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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.
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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.
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Papadopoulou V, Schoumans J, Basset V, Solly F, Pasquier J, Blum S, Spertini O. Single-center, observational study of AML/MDS-EB with IDH1/2 mutations: genetic profile, immunophenotypes, mutational kinetics and outcomes. Hematology 2023; 28:2180704. [PMID: 36815747 DOI: 10.1080/16078454.2023.2180704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
OBJECTIVE IDH1/2 mutations, intervening in epigenetic procedures, are frequently encountered in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). Knowledge of the genetics, immunophenotypes, and mutational kinetics of IDH1/2-mutated AML can contribute to the understanding of AML clonal architecture and inform therapeutics and monitoring. METHODS We retrospectively analyzed 50 IDH1/2-mutated AML/MDS-EB cases of our institution, to identify recurrent co-mutations, immunophenotypes, patterns of co-variance of IDH1/2 allele burdens with those of recurrent co-mutations, frequency of persistent IDH1/2 mutation as clonal hematopoiesis of indeterminate potential (CHIP) in remission and response to hypomethylating agents. RESULTS Most frequently co-mutated genes were DNMT3A, SRSF2 and NPM1. Most cases with co-existent IDH1/2 and NPM1 mutations (11/13) showed an 'APL-like' immunophenotype (CD34-HLADR-). Allele burdens of mutated IDH1/2 were identical to mutated SRSF2 allele burdens at diagnosis and remission, but not always to mutated NPM1 allele burden in remission. We show persistence of significant mutIDH1/2 allele burden in approximately one-fourth of patients with deep remissions. IDH1/2 mutations were significantly more frequent among responders to first-line HMA-based regimens than among non-responders, in patients treated for myeloid neoplasms with excess blasts. CONCLUSIONS IDH1/2 mutations are most frequently accompanied by DNMT3A, SRSF2 and NPM1 mutations. NPM1-IDH1/2 mutated AML has a mature phenotype possibly amenable to differentiation therapies. IDH1/2 and SRSF2 mutations probably arise at the same developmental stage of the disease, as their allele burdens covariate. IDH1/2 mutation represents CHIP in a substantial proportion of cases and is therefore no reliable residual disease marker. The preferential presence of IDH1/2 mutations among HMA-responders could inform therapeutic decisions if confirmed in larger series.
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Affiliation(s)
- Vasiliki Papadopoulou
- Service and Laboratory of Hematology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Jacqueline Schoumans
- Service and Laboratory of Hematology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Valentin Basset
- Service and Laboratory of Hematology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Françoise Solly
- Service and Laboratory of Hematology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Jérôme Pasquier
- Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
| | - Sabine Blum
- Service and Laboratory of Hematology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Olivier Spertini
- Service and Laboratory of Hematology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
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3
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Beneyto-Calabuig S, Merbach AK, Kniffka JA, Antes M, Szu-Tu C, Rohde C, Waclawiczek A, Stelmach P, Gräßle S, Pervan P, Janssen M, Landry JJM, Benes V, Jauch A, Brough M, Bauer M, Besenbeck B, Felden J, Bäumer S, Hundemer M, Sauer T, Pabst C, Wickenhauser C, Angenendt L, Schliemann C, Trumpp A, Haas S, Scherer M, Raffel S, Müller-Tidow C, Velten L. Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia. Cell Stem Cell 2023; 30:706-721.e8. [PMID: 37098346 DOI: 10.1016/j.stem.2023.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 02/05/2023] [Accepted: 03/30/2023] [Indexed: 04/27/2023]
Abstract
Inter-patient variability and the similarity of healthy and leukemic stem cells (LSCs) have impeded the characterization of LSCs in acute myeloid leukemia (AML) and their differentiation landscape. Here, we introduce CloneTracer, a novel method that adds clonal resolution to single-cell RNA-seq datasets. Applied to samples from 19 AML patients, CloneTracer revealed routes of leukemic differentiation. Although residual healthy and preleukemic cells dominated the dormant stem cell compartment, active LSCs resembled their healthy counterpart and retained erythroid capacity. By contrast, downstream myeloid progenitors constituted a highly aberrant, disease-defining compartment: their gene expression and differentiation state affected both the chemotherapy response and leukemia's ability to differentiate into transcriptomically normal monocytes. Finally, we demonstrated the potential of CloneTracer to identify surface markers misregulated specifically in leukemic cells. Taken together, CloneTracer reveals a differentiation landscape that mimics its healthy counterpart and may determine biology and therapy response in AML.
