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Jafari PA, Bagheri R, Lavasani S, Goudarzi S. DNMT3A-R882: a mutation with many paradoxes. Ann Hematol 2024:10.1007/s00277-024-05874-x. [PMID: 38969930 DOI: 10.1007/s00277-024-05874-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
Understanding the underlying mechanism of acute myeloid leukemia (AML) has led to the discovery of novel biomarkers to help predict, treat and monitor leukemia. DNA (cytosine-5)-methyltransferase 3 A (DNMT3A) is considered a prognostic and therapeutic epigenetic target in AML patients with a hotspot mutation of R882. R882 mutation is associated with impaired differentiation of Hematopoietic stem cells in the bone marrow and disease progression. The prevalence of R882 mutation varied in different ethnicities and countries, and similarly, its prognostic impact differed among numerous studies. Nevertheless, the co-occurrence of mutations in R882 with NPM1 and FLT3 has been reported more frequently and is associated with a worse prognosis. These studies also suggest diverse results regarding bone marrow transplantation response as a treatment, while chemoresistance is reached as a conclusive outcome These findings highlight the crucial need for an in-depth discussion on the significance of the R882 mutation in AML patients. Understanding its impact on leukemic transformation, prognosis, and treatment is vital for advancing clinical implications.
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Affiliation(s)
| | - Ramin Bagheri
- Mashhad University of Medical Sciences, Mashhad, Iran
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2
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Dhuri K, Alachkar H. Differences in the mutational landscape of clonal hematopoiesis of indeterminate potential among Races and between Male and Female patients with cancer. Exp Hematol 2024:104271. [PMID: 38969020 DOI: 10.1016/j.exphem.2024.104271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 07/07/2024]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) has emerged as a significant precursor to hematological malignancies and is associated with several age-related diseases. We leveraged public data to explore differences in the mutational landscape of CHIP between males and females and across diverse racial populations. DNMT3A mutations were substantially more prevalent in females than in males (38.94% vs. 31.37%, p-value: <0.001, q-value: <0.001). While ASXL1 mutations were more frequent in males than females (5.82% vs 2.69%, p-value: <0.001, q-value: <0.001). In the racial cohorts with sufficient sample sizes, STAT5B and CSF1R mutations were most frequent in Asian (1.40% and 0.84%), followed by Black (0.98% and 0.24%) and White populations (0.29% and 0.09%), (p-value: 0.001 and 0.001, q-value: 0.023 and 0.023). Several other CHIP mutations were enriched in Black: RARA, SMAD2, CDKN1B, CENPA, CTLA4, EIF1AX, ELF3, MSI1, MYC, SOX17, AURKA. On the other hand, H3C1, H3C4, MYCL were enriched in the Asian cohort. Our analysis highlights sex and racial differences in the CHIP mutations among patients with cancer. As CHIP continues to gain recognition as a critical precursor to malignancies and other diseases, understanding how these differences contribute to CHIP underlying mechanisms and clinical implications is critical.
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Affiliation(s)
- Kanaka Dhuri
- USC Alfred E. Mann School of Pharmacy and Pharmaceutical sciences, University of Southern California, Los Angeles, CA
| | - Houda Alachkar
- USC Alfred E. Mann School of Pharmacy and Pharmaceutical sciences, University of Southern California, Los Angeles, CA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA.
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3
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Choudhury S, Anne A, Singh M, Chaillet JR, Mohan KN. DNMT1 Y495C mutation interferes with maintenance methylation of imprinting control regions. Int J Biochem Cell Biol 2024; 169:106535. [PMID: 38281697 DOI: 10.1016/j.biocel.2024.106535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/05/2024] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
Hereditary Sensory and Autonomic Neuropathy Type 1E (HSAN1E) is a rare autosomal dominant neurological disorder due to missense mutations in DNA methyltransferase 1 (DNMT1). To investigate the nature of the dominant effect, we compared methylomes of transgenic R1wtDnmt1 and R1Dnmt1Y495C mouse embryonic stem cells (mESCs) overexpressing WT and the mutant mouse proteins respectively, with the R1 (wild-type) cells. In case of R1Dnmt1Y495C, 15 out of the 20 imprinting control regions were hypomethylated with transcript level dysregulation of multiple imprinted genes in ESCs and neurons. Non-imprinted regions, minor satellites, major satellites, LINE1 and IAP repeats were unaffected. These data mirror the specific imprinting defects associated with transient removal of DNMT1 in mESCs, deletion of the maternal-effect DNMT1o variant in preimplantation mouse embryos, and in part, reprogramming to naïve human iPSCs. This is the first DNMT1 mutation demonstrated to specifically affect Imprinting Control Regions (ICRs), and reinforces the differences in maintenance methylation of ICRs over non-imprinted regions. Consistent with nervous system abnormalities in the HSAN1E disorder and involvement of imprinted genes in normal development and neurogenesis, R1Dnmt1Y495C cells showed dysregulated pluripotency and neuron marker genes, and yielded more slender, shorter, and extensively branched neurons. We speculate that R1Dnmt1Y495C cells produce predominantly dimers containing mutant proteins, leading to a gradual and specific loss of ICR methylation during early human development.
