101
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Asada S, Kitamura T. Clonal hematopoiesis and associated diseases: A review of recent findings. Cancer Sci 2021; 112:3962-3971. [PMID: 34328684 PMCID: PMC8486184 DOI: 10.1111/cas.15094] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Recent genome‐wide studies have revealed that aging or chronic inflammation can cause clonal expansion of cells in normal tissues. Clonal hematopoiesis has been the most intensively studied form of clonal expansion in the last decade. Clonal hematopoiesis of indeterminate potential (CHIP) is an age‐related phenomenon observed in elderly individuals with no history of hematological malignancy. The most frequently mutated genes in CHIP are DNMT3A, TET2, and ASXL1, which are associated with initiation of leukemia. Importantly, CHIP has been the focus of a number of studies because it is an independent risk factor for myeloid malignancy, cardiovascular disease (CVD), and all‐cause mortality. Animal models recapitulating human CHIP revealed that CHIP‐associated mutations alter the number and function of hematopoietic stem and progenitor cells (HSPCs) and promote leukemic transformation. Moreover, chronic inflammation caused by infection or aging confers a fitness advantage to the CHIP‐associated mutant HSPCs. Myeloid cells, such as macrophages with a CHIP‐associated mutation, accelerate chronic inflammation and are associated with increased levels of inflammatory cytokines. This positive feedback loop between CHIP and chronic inflammation promotes development of atherosclerosis and chronic heart failure and thereby increases the risk for CVD. Notably, HSPCs with a CHIP‐associated mutation may alter not only innate but also acquired immune cells. This suggests that CHIP is involved in the development of solid cancers or immune disorders, such as aplastic anemia. In this review, we provide an overview of recent findings on CHIP. We also discuss potential interventions for treating CHIP and preventing myeloid transformation and CVD progression.
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Affiliation(s)
- Shuhei Asada
- The Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, Japan.,Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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102
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DNA Methylation and Intra-Clonal Heterogeneity: The Chronic Myeloid Leukemia Model. Cancers (Basel) 2021; 13:cancers13143587. [PMID: 34298798 PMCID: PMC8307727 DOI: 10.3390/cancers13143587] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 01/24/2023] Open
Abstract
Chronic Myeloid Leukemia (CML) is a model to investigate the impact of tumor intra-clonal heterogeneity in personalized medicine. Indeed, tyrosine kinase inhibitors (TKIs) target the BCR-ABL fusion protein, which is considered the major CML driver. TKI use has highlighted the existence of intra-clonal heterogeneity, as indicated by the persistence of a minority subclone for several years despite the presence of the target fusion protein in all cells. Epigenetic modifications could partly explain this heterogeneity. This review summarizes the results of DNA methylation studies in CML. Next-generation sequencing technologies allowed for moving from single-gene to genome-wide analyses showing that methylation abnormalities are much more widespread in CML cells. These data showed that global hypomethylation is associated with hypermethylation of specific sites already at diagnosis in the early phase of CML. The BCR-ABL-independence of some methylation profile alterations and the recent demonstration of the initial intra-clonal DNA methylation heterogeneity suggests that some DNA methylation alterations may be biomarkers of TKI sensitivity/resistance and of disease progression risk. These results also open perspectives for understanding the epigenetic/genetic background of CML predisposition and for developing new therapeutic strategies.
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103
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Cristall K, Bidard FC, Pierga JY, Rauh MJ, Popova T, Sebbag C, Lantz O, Stern MH, Mueller CR. A DNA methylation-based liquid biopsy for triple-negative breast cancer. NPJ Precis Oncol 2021; 5:53. [PMID: 34135468 PMCID: PMC8209161 DOI: 10.1038/s41698-021-00198-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
Here, we present a next-generation sequencing (NGS) methylation-based blood test called methylation DETEction of Circulating Tumour DNA (mDETECT) designed for the optimal detection and monitoring of metastatic triple-negative breast cancer (TNBC). Based on a highly multiplexed targeted sequencing approach, this assay incorporates features that offer superior performance and included 53 amplicons from 47 regions. Analysis of a previously characterised cohort of women with metastatic TNBC with limited quantities of plasma (<2 ml) produced an AUC of 0.92 for detection of a tumour with a sensitivity of 76% for a specificity of 100%. mDETECTTNBC was quantitative and showed superior performance to an NGS TP53 mutation-based test carried out on the same patients and to the conventional CA15-3 biomarker. mDETECT also functioned well in serum samples from metastatic TNBC patients where it produced an AUC of 0.97 for detection of a tumour with a sensitivity of 93% for a specificity of 100%. An assay for BRCA1 promoter methylation was also incorporated into the mDETECT assay and functioned well but its clinical significance is currently unclear. Clonal Hematopoiesis of Indeterminate Potential was investigated as a source of background in control subjects but was not seen to be significant, though a link to adiposity may be relevant. The mDETECTTNBC assay is a liquid biopsy able to quantitatively detect all TNBC cancers and has the potential to improve the management of patients with this disease.
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Affiliation(s)
- Katrina Cristall
- Queen's Cancer Research Institute, Queen's University, Kingston, ON, Canada.,Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Francois-Clement Bidard
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, Paris, France.,Department of Medical Oncology, Institut Curie, Paris, France
| | - Jean-Yves Pierga
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, Paris, France.,Department of Medical Oncology, Institut Curie, Paris, France.,Université Paris Descartes, Paris, France
| | - Michael J Rauh
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Tatiana Popova
- INSERM U830 Cancer, Heterogeneity, Instability and Plasticity (CHIP), Institut Curie, Paris, France
| | - Clara Sebbag
- Department of Medical Oncology, Institut Curie, Paris, France
| | - Olivier Lantz
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, Paris, France.,INSERM CIC BT 1428, Institut Curie, Paris, France.,INSERM U932, Institut Curie, Paris, France
| | - Marc-Henri Stern
- INSERM U830 Cancer, Heterogeneity, Instability and Plasticity (CHIP), Institut Curie, Paris, France
| | - Christopher R Mueller
- Queen's Cancer Research Institute, Queen's University, Kingston, ON, Canada. .,Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada. .,Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.