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Affiliation(s)
- Sergi Beneyto-Calabuig
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Anne Kathrin Merbach
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, 69117 Heidelberg, Germany
| | - Jonas-Alexander Kniffka
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Magdalena Antes
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Chelsea Szu-Tu
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Christian Rohde
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, 69117 Heidelberg, Germany
| | - Alexander Waclawiczek
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Patrick Stelmach
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Sarah Gräßle
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
| | - Philip Pervan
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Maike Janssen
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, 69117 Heidelberg, Germany
| | - Jonathan J M Landry
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Anna Jauch
- Institute of Human Genetics, University of Heidelberg, 69120 Heidelberg, Germany
| | - Michaela Brough
- Institute of Human Genetics, University of Heidelberg, 69120 Heidelberg, Germany
| | - Marcus Bauer
- Institute of Pathology, University Hospital Halle (Saale), Martin-Luther-University Halle-Wittenberg, 06112 Halle, Germany
| | - Birgit Besenbeck
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Julia Felden
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Sebastian Bäumer
- Department of Medicine A, Hematology and Oncology, University Hospital, Muenster, Germany
| | - Michael Hundemer
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Tim Sauer
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Caroline Pabst
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, 69117 Heidelberg, Germany
| | - Claudia Wickenhauser
- Institute of Pathology, University Hospital Halle (Saale), Martin-Luther-University Halle-Wittenberg, 06112 Halle, Germany
| | - Linus Angenendt
- Department of Medicine A, Hematology and Oncology, University Hospital, Muenster, Germany; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Christoph Schliemann
- Department of Medicine A, Hematology and Oncology, University Hospital, Muenster, Germany
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Simon Haas
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
| | - Michael Scherer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Simon Raffel
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, 69117 Heidelberg, Germany.
| | - Lars Velten
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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5
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Urabe A, Chi S, Minami Y. The Immuno-Oncology and Genomic Aspects of DNA-Hypomethylating Therapeutics in Acute Myeloid Leukemia. Int J Mol Sci 2023; 24:ijms24043727. [PMID: 36835136 PMCID: PMC9961620 DOI: 10.3390/ijms24043727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Hypomethylating agents (HMAs) have been used for decades in the treatment of hematologic neoplasms, and now, have gathered attention again in terms of their combination with potent molecular-targeted agents such as a BCL-6 inhibitor venetoclax and an IDH1 inhibitor ivosidenib, as well as a novel immune-checkpoint inhibitor (anit-CD47 antibody) megrolimab. Several studies have shown that leukemic cells have a distinct immunological microenvironment, which is at least partially due to genetic alterations such as the TP53 mutation and epigenetic dysregulation. HMAs possibly improve intrinsic anti-leukemic immunity and sensitivity to immune therapies such as PD-1/PD-L1 inhibitors and anti-CD47 agents. This review describes the immuno-oncological backgrounds of the leukemic microenvironment and the therapeutic mechanisms of HMAs, as well as current clinical trials of HMAs and/or venetoclax-based combination therapies.
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Affiliation(s)
| | | | - Yosuke Minami
- Correspondence: ; Tel.: +81-4-7133-1111; Fax: +81-7133-6502
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6
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Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukemia. Oncogene 2023; 42:1272-1281. [PMID: 36739363 PMCID: PMC10101851 DOI: 10.1038/s41388-023-02611-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/06/2023]
Abstract
Isocitrate dehydrogenase 2 (IDH2) mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia (CN-AML) but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2R172K and IDH2R140Q AML and reported their pathologic, functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co-expressing FLT3ITD and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to adulthood, full-blown leukemia ensued with multi-lineage dysplasia, increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. Tg(Runx1:FLT3ITDIDH2R172K) but not Tg(Runx1:FLT3ITDIDH2R140Q) zebrafish showed an increase in T-cell development at embryonic and adult stages. Single-cell transcriptomic analysis revealed increased myeloid skewing, differentiation blockade and enrichment of leukemia-associated gene signatures in both zebrafish models. Tg(Runx1:FLT3ITDIDH2R172K) but not Tg(Runx1:FLT3ITDIDH2R140Q) zebrafish showed an increase in interferon signals at the adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion, the zebrafish models of IDH2 mutated AML recapitulated the morphologic, clinical, functional and transcriptomic characteristics of human diseases, and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening.