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Affiliation(s)
- Sumana Choudhury
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India; Centre for Human Disease Research, BITS Pilani Hyderabad Campus, Hyderabad 500078, India
| | - Anuhya Anne
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India; Centre for Human Disease Research, BITS Pilani Hyderabad Campus, Hyderabad 500078, India
| | - Minali Singh
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India
| | - John Richard Chaillet
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kommu Naga Mohan
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India; Centre for Human Disease Research, BITS Pilani Hyderabad Campus, Hyderabad 500078, India.
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4
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Tibben BM, Rothbart SB. Mechanisms of DNA Methylation Regulatory Function and Crosstalk with Histone Lysine Methylation. J Mol Biol 2024; 436:168394. [PMID: 38092287 PMCID: PMC10957332 DOI: 10.1016/j.jmb.2023.168394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
DNA methylation is a well-studied epigenetic modification that has key roles in regulating gene expression, maintaining genome integrity, and determining cell fate. Precisely how DNA methylation patterns are established and maintained in specific cell types at key developmental stages is still being elucidated. However, research over the last two decades has contributed to our understanding of DNA methylation regulation by other epigenetic processes. Specifically, lysine methylation on key residues of histone proteins has been shown to contribute to the allosteric regulation of DNA methyltransferase (DNMT) activities. In this review, we discuss the dynamic interplay between DNA methylation and histone lysine methylation as epigenetic regulators of genome function by synthesizing key recent studies in the field. With a focus on DNMT3 enzymes, we discuss mechanisms of DNA methylation and histone lysine methylation crosstalk in the regulation of gene expression and the maintenance of genome integrity. Further, we discuss how alterations to the balance of various sites of histone lysine methylation and DNA methylation contribute to human developmental disorders and cancers. Finally, we provide perspectives on the current direction of the field and highlight areas for continued research and development.
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Affiliation(s)
- Bailey M Tibben
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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Lai X, Xiao J, Wang T, Hou C, Chen J, Wu D, Xu Y. Prognostic significance of persisting DNMT3A, ASXL1, and TET2 mutation burden in acute myeloid leukemia patients with allogeneic hematopoietic stem cell transplantation during complete remission. Leuk Lymphoma 2024; 65:363-371. [PMID: 37990829 DOI: 10.1080/10428194.2023.2284089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/12/2023] [Indexed: 11/23/2023]
Abstract
We retrospectively analyzed 155 AML patients with DAT mutations at diagnosis who underwent allogeneic hematopoietic stem cell transplantation (allo-HSCT) at complete remission. Of the 155 AML patients with DAT mutations at diagnosis, 59 (38.1%) patients had persisting DAT mutations pretransplantation. Compared to patients with pretransplant DAT transitions, patients with persisting DAT mutation burden were shown to be older (p = 0.004), and fewer patients had TET2 mutations at diagnosis (p = 0.033). Patients with persistent DAT mutation burden had shorter overall survival (OS) (3-year OS: 59.3% vs. 83.0%, p < 0.001) and disease-free survival (DFS) (3-year DFS: 56.1% vs. 83.0%, p < 0.001) with a higher cumulative incidence of relapse (CIR) (24.6% vs. 17.4%, p = 0.002) than those with DAT transitions. Additionally, multivariate analysis confirmed that persisting DAT mutations were an independent adverse factor for relapse, OS, and DFS. Collectively, persisting DAT mutations prior to allo-HSCT at complete remission for AML correlated with negative outcomes.