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104
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Abstract
The observation and analysis of intra-tumour heterogeneity (ITH), particularly in genomic studies, has advanced our understanding of the evolutionary forces that shape cancer growth and development. However, only a subset of the variation observed in a single tumour will have an impact on cancer evolution, highlighting the need to distinguish between functional and non-functional ITH. Emerging studies highlight a role for the cancer epigenome, transcriptome and immune microenvironment in functional ITH. Here, we consider the importance of both genetic and non-genetic ITH and their role in tumour evolution, and present the rationale for a broad research focus beyond the cancer genome. Systems-biology analytical approaches will be necessary to outline the scale and importance of functional ITH. By allowing a deeper understanding of tumour evolution this will, in time, encourage development of novel therapies and improve outcomes for patients.
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Affiliation(s)
- James R M Black
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Center of Excellence, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Center of Excellence, University College London Cancer Institute, London, UK.
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105
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Rossmann MP, Zon LI. 'Enhancing' red cell fate through epigenetic mechanisms. Curr Opin Hematol 2021; 28:129-137. [PMID: 33741760 PMCID: PMC8695091 DOI: 10.1097/moh.0000000000000654] [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] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Transcription of erythroid-specific genes is regulated by the three-dimensional (3D) structure and composition of chromatin, which dynamically changes during erythroid differentiation. Chromatin organization and dynamics are regulated by several epigenetic mechanisms involving DNA (de-)methylation, posttranslational modifications (PTMs) of histones, chromatin-associated structural proteins, and higher-order structural changes and interactions. This review addresses examples of recent developments in several areas delineating the interface of chromatin regulation and erythroid-specific lineage transcription. RECENT FINDINGS We survey and discuss recent studies that focus on the erythroid chromatin landscape, erythroid enhancer-promotor interactions, super-enhancer functionality, the role of chromatin modifiers and epigenetic crosstalk, as well as the progress in mapping red blood cell (RBC) trait-associated genetic variants within cis-regulatory elements (CREs) identified in genome-wide association study (GWAS) efforts as a step toward determining their impact on erythroid-specific gene expression. SUMMARY As one of the best characterized and accessible cell differentiation systems, erythropoiesis has been at the forefront of studies aiming to conceptualize how chromatin dynamics regulate transcription. New emerging technologies that bring a significantly enhanced spatial and temporal resolution of chromatin structure, and allow investigation of small cell numbers, have advanced our understanding of chromatin dynamics during erythroid differentiation in vivo.
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Affiliation(s)
- Marlies P. Rossmann
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Leonard I. Zon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA 02115, USA
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106
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Abstract
Malignancies of the erythroid lineage are rare but aggressive diseases. Notably, the first insights into their biology emerged over half a century ago from avian and murine tumor viruses-induced erythroleukemia models providing the rationale for several transgenic mouse models that unraveled the transforming potential of signaling effectors and transcription factors in the erythroid lineage. More recently, genetic roadmaps have fueled efforts to establish models that are based on the epigenomic lesions observed in patients with erythroid malignancies. These models, together with often unexpected erythroid phenotypes in genetically modified mice, provided further insights into the molecular mechanisms of disease initiation and maintenance. Here, we review how the increasing knowledge of human erythroleukemia genetics combined with those from various mouse models indicate that the pathogenesis of the disease is based on the interplay between signaling mutations, impaired TP53 function, and altered chromatin organization. These alterations lead to aberrant activity of erythroid transcriptional master regulators like GATA1, indicating that erythroleukemia will most likely require combinatorial targeting for efficient therapeutic interventions.
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107
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Veiga CB, Lawrence EM, Murphy AJ, Herold MJ, Dragoljevic D. Myelodysplasia Syndrome, Clonal Hematopoiesis and Cardiovascular Disease. Cancers (Basel) 2021; 13:cancers13081968. [PMID: 33921778 PMCID: PMC8073047 DOI: 10.3390/cancers13081968] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The development of blood cancers is a complex process that involves the acquisition of specific blood disorders that precede cancer. These blood disorders are often driven by the accumulation of genetic abnormalities, which are discussed in this review. Likewise, predicting the rate of progression of these diseases is difficult, but it appears to be linked to which specific gene mutations are present in blood cells. In this review, we discuss a variety of genetic abnormalities that drive blood cancer, conditions that precede clinical symptoms of blood cancer, and how alterations in these genes change blood cell function. Additionally, we discuss the novel links between blood cancer development and heart disease. Abstract The development of myelodysplasia syndromes (MDS) is multiphasic and can be driven by a plethora of genetic mutations and/or abnormalities. MDS is characterized by a hematopoietic differentiation block, evidenced by increased immature hematopoietic cells, termed blast cells and decreased mature circulating leukocytes in at least one lineage (i.e., cytopenia). Clonal hematopoiesis of indeterminate potential (CHIP) is a recently described phenomenon preceding MDS development that is driven by somatic mutations in hemopoietic stem cells (HSCs). These mutant HSCs have a competitive advantage over healthy cells, resulting in an expansion of these clonal mutated leukocytes. In this review, we discuss the multiphasic development of MDS, the common mutations found in both MDS and CHIP, how a loss-of-function in these CHIP-related genes can alter HSC function and leukocyte development and the potential disease outcomes that can occur with dysfunctional HSCs. In particular, we discuss the novel connections between MDS development and cardiovascular disease.
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Affiliation(s)
- Camilla Bertuzzo Veiga
- Division of Immunometabolism, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; (C.B.V.); (A.J.M.)
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Melbourne, VIC 3010, Australia
| | - Erin M. Lawrence
- Walter and Eliza Hall Institute of Medical Research, 1 G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; (E.M.L.); (M.J.H.)
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC 3052, Australia
| | - Andrew J. Murphy
- Division of Immunometabolism, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; (C.B.V.); (A.J.M.)
- Department of Diabetes, Department of Immunology, Monash University, Clayton, VIC 3004, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Marco J. Herold
- Walter and Eliza Hall Institute of Medical Research, 1 G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; (E.M.L.); (M.J.H.)
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC 3052, Australia
| | - Dragana Dragoljevic
- Division of Immunometabolism, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; (C.B.V.); (A.J.M.)