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MIR retrotransposons link the epigenome and the transcriptome of coding genes in acute myeloid leukemia. Nat Commun 2022; 13:6524. [PMID: 36316347 PMCID: PMC9622910 DOI: 10.1038/s41467-022-34211-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
DNMT3A and IDH1/2 mutations combinatorically regulate the transcriptome and the epigenome in acute myeloid leukemia; yet the mechanisms of this interplay are unknown. Using a systems approach within topologically associating domains, we find that genes with significant expression-methylation correlations are enriched in signaling and metabolic pathways. The common denominator across these methylation-regulated genes is the density in MIR retrotransposons of their introns. Moreover, a discrete number of CpGs overlapping enhancers are responsible for regulating most of these genes. Established mouse models recapitulate the dependency of MIR-rich genes on the balanced expression of epigenetic modifiers, while projection of leukemic profiles onto normal hematopoiesis ones further consolidates the dependencies of methylation-regulated genes on MIRs. Collectively, MIR elements on genes and enhancers are susceptible to changes in DNA methylation activity and explain the cooperativity of proteins in this pathway in normal and malignant hematopoiesis.
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8
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Transcriptome-wide subtyping of pediatric and adult T cell acute lymphoblastic leukemia in an international study of 707 cases. Proc Natl Acad Sci U S A 2022; 119:e2120787119. [PMID: 35385357 PMCID: PMC9169777 DOI: 10.1073/pnas.2120787119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We provide transcriptomic insights into differences between pediatric and adult T cell acute lymphoblastic leukemia (T-ALL) patients through an international collaborative effort integrating RNA-sequencing data of 707 patients. Ten subtypes were identified, each characterized by distinct gene mutation profiles and dysregulated expression signatures of leukemogenic factors, and associated with T cell development stages. Adult T-ALL tends to have characteristics of early T cell precursor ALL, mostly corresponding to the mixed phenotype acute leukemia, whereas pediatric T-ALL shows a wide spectrum of aberrant molecular features, from early T cell precursor to mature T cell compartments. Our findings have important implications for disease mechanism of T-ALL that differs between pediatric and adult patients, facilitating further refined targeted therapy. T cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy of T cell progenitors, known to be a heterogeneous disease in pediatric and adult patients. Here we attempted to better understand the disease at the molecular level based on the transcriptomic landscape of 707 T-ALL patients (510 pediatric, 190 adult patients, and 7 with unknown age; 599 from published cohorts and 108 newly investigated). Leveraging the information of gene expression enabled us to identify 10 subtypes (G1–G10), including the previously undescribed one characterized by GATA3 mutations, with GATA3R276Q capable of affecting lymphocyte development in zebrafish. Through associating with T cell differentiation stages, we found that high expression of LYL1/LMO2/SPI1/HOXA (G1–G6) might represent the early T cell progenitor, pro/precortical/cortical stage with a relatively high age of disease onset, and lymphoblasts with TLX3/TLX1 high expression (G7–G8) could be blocked at the cortical/postcortical stage, while those with high expression of NKX2-1/TAL1/LMO1 (G9–G10) might correspond to cortical/postcortical/mature stages of T cell development. Notably, adult patients harbored more cooperative mutations among epigenetic regulators, and genes involved in JAK-STAT and RAS signaling pathways, with 44% of patients aged 40 y or above in G1 bearing DNMT3A/IDH2 mutations usually seen in acute myeloid leukemia, suggesting the nature of mixed phenotype acute leukemia.