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Affiliation(s)
- Xiaoxuan Lai
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Jinyan Xiao
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Tanzhen Wang
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Chang Hou
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Jia Chen
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Depei Wu
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Yang Xu
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
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6
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Bae SG, Kim HJ, Kim MY, Kim DDH, Shin SI, Ahn JS, Park J. Identification of Cell Type-Specific Effects of DNMT3A Mutations on Relapse in Acute Myeloid Leukemia. Mol Cells 2023; 46:611-626. [PMID: 37853686 PMCID: PMC10590706 DOI: 10.14348/molcells.2023.0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 10/20/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease caused by distinctive mutations in individual patients; therefore, each patient may display different cell-type compositions. Although most patients with AML achieve complete remission (CR) through intensive chemotherapy, the likelihood of relapse remains high. Several studies have attempted to characterize the genetic and cellular heterogeneity of AML; however, our understanding of the cellular heterogeneity of AML remains limited. In this study, we performed single-cell RNA sequencing (scRNAseq) of bone marrow-derived mononuclear cells obtained from same patients at different AML stages (diagnosis, CR, and relapse). We found that hematopoietic stem cells (HSCs) at diagnosis were abnormal compared to normal HSCs. By improving the detection of the DNMT3A R882 mutation with targeted scRNAseq, we identified that DNMT3A-mutant cells that mainly remained were granulocyte-monocyte progenitors (GMPs) or lymphoid-primed multipotential progenitors (LMPPs) from CR to relapse and that DNMT3A-mutant cells have gene signatures related to AML and leukemic cells. Copy number variation analysis at the single-cell level indicated that the cell type that possesses DNMT3A mutations is an important factor in AML relapse and that GMP and LMPP cells can affect relapse in patients with AML. This study advances our understanding of the role of DNMT3A in AML relapse and our approach can be applied to predict treatment outcomes.
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Affiliation(s)
- Seo-Gyeong Bae
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Hyeoung-Joon Kim
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Chonnam National University, Hwasun 58128, Korea
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun 58128, Korea
| | - Mi Yeon Kim
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Chonnam National University, Hwasun 58128, Korea
| | - Dennis Dong Hwan Kim
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - So-I Shin
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Jae-Sook Ahn
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Chonnam National University, Hwasun 58128, Korea
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun 58128, Korea
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
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Park MN. The Therapeutic Potential of a Strategy to Prevent Acute Myeloid Leukemia Stem Cell Reprogramming in Older Patients. Int J Mol Sci 2023; 24:12037. [PMID: 37569414 PMCID: PMC10418941 DOI: 10.3390/ijms241512037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Acute myeloid leukemia (AML) is the most common and incurable leukemia subtype. Despite extensive research into the disease's intricate molecular mechanisms, effective treatments or expanded diagnostic or prognostic markers for AML have not yet been identified. The morphological, immunophenotypic, cytogenetic, biomolecular, and clinical characteristics of AML patients are extensive and complex. Leukemia stem cells (LSCs) consist of hematopoietic stem cells (HSCs) and cancer cells transformed by a complex, finely-tuned interaction that causes the complexity of AML. Microenvironmental regulation of LSCs dormancy and the diagnostic and therapeutic implications for identifying and targeting LSCs due to their significance in the pathogenesis of AML are discussed in this review. It is essential to perceive the relationship between the niche for LSCs and HSCs, which together cause the progression of AML. Notably, methylation is a well-known epigenetic change that is significant in AML, and our data also reveal that microRNAs are a unique factor for LSCs. Multiple-targeted approaches to reduce the risk of epigenetic factors, such as the administration of natural compounds for the elimination of local LSCs, may prevent potentially fatal relapses. Furthermore, the survival analysis of overlapping genes revealed that specific targets had significant effects on the survival and prognosis of patients. We predict that the multiple-targeted effects of herbal products on epigenetic modification are governed by different mechanisms in AML and could prevent potentially fatal relapses. Thus, these strategies can facilitate the incorporation of herbal medicine and natural compounds into the advanced drug discovery and development processes achievable with Network Pharmacology research.