- Department of Diabetes, Department of Immunology, Monash University, Clayton, VIC 3004, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC 3052, Australia
- Correspondence:
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108
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The regulation mechanisms and the Lamarckian inheritance property of DNA methylation in animals. Mamm Genome 2021; 32:135-152. [PMID: 33860357 DOI: 10.1007/s00335-021-09870-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/05/2021] [Indexed: 12/19/2022]
Abstract
DNA methylation is a stable and heritable epigenetic mechanism, of which the main functions are stabilizing the transcription of genes and promoting genetic conservation. In animals, the direct molecular inducers of DNA methylation mainly include histone covalent modification and non-coding RNA, whereas the fundamental regulators of DNA methylation are genetic and environmental factors. As is well known, competition is present everywhere in life systems, and will finally strike a balance that is optimal for the animal's survival and reproduction. The same goes for the regulation of DNA methylation. Genetic and environmental factors, respectively, are responsible for the programmed and plasticity changes of DNA methylation, and keen competition exists between genetically influenced procedural remodeling and environmentally influenced plastic alteration. In this process, genetic and environmental factors collaboratively decide the methylation patterns of corresponding loci. DNA methylation alterations induced by environmental factors can be transgenerationally inherited, and exhibit the characteristic of Lamarckian inheritance. Further research on regulatory mechanisms and the environmental plasticity of DNA methylation will provide strong support for understanding the biological function and evolutionary effects of DNA methylation.
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109
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Gonzalez Castro LN, Tirosh I, Suvà ML. Decoding Cancer Biology One Cell at a Time. Cancer Discov 2021; 11:960-970. [PMID: 33811126 PMCID: PMC8030694 DOI: 10.1158/2159-8290.cd-20-1376] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 11/16/2022]
Abstract
Human tumors are composed of diverse malignant and nonmalignant cells, generating a complex ecosystem that governs tumor biology and response to treatments. Recent technological advances have enabled the characterization of tumors at single-cell resolution, providing a compelling strategy to dissect their intricate biology. Here we describe recent developments in single-cell expression profiling and the studies applying them in clinical settings. We highlight some of the powerful insights gleaned from these studies for tumor classification, stem cell programs, tumor microenvironment, metastasis, and response to targeted and immune therapies. SIGNIFICANCE: Intratumor heterogeneity (ITH) has been a major barrier to our understanding of cancer. Single-cell genomics is leading a revolution in our ability to systematically dissect ITH. In this review, we focus on single-cell expression profiling and lessons learned in key aspects of human tumor biology.
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Affiliation(s)
- L Nicolas Gonzalez Castro
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Mario L Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
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110
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Iacobucci I, Qu C, Varotto E, Janke LJ, Yang X, Seth A, Shelat A, Friske JD, Fukano R, Yu J, Freeman BB, Kennedy JA, Sperling AS, Zheng R, Wang Y, Jogiraju H, Dickerson KM, Payne-Turner D, Morris SM, Hollis ES, Ghosn N, Haggard GE, Lindsley RC, Ebert BL, Mullighan CG. Modeling and targeting of erythroleukemia by hematopoietic genome editing. Blood 2021; 137:1628-1640. [PMID: 33512458 PMCID: PMC7995291 DOI: 10.1182/blood.2020009103] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/17/2020] [Indexed: 12/15/2022] Open
Abstract
Acute erythroid leukemia (AEL) is characterized by a distinct morphology, mutational spectrum, lack of preclinical models, and poor prognosis. Here, using multiplexed genome editing of mouse hematopoietic stem and progenitor cells and transplant assays, we developed preclinical models of AEL and non-erythroid acute leukemia and describe the central role of mutational cooperativity in determining leukemia lineage. Different combination of mutations in Trp53, Bcor, Dnmt3a, Rb1, and Nfix resulted in the development of leukemia with an erythroid phenotype, accompanied by the acquisition of alterations in signaling and transcription factor genes that recapitulate human AEL by cross-species genomic analysis. Clonal expansion during tumor evolution was driven by mutational cooccurrence, with clones harboring a higher number of founder and secondary lesions (eg, mutations in signaling genes) showing greater evolutionary fitness. Mouse and human AEL exhibited deregulation of genes regulating erythroid development, notably Gata1, Klf1, and Nfe2, driven by the interaction of mutations of the epigenetic modifiers Dnmt3a and Tet2 that perturbed methylation and thus expression of lineage-specific transcription factors. The established mouse leukemias were used as a platform for drug screening. Drug sensitivity was associated with the leukemia genotype, with the poly (ADP-ribose) polymerase inhibitor talazoparib and the demethylating agent decitabine efficacious in Trp53/Bcor-mutant AEL, CDK7/9 inhibitors in Trp53/Bcor/Dnmt3a-mutant AEL, and gemcitabine and bromodomain inhibitors in NUP98-KDM5A leukemia. In conclusion, combinatorial genome editing has shown the interplay of founding and secondary genetic alterations in phenotype and clonal evolution, epigenetic regulation of lineage-specific transcription factors, and therapeutic tractability in erythroid leukemogenesis.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Chunxu Qu
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Elena Varotto
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
- Pediatric Hematology-Oncology, Department of Woman's and Child's Health, University of Padova, Padova, Italy
| | - Laura J Janke
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Xu Yang
- Department of Computational Biology
| | - Aman Seth
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Anang Shelat
- Department of Chemical Biology and Therapeutics, and
| | - Jake D Friske
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Reiji Fukano
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | | | - Burgess B Freeman
- Preclinical Pharmacokinetics Shared Resource, St Jude Children's Research Hospital, Memphis, TN
| | - James A Kennedy
- Brigham and Women's Hospital, Boston, MA
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Adam S Sperling
- Brigham and Women's Hospital, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Rena Zheng
- Department of Medicine, Section of Hematology and Medical Oncology, Boston University Medical Center, Boston MA
| | - Yingzhe Wang
- Preclinical Pharmacokinetics Shared Resource, St Jude Children's Research Hospital, Memphis, TN
| | - Harini Jogiraju
- Preclinical Pharmacokinetics Shared Resource, St Jude Children's Research Hospital, Memphis, TN
| | | | | | - Sarah M Morris
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Emily S Hollis
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Nina Ghosn
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Georgia E Haggard
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - R Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Howard Hughes Medical Institute, Dana-Farber Cancer Institute, Boston, MA; and
| | - Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, St Jude Children's Research Hospital, Memphis, TN
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111
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Policarpi C, Dabin J, Hackett JA. Epigenetic editing: Dissecting chromatin function in context. Bioessays 2021; 43:e2000316. [PMID: 33724509 DOI: 10.1002/bies.202000316] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/06/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022]
Abstract
How epigenetic mechanisms regulate genome output and response to stimuli is a fundamental question in development and disease. Past decades have made tremendous progress in deciphering the regulatory relationships involved by correlating aggregated (epi)genomics profiles with global perturbations. However, the recent development of epigenetic editing technologies now enables researchers to move beyond inferred conclusions, towards explicit causal reasoning, through 'programing' precise chromatin perturbations in single cells. Here, we first discuss the major unresolved questions in the epigenetics field that can be addressed by programable epigenome editing, including the context-dependent function and memory of chromatin states. We then describe the epigenetic editing toolkit focusing on CRISPR-based technologies, and highlight its achievements, drawbacks and promise. Finally, we consider the potential future application of epigenetic editing to the study and treatment of specific disease conditions.