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9
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Fang X, Miao C, Zeng T, Chu W, Zheng Y, Sun X, Yin X, Li Y. Role of m 5 C RNA methylation regulators in colorectal cancer prognosis and immune microenvironment. J Clin Lab Anal 2022; 36:e24303. [PMID: 35212022 PMCID: PMC8993619 DOI: 10.1002/jcla.24303] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 12/24/2022] Open
Abstract
Background RNA modification has become one of the hot topics of research as it can be used for tumor prognosis. However, its role in various biological processes is still poorly understood. The aim of this study was to investigate the role of m5C and m1A regulators on colorectal cancer prognosis using bioinformatics tools. The association between these regulators and differences in patient survival as well as the clinicopathological characteristics and tumor immune microenvironment in colorectal cancer tissues were assessed. Methods We selected publicly available colorectal cancer data sets from The Cancer Genome Atlas and used the “limma” package in R to identify differentially expressed genes. The least absolute shrinkage and selection operator regression model was used to calculate the prognostic risk, and a risk prediction model was constructed, to help assess the prognostic values of the differentially expressed genes. Finally, using TISCH and TIMER, we assessed the extent of cellular infiltration in colorectal cancer. Results We explored NSUN6 and DNMT3A expression using UALCAN and HPA and found that their expression is significantly increased in colorectal cancer tissues and correlated with sex and TP53 mutation status. Moreover, we found NSUN6 and DNMT3A were related to the infiltration of six major immune cells, with DNMT3A being closely related to dendritic cells, CD4+ T cells, and B cells, whereas NSUN6 to B cells and CD8+ T cells. Conclusion Our findings suggest that m5C regulators can predict the clinical prognostic risk and regulate the tumor immune microenvironment in colorectal cancer.
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Affiliation(s)
- Xiaojie Fang
- Department of Anorectal Surgery, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Chenyun Miao
- Department of TCM Gynecology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Tianni Zeng
- Department of Medical Oncology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Weijian Chu
- Department of Anorectal Surgery, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Yi Zheng
- Department of Anorectal Surgery, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Xi Sun
- Department of Anorectal Surgery, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Xin Yin
- Department of Anorectal Surgery, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Yanyan Li
- Department of Anorectal Surgery, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
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10
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Chen TC, Yao CY, Chen YR, Yuan CT, Lin CC, Hsu YC, Chuang PH, Kao CJ, Li YH, Hou HA, Chou WC, Tien HF. Oncogenesis induced by combined Phf6 and Idh2 mutations through increased oncometabolites and impaired DNA repair. Oncogene 2022; 41:1576-1588. [PMID: 35091680 DOI: 10.1038/s41388-022-02193-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/22/2021] [Accepted: 01/13/2022] [Indexed: 11/09/2022]
Abstract
The pathogenesis of acute leukemia involves interaction among genetic alterations. Mutations of IDH1/2 and PHF6 are common and co-exist in some patients of hematopoietic malignancies, but their cooperative effects remain unexplored. In this study, we addressed the question by characterizing the hematopoietic phenotypes of mice harboring neither, Phf6 knockout, Idh2 R172K, or combined mutations. We found that the combined Phf6KOIdh2R172K mice showed biased hematopoietic differentiation toward myeloid lineages and reduced long-term hematopoietic stem cells. They rapidly developed neoplasms of myeloid and lymphoid lineages, with much shorter survival compared with single mutated and wild-type mice. The marrow and spleen cells of the combined mutated mice produced a drastically increased amount of 2-hydroxyglutarate compared with mice harboring Idh2 R172K. Single-cell RNA sequencing revealed distinct patterns of transcriptome of the hematopoietic stem/progenitor cells from the combined mutated mice, including aberrant expression of metabolic enzymes, increased expression of several oncogenes, and impairment of DNA repairs, as confirmed by the enhanced γH2AX expression in the marrow and spleen cells. We conclude that Idh2 and Phf6 mutations are synergistic in leukemogenesis, at least through overproduction of 2-hydroxyglutarate and impairment of DNA repairs.
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Affiliation(s)
- Tsung-Chih Chen
- Division of Hematology/Medical Oncology, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chi-Yuan Yao
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Ren Chen
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chang-Tsu Yuan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Pathology, National Taiwan University Cancer Center, Taipei, Taiwan.,Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Chin Lin
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yueh-Chwen Hsu
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Po-Han Chuang
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chein-Jun Kao
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Hung Li
- Department of Animal Science, Chinese Culture University, Taipei, Taiwan
| | - Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Wen-Chien Chou
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan. .,Department of Pathology, National Taiwan University Cancer Center, Taipei, Taiwan.