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Affiliation(s)
- Moon Nyeo Park
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 05253, Republic of Korea
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8
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Schandl CA, Mazzoni S, Znoyko I, Nahhas GJ, Chung D, Ding Y, Hess B, Wolff DJ. Novel high-risk acute myeloid leukemia subgroup with ERG amplification and Biallelic loss of TP53. Cancer Genet 2023; 272-273:23-28. [PMID: 36657266 DOI: 10.1016/j.cancergen.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/21/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
ETS-related gene (ERG) amplification, observed in 4-6% of acute myeloid leukemia (AML), is associated with unfavorable prognosis. To determine coincident effects of additional genomic abnormalities in AML with ERG amplification (ERGamp), we examined 11 ERGamp cases of 205 newly diagnosed AML using chromosomal microarray analysis and next generation sequencing. ERGamp cases demonstrated a distinct pattern of high genetic complexity: loss of 5q, chromothripsis and TP53 loss of function variants. Remarkably, allelic TP53 loss or loss of heterozygosity (LOH) co-occurring with TP53 inactivating mutation dramatically effected ERGamp tumor patient outcome. In the presence of homozygous TP53 loss of function, ERGamp patients demonstrated no response to induction chemotherapy with median overall survival (OS) of 3.8 months (N = 9). Two patients with heterozygous loss of TP53 function underwent alloSCT without evidence of relapse at one year. Similarly, a validation TCGA cohort, 6 of the 8 ERGamp cases with TP53 loss of function demonstrated median OS of 2.5 months. This suggests that with TP53 mutant ERGamp AML, successive loss of the second TP53 allele, typically by 17p deletion or LOH identifies a specific high-risk subtype of AML patients who are resistant to standard induction chemotherapy and need novel approaches to avert the very poor prognosis.
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Affiliation(s)
- Cynthia A Schandl
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Sandra Mazzoni
- Departmant of Hematology and Oncology, Cleveland Clinic Taussig Cancer Center, Cleveland, OH, USA.
| | - Iya Znoyko
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Georges J Nahhas
- Department of Public Health-Division of Biostatistics and Bioinformatics, Medical University of South Carolina, Charleston, SC, USA
| | - Dongjun Chung
- Department of Public Health-Division of Biostatistics and Bioinformatics, Medical University of South Carolina, Charleston, SC, USA
| | - Yanna Ding
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Brian Hess
- Department of Hematology and Oncology, Medical University of South Carolina Hollings Cancer Center, Charleston, SC, USA
| | - Daynna J Wolff
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
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Li W, Liu S, Wang C, Cui L, Zhao X, Liu W, Zhang R, Li Z. DNMT3A low-expression is correlated to poor prognosis in childhood B-ALL and confers resistance to daunorubicin on leukemic cells. BMC Cancer 2023; 23:255. [PMID: 36934225 PMCID: PMC10024838 DOI: 10.1186/s12885-023-10724-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 03/08/2023] [Indexed: 03/19/2023] Open
Abstract
BACKGROUND Little is known about DNMT3A expression and its prognostic significance in childhood B cell acute lymphoblastic leukemia (B-ALL). METHODS We determined DNMT3A mRNA expression in 102 children with B-ALL. Correlations with relapse-free survival (RFS) and common clinical characteristics were analyzed. DNMT3A was stably knocked out by CRISPR/Cas9 gene editing technology in Reh and 697 B-ALL cell lines. Cell proliferation activity after treated with daunorubicin (DNR) was determined by CCK8 assay in DNMT3A KO Reh and 697 cell lines. RESULTS DNMT3A expression in B-ALL patients who were in continuous complete remission (CCR) was higher than in those who got relapse (P = 0.0111). Receiver operating characteristic curve showed prognostic significance of DNMT3A expression (P = 0.003). Low expression of DNMT3A (≤ 0.197) was significantly correlated with poor RFS (P < 0.001) in children with B-ALL. Knock-out of DNMT3A in Reh and 697 cell lines significantly increased IC50 of DNR (P = 0.0201 and 0.0022 respectively), indicating elevated resistance to DNR. CONCLUSION Low expression of DNMT3A associates with poor prognosis in children with B-ALL. Knock-out of DNMT3A confers resistance to DNR on leukemic cells.
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Affiliation(s)
- Weijing Li
- Laboratory of Hematologic Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Shugang Liu
- Laboratory of Hematologic Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Chanjuan Wang
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Lei Cui
- Laboratory of Hematologic Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Xiaoxi Zhao
- Laboratory of Hematologic Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Wei Liu
- Department of Hematology Oncology, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, China.
| | - Ruidong Zhang
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing, China.