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Affiliation(s)
- Cristina Policarpi
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Juliette Dabin
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Jamie A Hackett
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
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112
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Transcriptional and epigenetic control of hematopoietic stem cell fate decisions in vertebrates. Dev Biol 2021; 475:156-164. [PMID: 33689804 DOI: 10.1016/j.ydbio.2021.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/24/2021] [Accepted: 03/04/2021] [Indexed: 12/20/2022]
Abstract
Hematopoietic stem cells (HSCs) are the foundation of adult hematopoiesis that produce all types of mature blood lineages. In vertebrates, HSC development is a stepwise process, coordinately regulated by chromatin architectures and a group of transcriptional and epigenetic regulators. A deeper understanding of the molecular mechanisms governing the generation, expansion, and function of HSCs holds great promise in the generation and expansion of engraftable HSCs in vitro for clinical applications. This study reviewed recent advances in transcriptional and epigenetic control of hematopoietic stem cell fate decisions in vertebrates.
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113
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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] [MESH Headings] [Grants] [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.
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Affiliation(s)
| | - Lev M Kats
- The Peter MacCallum Cancer CentreMelbourneVICAustralia
- The Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVICAustralia
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114
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Velten L, Story BA, Hernández-Malmierca P, Raffel S, Leonce DR, Milbank J, Paulsen M, Demir A, Szu-Tu C, Frömel R, Lutz C, Nowak D, Jann JC, Pabst C, Boch T, Hofmann WK, Müller-Tidow C, Trumpp A, Haas S, Steinmetz LM. Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics. Nat Commun 2021; 12:1366. [PMID: 33649320 PMCID: PMC7921413 DOI: 10.1038/s41467-021-21650-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 02/05/2021] [Indexed: 01/07/2023] Open
Abstract
Cancer stem cells drive disease progression and relapse in many types of cancer. Despite this, a thorough characterization of these cells remains elusive and with it the ability to eradicate cancer at its source. In acute myeloid leukemia (AML), leukemic stem cells (LSCs) underlie mortality but are difficult to isolate due to their low abundance and high similarity to healthy hematopoietic stem cells (HSCs). Here, we demonstrate that LSCs, HSCs, and pre-leukemic stem cells can be identified and molecularly profiled by combining single-cell transcriptomics with lineage tracing using both nuclear and mitochondrial somatic variants. While mutational status discriminates between healthy and cancerous cells, gene expression distinguishes stem cells and progenitor cell populations. Our approach enables the identification of LSC-specific gene expression programs and the characterization of differentiation blocks induced by leukemic mutations. Taken together, we demonstrate the power of single-cell multi-omic approaches in characterizing cancer stem cells.
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Affiliation(s)
- Lars Velten
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Benjamin A Story
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Swiss Federal Institute of Technology (ETH) Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - Pablo Hernández-Malmierca
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Simon Raffel
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Daniel R Leonce
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Jennifer Milbank
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Malte Paulsen
- European Molecular Biology Laboratory (EMBL), Flow Cytometry Core Facility, Heidelberg, Germany
| | - Aykut Demir
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Chelsea Szu-Tu
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Robert Frömel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Christoph Lutz
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Daniel Nowak
- Department of Hematology and Oncology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Johann-Christoph Jann
- Department of Hematology and Oncology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Caroline Pabst
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Tobias Boch
- Swiss Federal Institute of Technology (ETH) Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- Department of Hematology and Oncology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Wolf-Karsten Hofmann
- Department of Hematology and Oncology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carsten Müller-Tidow
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Simon Haas
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Genome Technology Center, Palo Alto, CA, USA.
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Zhang Y, Hu J, Zou X, Ma F, Qiu JG, Zhang CY. Integration of single-molecule detection with endonuclease IV-assisted signal amplification for sensitive DNA methylation assay. Chem Commun (Camb) 2021; 57:2073-2076. [PMID: 33507186 DOI: 10.1039/d0cc08306b] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We demonstrate the development of a new fluorescent biosensor for sensitive DNA methylation assay by integrating single-molecule detection with endo IV-assisted signal amplification. This biosensor possesses the characteristics of good selectivity and high sensitivity with a detection limit of 7.3 × 10-17 M. It can distinguish as low as 0.01% methylation level, and can analyze genomic DNA methylation even in a single cancer cell.
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Affiliation(s)
- Yan Zhang
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
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116
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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.