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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11
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Wang XY, Zhu WW, Wang Z, Huang JB, Wang SH, Bai FM, Li TE, Zhu Y, Zhao J, Yang X, Lu L, Zhang JB, Jia HL, Dong QZ, Chen JH, Andersen JB, Ye D, Qin LX. Driver mutations of intrahepatic cholangiocarcinoma shape clinically relevant genomic clusters with distinct molecular features and therapeutic vulnerabilities. Am J Cancer Res 2022; 12:260-276. [PMID: 34987644 PMCID: PMC8690927 DOI: 10.7150/thno.63417] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/22/2021] [Indexed: 12/15/2022] Open
Abstract
Purpose: To establish a clinically applicable genomic clustering system, we investigated the interactive landscape of driver mutations in intrahepatic cholangiocarcinoma (ICC). Methods: The genomic data of 1481 ICCs from diverse populations was analyzed to investigate the pair-wise co-occurrences or mutual exclusivities among recurrent driver mutations. Clinicopathological features and outcomes were compared among different clusters. Gene expression and DNA methylation profiling datasets were analyzed to investigate the molecular distinctions among mutational clusters. ICC cell lines with different gene mutation backgrounds were used to evaluate the cluster specific biological behaviors and drug sensitivities. Results: Statistically significant mutation-pairs were identified across 21 combinations of genes. Seven most recurrent driver mutations (TP53, KRAS, SMAD4, IDH1/2, FGFR2-fus and BAP1) showed pair-wise co-occurrences or mutual exclusivities and could aggregate into three genetic clusters: Cluster1: represented by tripartite interaction of KRAS, TP53 and SMAD4 mutations, exhibited large bile duct histological phenotype with high CA19-9 level and dismal prognosis; Cluster2: co-association of IDH/BAP1 or FGFR2-fus/BAP1 mutation, was characterized by small bile duct phenotype, low CA19-9 level and optimal prognosis; Cluster3: mutation-free ICC cases with intermediate clinicopathological features. These clusters showed distinct molecular traits, biological behaviors and responses to therapeutic drugs. Finally, we identified S100P and KRT17 as “cluster-specific”, “lineage-dictating” and “prognosis-related” biomarkers, which in combination with CA19-9 could well stratify Cluster3 ICCs into two biologically and clinically distinct subtypes. Conclusions: This clinically applicable clustering system can be instructive to ICC prognostic stratification, molecular classification, and therapeutic optimization.
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12
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Kurtz KJ, Conneely SE, O'Keefe M, Wohlan K, Rau RE. Murine Models of Acute Myeloid Leukemia. Front Oncol 2022; 12:854973. [PMID: 35756660 PMCID: PMC9214208 DOI: 10.3389/fonc.2022.854973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/16/2022] [Indexed: 01/27/2023] Open
Abstract
Acute myeloid leukemia (AML) is a phenotypically and genetically heterogeneous hematologic malignancy. Extensive sequencing efforts have mapped the genomic landscape of adult and pediatric AML revealing a number of biologically and prognostically relevant driver lesions. Beyond identifying recurrent genetic aberrations, it is of critical importance to fully delineate the complex mechanisms by which they contribute to the initiation and evolution of disease to ultimately facilitate the development of targeted therapies. Towards these aims, murine models of AML are indispensable research tools. The rapid evolution of genetic engineering techniques over the past 20 years has greatly advanced the use of murine models to mirror specific genetic subtypes of human AML, define cell-intrinsic and extrinsic disease mechanisms, study the interaction between co-occurring genetic lesions, and test novel therapeutic approaches. This review summarizes the mouse model systems that have been developed to recapitulate the most common genomic subtypes of AML. We will discuss the strengths and weaknesses of varying modeling strategies, highlight major discoveries emanating from these model systems, and outline future opportunities to leverage emerging technologies for mechanistic and preclinical investigations.
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Affiliation(s)
- Kristen J Kurtz
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, United States
| | - Shannon E Conneely
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, United States
| | - Madeleine O'Keefe
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, United States
| | - Katharina Wohlan
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Rachel E Rau
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, United States
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13
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Mouse Models of Frequently Mutated Genes in Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13246192. [PMID: 34944812 PMCID: PMC8699817 DOI: 10.3390/cancers13246192] [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: 09/30/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 01/19/2023] Open
Abstract
Acute myeloid leukemia is a clinically and biologically heterogeneous blood cancer with variable prognosis and response to conventional therapies. Comprehensive sequencing enabled the discovery of recurrent mutations and chromosomal aberrations in AML. Mouse models are essential to study the biological function of these genes and to identify relevant drug targets. This comprehensive review describes the evidence currently available from mouse models for the leukemogenic function of mutations in seven functional gene groups: cell signaling genes, epigenetic modifier genes, nucleophosmin 1 (NPM1), transcription factors, tumor suppressors, spliceosome genes, and cohesin complex genes. Additionally, we provide a synergy map of frequently cooperating mutations in AML development and correlate prognosis of these mutations with leukemogenicity in mouse models to better understand the co-dependence of mutations in AML.