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China.
- Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.
| | - Zhigang Li
- Laboratory of Hematologic Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing, China.
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China.
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China.
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Deregulated Gene Expression Profiles and Regulatory Networks in Adult and Pediatric RUNX1/RUNX1T1-Positive AML Patients. Cancers (Basel) 2023; 15:cancers15061795. [PMID: 36980682 PMCID: PMC10046396 DOI: 10.3390/cancers15061795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous and complex disease concerning molecular aberrations and prognosis. RUNX1/RUNX1T1 is a fusion oncogene that results from the chromosomal translocation t(8;21) and plays a crucial role in AML. However, its impact on the transcriptomic profile of different age groups of AML patients is not completely understood. Here, we investigated the deregulated gene expression (DEG) profiles in adult and pediatric RUNX1/RUNX1T1-positive AML patients, and compared their functions and regulatory networks. We retrospectively analyzed gene expression data from two independent Gene Expression Omnibus (GEO) datasets (GSE37642 and GSE75461) and computed their differentially expressed genes and upstream regulators, using limma, GEO2Enrichr, and X2K. For validation purposes, we used the TCGA-LAML (adult) and TARGET-AML (pediatric) patient cohorts. We also analyzed the protein–protein interaction (PPI) networks, as well as those composed of transcription factors (TF), intermediate proteins, and kinases foreseen to regulate the top deregulated genes in each group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses were further performed for the DEGs in each dataset. We found that the top upregulated genes in (both adult and pediatric) RUNX1/RUNX1T1-positive AML patients are enriched in extracellular matrix organization, the cell projection membrane, filopodium membrane, and supramolecular fiber. Our data corroborate that RUNX1/RUNX1T1 reprograms a large transcriptional network to establish and maintain leukemia via intricate PPI interactions and kinase-driven phosphorylation events.
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11
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Subbotina TN, Maslyukova IE, Semashchenko KS, Khodos GA, Kurochkin DV, Shalyova AA, Mikhalev MA, Vasiliev EV, Osadchaya MG, Dunaeva EA, Esman AS, Mironov KO. Analysis of somatic mutations in the <i>JAK2</i>, <i>CALR</i>, <i>MPL</i> and <i>ASXL1</i> genes and evaluation of their impact on the survival of patients with myelofibrosis. ONCOHEMATOLOGY 2023. [DOI: 10.17650/1818-8346-2023-18-1-63-75] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Background. The development of myelofibrosis (MF) is driven by complex molecular genetic events that include driver somatic mutations responsible for the constitutive activation of the JAK/STAT signaling pathway (JAK2, CALR, and MPL), additional mutations affecting epigenetic regulators (TET2, ASXL1, IDH1/2, etc.) and RNA splicing (SRSF2, U2AF1, SF3B1, etc.), as well as genetic aberrations that contribute to genomic instability and disease progression.Aim. To analyze driver (JAK2, CALR, MPL) and prognostic (ASXL1) somatic mutations in patients with MF and evaluate their impact on survival.Materials and methods. The study included 29 patients diagnosed with MF, selected by hematologists from the City Clinical Hospital No. 7 and Regional Clinical Hospital (Krasnoyarsk).Results. 26 (89.6 %) out of 29 examined patients had some driver mutations in JAK2, CALR, MPL genes. The p.V617F mutation in the JAK2 gene was found in 20 (68.9 %) patients. Mutations in the CALR gene were detected in 4 (13.8 %) patients, mutations in the MPL gene were found in 3 patients (10.3 %). In 1 of 26 patients, 2 driver mutations were present simultaneously. 3 (10.3 %) patients were triple negative. Mutations in the ASXL1 gene were detected in 12 (41.4 %) out of 29 examined patients. Conducted targeted NGS (next generation sequencing) for 13 out of 29 patients revealed additional genetic variants that contribute to the understanding of the development mechanism and disease course. When evaluating the overall survival in the groups of patients diagnosed with MF examined by us, depending on the combination of driver (JAK2, CALR, MPL) and prognostic (ASXL1) mutations, no statistically significant differences were found (p = 0.12). This appears to be due to the small sample size. At the same time, assessment of patient survival depending on ASXL1 status showed that in the presence of mutations in the ASXL1 gene, the median survival was 45 months (range 7–120 months), while in the absence of mutations it was 48 months (range 21–359 months) (p = 0.03).Conclusion. The results obtained allow us to assume that the presence of mutations in the ASXL1 gene is an unfavorable factor in the course of the disease.