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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
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117
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Abstract
PURPOSE OF REVIEW In hematopoiesis, rapid cell fate decisions are necessary for timely responses to environmental stimuli resulting in the production of diverse types of blood cells. Early studies have led to a hierarchical, tree-like view of hematopoiesis with hematopoietic stem cells residing at the apex and serially branching out to give rise to bipotential progenitors with increasingly restricted lineage potential. Recent single-cell studies have challenged some aspects of the classical model of hematopoiesis. Here, we review the latest articles on cell fate decision in hematopoietic progenitors, highlighting single-cell studies that have questioned previously established concepts and those that have reaffirmed them. RECENT FINDINGS The hierarchical organization of hematopoiesis and the importance of transcription factors have been largely validated at the single-cell level. In contrast, single-cell studies have shown that lineage commitment is progressive rather than switch-like as originally proposed. Furthermore, the reconstruction of cell fate paths suggested the existence of a gradient of hematopoietic progenitors that are in a continuum of changing fate probabilities rather than in a static bipotential state, leading us to reconsider the notion of bipotential progenitors. SUMMARY Single-cell transcriptomic and proteomic studies have transformed our view of lineage commitment and offer a drastically different perspective on hematopoiesis.
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118
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Hill B, Jagadeesh D, Pohlman B, Dean R, Parameswaran N, Chen J, Radivoyevitch T, Morrison A, Fada S, Dever M, Robinson S, Lindner D, Smith M, Saunthararajah Y. A pilot clinical trial of oral tetrahydrouridine/decitabine for noncytotoxic epigenetic therapy of chemoresistant lymphoid malignancies. Semin Hematol 2021; 58:35-44. [PMID: 33509441 PMCID: PMC7847482 DOI: 10.1053/j.seminhematol.2020.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/29/2020] [Indexed: 11/11/2022]
Abstract
One mechanism by which lymphoid malignancies resist standard apoptosis-intending (cytotoxic) treatments is genetic attenuation of the p53/p16-CDKN2A apoptosis axis. Depletion of the epigenetic protein DNA methyltransferase 1 (DNMT1) using the deoxycytidine analog decitabine is a validated approach to cytoreduce malignancy independent of p53/p16. In vivo decitabine activity, however, is restricted by rapid catabolism by cytidine deaminase (CDA). We, therefore, combined decitabine with the CDA-inhibitor tetrahydrouridine and conducted a pilot clinical trial in patients with relapsed lymphoid malignancies: the doses of tetrahydrouridine/decitabine used (∼10/0.2 mg/kg orally (PO) 2×/week) were selected for the molecular pharmacodynamic objective of non-cytotoxic, S-phase dependent, DNMT1-depletion, guided by previous Phase 1 studies. Patients with relapsed/refractory B- or T-cell malignancies (n = 7) were treated for up to 18 weeks. Neutropenia without concurrent thrombocytopenia is an expected toxicity of DNMT1-depletion and occurred in all patients (Grade 3/4). Subjective and objective clinical improvements occurred in 4 of 7 patients, but these responses were lost upon treatment interruptions and reductions to manage neutropenia. We thus performed parallel experiments in a preclinical in vivo model of lymphoma to identify regimen refinements that might sustain DNMT1-targeting in malignant cells but limit neutropenia. We found that timed-alternation of decitabine with the related molecule 5-azacytidine, and combination with inhibitors of CDA and de novo pyrimidine synthesis could leverage feedback responses of pyrimidine metabolism to substantially increase lymphoma cytoreduction but with less neutropenia. In sum, regimen innovations beyond incorporation of a CDA-inhibitor are needed to sustain decitabine DNMT1-targeting and efficacy against chemo-resistant lymphoid malignancy. Such potential solutions were explored in preclinical in vivo studies.
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Affiliation(s)
- Brian Hill
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH.
| | - Deepa Jagadeesh
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Brad Pohlman
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Robert Dean
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Neetha Parameswaran
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Joel Chen
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | | | - Ashley Morrison
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Sherry Fada
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Meredith Dever
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Shelley Robinson
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Daniel Lindner
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Mitchell Smith
- Department of Hematology and Oncology, George Washington University, DC
| | - Yogen Saunthararajah
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH; Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH.
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119
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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.
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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
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120
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Sturgess KHM, Calero-Nieto FJ, Göttgens B, Wilson NK. Single-Cell Analysis of Hematopoietic Stem Cells. Methods Mol Biol 2021; 2308:301-337. [PMID: 34057731 DOI: 10.1007/978-1-0716-1425-9_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The study of hematopoiesis has been revolutionized in recent years by the application of single-cell RNA sequencing technologies. The technique coupled with rapidly developing bioinformatic analysis has provided great insight into the cell type compositions of many populations previously defined by their cell surface phenotype. Moreover, transcriptomic information enables the identification of individual molecules and pathways which define novel cell populations and their transitions including cell lineage decisions. Combining single-cell transcriptional profiling with molecular perturbations allows functional analysis of individual factors in gene regulatory networks and better understanding of the earliest stages of malignant transformation. In this chapter we describe a comprehensive protocol for scRNA-Seq analysis of the mouse bone marrow, using both plate-based (low throughput) and droplet-based (high throughput) methods. The protocol includes instructions for sample preparation, an antibody panel for flow cytometric purification of hematopoietic progenitors with index sorting for plate-based analysis or in bulk for droplet-based methods. The plate-based protocol described in this chapter is a combination of the Smart-Seq2 and mcSCRB-Seq protocols, optimized in our laboratory. It utilizes off-the-shelf reagents for cDNA preparation, is amenable to automation using a liquid handler, and takes 4 days from preparation of the cells for sorting to producing a sequencing-ready library. The droplet-based method (using for instance the 10× Genomics platform) relies on the manufacturer's user guide and commercial reagents, and takes 3 days from isolation of the cells to the production of a library ready for sequencing.