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14
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Duchmann M, Laplane L, Itzykson R. Clonal Architecture and Evolutionary Dynamics in Acute Myeloid Leukemias. Cancers (Basel) 2021; 13:4887. [PMID: 34638371 PMCID: PMC8507870 DOI: 10.3390/cancers13194887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/19/2022] Open
Abstract
Acute myeloid leukemias (AML) results from the accumulation of genetic and epigenetic alterations, often in the context of an aging hematopoietic environment. The development of high-throughput sequencing-and more recently, of single-cell technologies-has shed light on the intratumoral diversity of leukemic cells. Taking AML as a model disease, we review the multiple sources of genetic, epigenetic, and functional heterogeneity of leukemic cells and discuss the definition of a leukemic clone extending its definition beyond genetics. After introducing the two dimensions contributing to clonal diversity, namely, richness (number of leukemic clones) and evenness (distribution of clone sizes), we discuss the mechanisms at the origin of clonal emergence (mutation rate, number of generations, and effective size of the leukemic population) and the causes of clonal dynamics. We discuss the possible role of neutral drift, but also of cell-intrinsic and -extrinsic influences on clonal fitness. After reviewing available data on the prognostic role of genetic and epigenetic diversity of leukemic cells on patients' outcome, we discuss how a better understanding of AML as an evolutionary process could lead to the design of novel therapeutic strategies in this disease.
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Affiliation(s)
- Matthieu Duchmann
- Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Université de Paris, 75010 Paris, France;
- Laboratoire d’Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 75010 Paris, France
| | - Lucie Laplane
- Institut d’Histoire et Philosophie des Sciences et des Techniques UMR 8590, CNRS, Université Paris 1 Panthéon-Sorbonne, 75010 Paris, France;
- Gustave Roussy Cancer Center, UMR1287, 94805 Villejuif, France
| | - Raphael Itzykson
- Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Université de Paris, 75010 Paris, France;
- Département Hématologie et Immunologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 75010 Paris, France
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15
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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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16
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Abstract
PURPOSE OF REVIEW Clonal heterogeneity is a significant obstacle to successful treatment of patients with acute myeloid leukemia (AML). Here, we review new advances in the understanding of genetic heterogeneity in AML using single-cell DNA-sequencing technology. RECENT FINDINGS New genomics and immunologic discovery tools have provided single-cell resolution maps of the clonal architecture of AML. The use of these technologies reveals the mutational landscape of AML at diagnosis, during treatment, and at relapse has an enormous degree of clonal complexity and diversity that is poised to adapt and evolve under environmental pressures. SUMMARY AML is a complex ecosystem of competing and cooperating clones undergoing constant evolution and selection.
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17
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Yang H, Sun B, Xu K, He Y, Zhang T, Hall SRR, Tan ST, Schmid RA, Peng RW, Hu G, Yao F. Pharmaco-transcriptomic correlation analysis reveals novel responsive signatures to HDAC inhibitors and identifies Dasatinib as a synergistic interactor in small-cell lung cancer. EBioMedicine 2021; 69:103457. [PMID: 34224975 PMCID: PMC8264109 DOI: 10.1016/j.ebiom.2021.103457] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Histone acetylation/deacetylase process is one of the most studied epigenetic modifications. Histone deacetylase inhibitors (HDACis) have shown clinical benefits in haematological malignancies but failed in solid tumours due to the lack of biomarker-driven stratification. METHODS We perform integrative pharmaco-transcriptomic analysis by correlating drug response profiles of five pan-HDACis with transcriptomes of solid cancer cell lines (n=659) to systematically identify generalizable gene signatures associated with HDACis sensitivity and resistance. The established signatures are then applied to identify cancer subtypes that are potentially sensitive or resistant to HDACis, and drugs that enhance the efficacy of HDACis. Finally, the reproductivity of the established HDACis signatures is evaluated by multiple independent drug response datasets and experimental assays. FINDINGS We successfully delineate generalizable gene signatures predicting sensitivity (containing 46 genes) and resistance (containing 53 genes) to all five HDACis, with their reproductivity confirmed by multiple external sources and independent internal assays. Using the gene signatures, we identify low-grade glioma harbouring isocitrate dehydrogenase 1/2 (IDH1/2) mutation and non-YAP1-driven subsets of small-cell lung cancer (SCLC) that particularly benefit from HDACis monotherapy. Further, based on the resistance gene signature, we identify clinically-approved Dasatinib as a synthetic lethal drug with HDACi, synergizing in inducing apoptosis and reactive oxygen species on a panel of SCLC. Finally, Dasatinib significantly enhances the therapeutic efficacy of Vorinostat in SCLC xenografts. INTERPRETATION Our work establishes robust gene signatures predicting HDACis sensitivity/resistance in solid cancer and uncovers combined Dasatinib/HDACi as a synthetic lethal combination therapy for SCLC. FUNDING This work was supported by the National Natural Science Foundation of China (82072570 to F. Yao; 82002941 to B. Sun).
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Affiliation(s)
- Haitang Yang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China.
| | - Beibei Sun
- Institute for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Ke Xu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Yunfei He
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China, Shanghai, 200030, People's Republic of China
| | - Tuo Zhang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Sean R R Hall
- Gillies McIndoe Research Institute, Wellington, 6242, New Zealand
| | - Swee T Tan
- Gillies McIndoe Research Institute, Wellington, 6242, New Zealand
| | - Ralph A Schmid
- Division of General Thoracic Surgery, Department of BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, 3008, Switzerland
| | - Ren-Wang Peng
- Division of General Thoracic Surgery, Department of BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, 3008, Switzerland
| | - Guohong Hu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China, Shanghai, 200030, People's Republic of China
| | - Feng Yao
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China.
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18
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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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19
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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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20
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Targeting LSD1 for acute myeloid leukemia (AML) treatment. Pharmacol Res 2020; 164:105335. [PMID: 33285227 DOI: 10.1016/j.phrs.2020.105335] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022]
Abstract
Targeted therapy for acute myeloid leukemia (AML) is an effective strategy, but currently there are very limited therapeutic targets for AML treatment. Histone lysine specific demethylase 1 (LSD1) is highly expressed in many cancers, impedes the differentiation of cancer cells, promotes the proliferation, metastasis and invasion of cancer cells, and is associated with poor prognosis. Targeting LSD1 has been recognized as a promising strategy for AML treatment in recent years. Based on these features, in the review, we discussed the main epigenetic drugs targeting LSD1 for AML therapy. Thus, this review focuses on the progress of LSD1 inhibitors in AML treatment, particularly those such as tranylcypromine (TCP), ORY-1001, GSK2879552, and IMG-7289 in clinical trials. These inhibitors provide novel scaffolds for designing new LSD1 inhibitors. Besides, combined therapies of LSD1 inhibitors with other drugs for AML treatment are also highlighted.
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21
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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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22
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Testa U, Castelli G, Pelosi E. Isocitrate Dehydrogenase Mutations in Myelodysplastic Syndromes and in Acute Myeloid Leukemias. Cancers (Basel) 2020; 12:E2427. [PMID: 32859092 PMCID: PMC7564409 DOI: 10.3390/cancers12092427] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/03/2020] [Accepted: 08/20/2020] [Indexed: 02/07/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease generated by the acquisition of multiple genetic and epigenetic aberrations which impair the proliferation and differentiation of hematopoietic progenitors and precursors. In the last years, there has been a dramatic improvement in the understanding of the molecular alterations driving cellular signaling and biochemical changes determining the survival advantage, stimulation of proliferation, and impairment of cellular differentiation of leukemic cells. These molecular alterations influence clinical outcomes and provide potential targets for drug development. Among these alterations, an important role is played by two mutant enzymes of the citric acid cycle, isocitrate dehydrogenase (IDH), IDH1 and IDH2, occurring in about 20% of AMLs, which leads to the production of an oncogenic metabolite R-2-hydroxy-glutarate (R-2-HG); this causes a DNA hypermethylation and an inhibition of hematopoietic stem cell differentiation. IDH mutations differentially affect prognosis of AML patients following the location of the mutation and other co-occurring genomic abnormalities. Recently, the development of novel therapies based on the specific targeting of mutant IDH may contribute to new effective treatments of these patients. In this review, we will provide a detailed analysis of the biological, clinical, and therapeutic implications of IDH mutations.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (G.C.); (E.P.)