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Affiliation(s)
- Katherine H M Sturgess
- Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Fernando J Calero-Nieto
- Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Nicola K Wilson
- Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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121
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Moroney JB, Chupp DP, Xu Z, Zan H, Casali P. Epigenetics of the antibody and autoantibody response. Curr Opin Immunol 2020; 67:75-86. [PMID: 33176228 PMCID: PMC7744442 DOI: 10.1016/j.coi.2020.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 11/20/2022]
Abstract
B cell differentiation driven by microbial antigens leads to production of anti-microbial antibodies, such as those neutralizing viruses, bacteria or bacterial toxin, that are class-switched (IgG and IgA) and somatically hypermutated (maturation of the antibody response) as well as secreted in large volume by plasma cells. Similar features characterize pathogenic antibodies to self-antigens in autoimmunity, reflecting the critical role of class switch DNA recombination (CSR), somatic hypermutation (SHM) and plasma cell differentiation in the generation of antibodies to not only foreign antigens but also self-antigens (autoantibodies). Central to CSR/SHM and plasma cell differentiation are AID, a potent DNA cytidine deaminase encoded by Aicda, and Blimp-1, a transcription factor encoded by Prdm1. B cell-intrinsic expression of Aicda and Prdm1 is regulated by epigenetic elements and processes, including DNA methylation, histone post-translational modifications and non-coding RNAs, particularly miRNAs. Here, we will discuss: B cell-intrinsic epigenetic processes that regulate antibody and autoantibody responses; how epigenetic dysregulation alters CSR/SHM and plasma cell differentiation, thereby leading to autoantibody responses, as in systemic lupus; and, how these can be modulated by nutrients, metabolites, and hormones through changes in B cell-intrinsic epigenetic mechanisms, which can provide therapeutic targets in autoimmunity.
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Affiliation(s)
- Justin B Moroney
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX 78229, USA
| | - Daniel P Chupp
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX 78229, USA
| | - Zhenming Xu
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX 78229, USA
| | - Hong Zan
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX 78229, USA
| | - Paolo Casali
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX 78229, USA.
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122
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Kunimoto H, Nakajima H. TET2: A cornerstone in normal and malignant hematopoiesis. Cancer Sci 2020; 112:31-40. [PMID: 33048426 PMCID: PMC7780023 DOI: 10.1111/cas.14688] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/04/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022] Open
Abstract
Regulation of genome‐wide DNA methylation is fundamental for a variety of biological processes such as mammalian development, stem cell function, cellular proliferation/differentiation, and oncogenesis. Among the regulators of DNA methylation, ten‐eleven translocation 2 (TET2) is one of the most frequently mutated genes in clonal hematopoiesis of indeterminate potential and in various hematological malignancies, underscoring a pivotal role for TET2 in blood homeostasis and hematopoietic transformation. TET2 oxidizes methylated cytosines to further modify cytosines, which behave as intermediates in active/passive DNA demethylation processes. TET2 itself associates with histone modifiers, thereby regulating histone modifications and expression of target genes. A number of studies have reported pleiotropic effects of TET2 on hematopoietic stem cell self‐renewal, hematopoietic differentiation, genome instability and inflammatory response. Recent single‐cell genomics studies have identified gene promoters as well as transcription factor binding sites as TET2‐targeted genetic loci in which disruption of DNA methylation can fundamentally modify hematopoietic differentiation and promote leukemogenesis. TET2 mutations show convergent cooperativity with other disease alleles in signaling molecules, epigenetic modifiers, and spliceosome factors in hematopoietic transformation. Future studies focusing on the molecular basis of stem cell and immune regulation by TET2 loss will further deepen our understanding of the entire landscape of pathophysiology and molecular vulnerabilities of TET2‐mutated hematological malignancies.
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Affiliation(s)
- Hiroyoshi Kunimoto
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hideaki Nakajima
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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123
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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.
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124
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Chauvistré H, Seré K. Epigenetic aspects of DC development and differentiation. Mol Immunol 2020; 128:116-124. [PMID: 33126080 DOI: 10.1016/j.molimm.2020.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 09/09/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023]
Abstract
In this review we introduce the basic principles of epigenetic gene regulation and discuss them in the context of dendritic cell (DC) development and differentiation. Epigenetic mechanisms control the accessibility of chromatin for DNA binding proteins and thus they control gene expression. These mechanisms comprise chemical modifications of DNA and histones, chromatin remodeling and chromatin conformation. The variety of epigenetic mechanisms allow high-end fine tuning and flexibility of gene expression, a prerequisite in the process of DC lineage development.
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Affiliation(s)
- Heike Chauvistré
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen and the German Cancer Consortium (DKTK), Essen, Germany
| | - Kristin Seré
- Institute of Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany.
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125
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Rodrigues CP, Shvedunova M, Akhtar A. Epigenetic Regulators as the Gatekeepers of Hematopoiesis. Trends Genet 2020; 37:S0168-9525(20)30251-1. [PMID: 34756331 DOI: 10.1016/j.tig.2020.09.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/12/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023]
Abstract
Hematopoiesis is the process by which both fetal and adult organisms derive the full repertoire of blood cells from a single multipotent progenitor cell type, the hematopoietic stem cells (HSCs). Correct enactment of this process relies on a synergistic interplay between genetically encoded differentiation programs and a host of cell-intrinsic and cell-extrinsic factors. These include the influence of the HSC niche microenvironment, action of specific transcription factors, and alterations in intracellular metabolic state. The consolidation of these inputs with the genetically encoded program into a coherent differentiation program for each lineage is thought to rely on epigenetic modifiers. Recent work has delineated the precise contributions of different classes of epigenetic modifiers to HSC self-renewal as well as lineage specification and differentiation into various cell types. Here, we bring together what is currently known about chromatin status and the development of cells in the hematopoietic system under normal and abnormal conditions.
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Affiliation(s)
- Cecilia Pessoa Rodrigues
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; University of Freiburg, Faculty of Biology, Schaenzlestrasse 1, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Maria Shvedunova
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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126
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Abstract
DNA methylation is a key layer of epigenetic regulation. The deposition of methylation marks relies on the catalytic activity of DNA methyltransferases (DNMTs), and their active removal relies on the activity of ten-eleven translocation (TET) enzymes. Paradoxically, in important biological contexts these antagonistic factors are co-expressed and target overlapping genomic regions. The ensuing cyclic biochemistry of cytosine modifications gives rise to a continuous, out-of-thermal equilibrium transition through different methylation states. But what is the purpose of this intriguing turnover of DNA methylation? Recent evidence demonstrates that methylation turnover is enriched at gene distal regulatory elements, including enhancers, and can give rise to large-scale oscillatory dynamics. We discuss this phenomenon and propose that DNA methylation turnover might facilitate key lineage decisions.
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127
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Clonal hematopoiesis: Molecular basis and clinical relevance. Leuk Res 2020; 98:106457. [PMID: 33010619 DOI: 10.1016/j.leukres.2020.106457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/15/2020] [Accepted: 09/20/2020] [Indexed: 12/17/2022]
Abstract
Recent genomics studies have revealed that clonal hematopoietic expansion due to recurrent somatic mutations in hematopoietic cells are common in older people without evidence of hematological malignancies. This phenomenon, termed clonal hematopoiesis of indeterminate potential (CHIP), is associated with greater risk for hematological malignancy and cardiovascular diseases, leading to decreased overall survival of the affected individuals. The most frequently mutated genes in CHIP cases include genes associated with epigenetic modification, cell signaling, DNA damage response and RNA splicing, which are all recurrently mutated in myeloid malignancies. Recent findings suggest that these genetic alleles exert pleiotropic effects on hematopoietic stem cell (HSC) functions, transcriptional regulations, DNA damage responses and resistance to cellular stresses. Recent studies have uncovered the clinical relevance of CHIP in various settings during the management of hematological malignancies. Elucidating overall picture of clonal evolution based on CHIP will help developing preventive measures and novel treatments for hematological malignancies.
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128
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Liggett LA, Sankaran VG. Unraveling Hematopoiesis through the Lens of Genomics. Cell 2020; 182:1384-1400. [PMID: 32946781 PMCID: PMC7508400 DOI: 10.1016/j.cell.2020.08.030] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/14/2020] [Accepted: 08/17/2020] [Indexed: 01/07/2023]
Abstract
Hematopoiesis has long served as a paradigm of stem cell biology and tissue homeostasis. In the past decade, the genomics revolution has ushered in powerful new methods for investigating the hematopoietic system that have provided transformative insights into its biology. As part of the advances in genomics, increasingly accurate deep sequencing and novel methods of cell tracking have revealed hematopoiesis to be more of a continuous and less of a discrete and punctuated process than originally envisioned. In part, this continuous nature of hematopoiesis is made possible by the emergent outcomes of vast, interconnected regulatory networks that influence cell fates and lineage commitment. It is also becoming clear how these mechanisms are modulated by genetic variation present throughout the population. This review describes how these recently uncovered complexities are reshaping our concept of tissue development and homeostasis while opening up a more comprehensive future understanding of hematopoiesis.
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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
| | - 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.
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129
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Abstract
We have uncovered a novel role for the nuclear receptor-binding SET domain protein 1 (NSD1) in human and murine erythroid differentiation. Mechanistically, we found that the histone methyltransferase activity of NSD1 is essential for chromatin binding, protein interactions and target gene activation of the erythroid transcriptional master regulator GATA1.
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Affiliation(s)
- Samantha Tauchmann
- University Children's Hospital Basel (UKBB), Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Marwa Almosailleakh
- University Children's Hospital Basel (UKBB), Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Juerg Schwaller
- University Children's Hospital Basel (UKBB), Department of Biomedicine, University of Basel, Basel, Switzerland
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130
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Weichenhan D, Lipka DB, Lutsik P, Goyal A, Plass C. Epigenomic technologies for precision oncology. Semin Cancer Biol 2020; 84:60-68. [PMID: 32822861 DOI: 10.1016/j.semcancer.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 12/15/2022]
Abstract
Epigenetic patterns in a cell control the expression of genes and consequently determine the phenotype of a cell. Cancer cells possess altered epigenomes which include aberrant patterns of DNA methylation, histone tail modifications, nucleosome positioning and of the three-dimensional chromatin organization within a nucleus. These altered epigenetic patterns are potential useful biomarkers to detect cancer cells and to classify tumor types. In addition, the cancer epigenome dictates the response of a cancer cell to therapeutic intervention and, therefore its knowledge, will allow to predict response to different therapeutic approaches. Here we review the current state-of-the-art technologies that have been developed to decipher epigenetic patterns on the genomic level and discuss how these methods are potentially useful for precision oncology.
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Affiliation(s)
- Dieter Weichenhan
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Daniel B Lipka
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, National Center for Tumor Diseases Heidelberg & German Cancer Research Center, Im Neuenheimer Feld 581, D-69120, Heidelberg, Germany; Faculty of Medicine, Medical Center, Otto-von-Guericke-University, Leipziger Straße 44, D-39120, Magdeburg, Germany.
| | - Pavlo Lutsik
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Ashish Goyal
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Christoph Plass
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
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131
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Nam AS, Chaligne R, Landau DA. Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics. Nat Rev Genet 2020; 22:3-18. [PMID: 32807900 DOI: 10.1038/s41576-020-0265-5] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2020] [Indexed: 12/17/2022]
Abstract
Cancer represents an evolutionary process through which growing malignant populations genetically diversify, leading to tumour progression, relapse and resistance to therapy. In addition to genetic diversity, the cell-to-cell variation that fuels evolutionary selection also manifests in cellular states, epigenetic profiles, spatial distributions and interactions with the microenvironment. Therefore, the study of cancer requires the integration of multiple heritable dimensions at the resolution of the single cell - the atomic unit of somatic evolution. In this Review, we discuss emerging analytic and experimental technologies for single-cell multi-omics that enable the capture and integration of multiple data modalities to inform the study of cancer evolution. These data show that cancer results from a complex interplay between genetic and non-genetic determinants of somatic evolution.
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Affiliation(s)
- Anna S Nam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.,New York Genome Center, New York, NY, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ronan Chaligne
- New York Genome Center, New York, NY, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dan A Landau
- New York Genome Center, New York, NY, USA. .,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA. .,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA. .,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
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132
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Epigenomic analysis of Parkinson's disease neurons identifies Tet2 loss as neuroprotective. Nat Neurosci 2020; 23:1203-1214. [PMID: 32807949 DOI: 10.1038/s41593-020-0690-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 07/07/2020] [Indexed: 01/08/2023]
Abstract
Parkinson's disease (PD) pathogenesis may involve the epigenetic control of enhancers that modify neuronal functions. Here, we comprehensively examine DNA methylation at enhancers, genome-wide, in neurons of patients with PD and of control individuals. We find a widespread increase in cytosine modifications at enhancers in PD neurons, which is partly explained by elevated hydroxymethylation levels. In particular, patients with PD exhibit an epigenetic and transcriptional upregulation of TET2, a master-regulator of cytosine modification status. TET2 depletion in a neuronal cell model results in cytosine modification changes that are reciprocal to those observed in PD neurons. Moreover, Tet2 inactivation in mice fully prevents nigral dopaminergic neuronal loss induced by previous inflammation. Tet2 loss also attenuates transcriptional immune responses to an inflammatory trigger. Thus, widespread epigenetic dysregulation of enhancers in PD neurons may, in part, be mediated by increased TET2 expression. Decreased Tet2 activity is neuroprotective, in vivo, and may be a new therapeutic target for PD.