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23
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Yu J, Li Y, Zhang D, Wan D, Jiang Z. Clinical implications of recurrent gene mutations in acute myeloid leukemia. Exp Hematol Oncol 2020; 9:4. [PMID: 32231866 PMCID: PMC7099827 DOI: 10.1186/s40164-020-00161-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 03/17/2020] [Indexed: 12/18/2022] Open
Abstract
Acute myeloid leukemia (AML) is a genetically heterogeneous clonal malignancy characterized by recurrent gene mutations. Genomic heterogeneity, patients’ individual variability, and recurrent gene mutations are the major obstacles among many factors that impact treatment efficacy of the AML patients. With the application of cost- and time-effective next-generation sequencing (NGS) technologies, an enormous diversity of genetic mutations has been identified. The recurrent gene mutations and their important roles in acute myeloid leukemia (AML) pathogenesis have been studied extensively. In this review, we summarize the recent development on the gene mutation in patients with AML.
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Affiliation(s)
- Jifeng Yu
- 1Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China.,2Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Yingmei Li
- 1Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Danfeng Zhang
- 1Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Dingming Wan
- 1Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Zhongxing Jiang
- 1Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
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24
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Cooperating mutations: joint forces, novel vulnerabilities. Blood 2020; 135:785-787. [DOI: 10.1182/blood.2019004679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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25
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Dai YJ, Hu F, He SY, Wang YY. Epigenetic landscape analysis of lncRNAs in acute myeloid leukemia with DNMT3A mutations. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:318. [PMID: 32355762 PMCID: PMC7186694 DOI: 10.21037/atm.2020.02.143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background Acute myeloid leukemia (AML) is a type of cancer that consists of a group of hematological malignancies with high heterogeneity. DNA methyltransferase 3A (DNMT3A)-mutated AML patients have a poor prognosis. Some long non-coding RNAs (lncRNAs) have been reported to enhance therapeutic sensitivity, and so could affect the overall survival rate of elderly cytogenetically normal acute myeloid leukemia (CN-AML) patients; however, studies on the lncRNA signature in DNMT3A-mutated AML are rare. Method The DNMT3A R878H conditional knock-in mouse model was constructed to explore the lncRNAs of DNMT3A mutation by using the Cuffcomparison method. Cis and trans regulation networks were used to predict candidate genes. The expression levels in leukemic cell lines and the prognostic index of these candidate genes were analyzed with the Broad Institute Cancer Cell Line Encyclopedia (CCLE) and OncoLnc databases. The data for each sample were statistically analyzed using GraphPad Prism. Results In this study, we applied the DNMT3A R878H conditional knock-in mouse model to explore the lncRNA epigenetic landscape of DNMT3A mutation by using the Cuffcomparison method. Twenty-three differentially expressed lncRNAs were identified in Dnmt3aR878H/WTMx1-Cre+ mice. We next predicted the downstream targetable genes regulated by these lncRNAs through cis and trans regulation networks and found 124 candidate genes are related to these lncRNAs. In further analysis of 124 genes, we found that increased mRNA expression levels of interleukin 1 receptor type 2 (IL1R2), Krüppel-like factor 13 (KLF13), ATPase H+ transporting V1 subunit A (ATP6V1A), proteasome 26S Subunit, non-ATPase 3 (PSMD3), and pyrroline-5-carboxylate reductase 2 (PYCR2) were associated with poor prognosis in AML. Functional analysis of these genes demonstrated that the pathways involved in autophagy, cell cycle, and hematopoietic stem cell differentiation were more enriched in Dnmt3aR878H/WTMx1-Cre+ mice. Conclusion Our study was the first to use DNMT3A R878H conditional knock-in mouse model to predict the specific lncRNAs regulated by the DNMT3A mutation in AML. Six candidate genes were found to be associated with DNMT3A mutation with poor prognosis. Our results provided a possible treatment strategy for this disease.
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Affiliation(s)
- Yu-Jun Dai
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510000, China.,Center State Key Laboratory of Oncology in South China, Guangzhou 510000, China.,Collaborative Innovation Center for Cancer Medicine, Guangzhou 510000, China
| | - Fang Hu
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510000, China.,Center State Key Laboratory of Oncology in South China, Guangzhou 510000, China.,Collaborative Innovation Center for Cancer Medicine, Guangzhou 510000, China
| | - Si-Yuan He
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Yue-Ying Wang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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