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133
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MPN: The Molecular Drivers of Disease Initiation, Progression and Transformation and their Effect on Treatment. Cells 2020; 9:cells9081901. [PMID: 32823933 PMCID: PMC7465511 DOI: 10.3390/cells9081901] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
Myeloproliferative neoplasms (MPNs) constitute a group of disorders identified by an overproduction of cells derived from myeloid lineage. The majority of MPNs have an identifiable driver mutation responsible for cytokine-independent proliferative signalling. The acquisition of coexisting mutations in chromatin modifiers, spliceosome complex components, DNA methylation modifiers, tumour suppressors and transcriptional regulators have been identified as major pathways for disease progression and leukemic transformation. They also confer different sensitivities to therapeutic options. This review will explore the molecular basis of MPN pathogenesis and specifically examine the impact of coexisting mutations on disease biology and therapeutic options.
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134
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Williams BP, Gehring M. Principles of Epigenetic Homeostasis Shared Between Flowering Plants and Mammals. Trends Genet 2020; 36:751-763. [PMID: 32711945 DOI: 10.1016/j.tig.2020.06.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022]
Abstract
In diverse eukaryotes, epigenetic information such as DNA methylation is stably propagated over many cell divisions and generations, and can remain the same over thousands or millions of years. However, this stability is the product of dynamic processes that add and remove DNA methylation by specialized enzymatic pathways. The activities of these dynamic pathways must therefore be finely orchestrated in order to ensure that the DNA methylation landscape is maintained with high fidelity - a concept we term epigenetic homeostasis. In this review, we summarize recent insights into epigenetic homeostasis mechanisms in flowering plants and mammals, highlighting analogous mechanisms that have independently evolved to achieve the same goal of stabilizing the epigenetic landscape.
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Affiliation(s)
- Ben P Williams
- Whitehead Institute for Biomedical Research, 455 Main St, Cambridge, MA 02142, USA.
| | - Mary Gehring
- Whitehead Institute for Biomedical Research, 455 Main St, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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135
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López-Moyado IF, Rao A. DNMT3A and TET2 mutations reshape hematopoiesis in opposing ways. Nat Genet 2020; 52:554-556. [DOI: 10.1038/s41588-020-0641-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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136
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Hematopoietic regeneration under the spell of epigenetic-epitranscriptomic factors and transposable elements. Curr Opin Hematol 2020; 27:264-272. [DOI: 10.1097/moh.0000000000000585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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137
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Norsworthy KJ, Mulkey F, Scott EC, Ward AF, Przepiorka D, Charlab R, Dorff SE, Deisseroth A, Kazandjian D, Sridhara R, Beaver JA, Farrell AT, de Claro RA, Pazdur R. Differentiation Syndrome with Ivosidenib and Enasidenib Treatment in Patients with Relapsed or Refractory IDH-Mutated AML: A U.S. Food and Drug Administration Systematic Analysis. Clin Cancer Res 2020; 26:4280-4288. [PMID: 32393603 DOI: 10.1158/1078-0432.ccr-20-0834] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/28/2020] [Accepted: 05/06/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE Differentiation syndrome (DS) is a serious adverse reaction of isocitrate dehydrogenase (IDH) inhibitors ivosidenib and enasidenib in patients with (IDH)1- and IDH2-mutated acute myeloid leukemia (AML), respectively. EXPERIMENTAL DESIGN During FDA review of marketing applications for ivosidenib and enasidenib, data from pivotal trials were queried to identify cases of DS in patients with relapsed or refractory (R/R) AML. One hundred seventy-nine patients with R/R AML received ivosidenib and 214 received enasidenib. Adverse events, labs, and vital signs in the first 90 days of treatment were screened per diagnostic criteria, and narratives were reviewed to adjudicate DS cases. RESULTS We identified 72 of 179 (40%) potential cases for ivosidenib and 86 of 214 (40%) for enasidenib; 34 of 179 (19%) and 41 of 214 (19%) were adjudicated as DS. Leukocytosis was present in 79% and 61% of cases, respectively. Median (range) time to onset was 20 (1-78) and 19 (1-86) days. Grade ≥ 3 adverse reactions occurred in 68% and 66%; 6% and 5% were fatal. Univariate analyses suggested baseline bone marrow blasts ≥ 48% and peripheral blood blasts ≥ 25% and 15% for ivosidenib and enasidenib, respectively, were associated with increased risk of DS. Complete remission (CR) + CR with partial hematologic recovery rates were lower in patients with versus without DS [ivosidenib 18% (95% confidence interval, 7%-35%) vs. 36% (28%-45%); enasidenib 18% (7%-33%) vs. 25% (18%-32%)]. CONCLUSIONS DS is a common and potentially fatal adverse reaction of IDH inhibitors, and use of standardized diagnostic criteria may aid in earlier diagnosis and treatment.See related commentary by Zeidner, p. 4174.
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Affiliation(s)
- Kelly J Norsworthy
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland.
| | - Flora Mulkey
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Emma C Scott
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Ashley F Ward
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Donna Przepiorka
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Rosane Charlab
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Sarah E Dorff
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Albert Deisseroth
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Dickran Kazandjian
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Rajeshwari Sridhara
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Julia A Beaver
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Ann T Farrell
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - R Angelo de Claro
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Richard Pazdur
- Oncology Center of Excellence, U.S. Food and Drug Administration, Silver Spring, Maryland
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