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Affiliation(s)
- T. N. Subbotina
- Siberian Federal University; Federal Siberian Research and Clinical Center, Federal Medical and Biological Agency
| | - I. E. Maslyukova
- Siberian Federal University; Federal Siberian Research and Clinical Center, Federal Medical and Biological Agency
| | | | | | - D. V. Kurochkin
- Siberian Federal University; Federal Siberian Research and Clinical Center, Federal Medical and Biological Agency
| | - A. A. Shalyova
- Siberian Federal University; Federal Siberian Research and Clinical Center, Federal Medical and Biological Agency
| | | | | | | | - E. A. Dunaeva
- Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
| | - A. S. Esman
- Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
| | - K. O. Mironov
- Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
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12
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Miyashita N, Onozawa M, Yoshida S, Kimura H, Takahashi S, Yokoyama S, Matsukawa T, Hirabayashi S, Fujisawa S, Mori A, Ota S, Kakinoki Y, Tsutsumi Y, Yamamoto S, Miyagishima T, Nagashima T, Ibata M, Wakasa K, Haseyama Y, Fujimoto K, Ishihara T, Sakai H, Kondo T, Teshima T. Prognostic impact of FLT3-ITD, NPM1 mutation and CEBPA bZIP domain mutation in cytogenetically normal acute myeloid leukemia: a Hokkaido Leukemia Net study. Int J Hematol 2023:10.1007/s12185-023-03567-1. [PMID: 36853451 DOI: 10.1007/s12185-023-03567-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 03/01/2023]
Abstract
Mutation status of FLT3, NPM1, and CEBPA is used to classify the prognosis of acute myeloid leukemia, but its significance in patients with cytogenetically normal (CN) AML is unclear. We prospectively analyzed these genes in 295 patients with CN-AML and identified 76 (25.8%) FLT3-ITD, 113 (38.3%) NPM1 mutations, and 30 (10.2%) CEBPA biallelic mutations. We found that patients with FLT3-ITD had a poor prognosis at any age, while patients with CEBPA biallelic mutation were younger and had a better prognosis. FLT3-ITD and NPM1 mutations were correlated, and the favorable prognostic impact of being FLT3-ITD negative and NPM1 mutation positive was evident only in patients aged 65 years or more. For CEBPA, 86.7% of the patients with biallelic mutation and 9.1% of patients with the single allele mutation had in-frame mutations in the bZIP domain, which were strongly associated with a favorable prognosis. Multivariate analysis showed that age < 65 years, FLT3-ITD and CEBPA bZIP in-frame mutation were independent prognostic factors. The results suggest that analyzing these gene mutations at diagnosis can inform selection of the optimal intensity of therapy for patients with CN-AML.
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Affiliation(s)
- Naoki Miyashita
- Department of Hematology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan
| | - Masahiro Onozawa
- Department of Hematology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan.
| | - Shota Yoshida
- Department of Hematology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan
| | - Hiroyuki Kimura
- Department of Hematology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan
| | - Shogo Takahashi
- Department of Hematology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan
| | - Shota Yokoyama
- Department of Hematology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan
| | - Toshihiro Matsukawa
- Department of Hematology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan
| | - Shinsuke Hirabayashi
- Department of Pediatrics, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Shinichi Fujisawa
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Akio Mori
- Blood Disorders Center, Aiiku Hospital, Sapporo, Japan
| | - Shuichi Ota
- Department of Hematology, Sapporo Hokuyu Hospital, Sapporo, Japan
| | | | - Yutaka Tsutsumi
- Department of Hematology, Hakodate Municipal Hospital, Hakodate, Japan
| | - Satoshi Yamamoto
- Department of Hematology, Sapporo City General Hospital, Sapporo, Japan
| | | | - Takahiro Nagashima
- Department of Internal Medicine/General Medicine, Kitami Red Cross Hospital, Kitami, Japan
| | - Makoto Ibata
- Department of Hematology, Sapporo Kosei General Hospital, Sapporo, Japan
| | - Kentaro Wakasa
- Department of Hematology, Obihiro Kosei Hospital, Obihiro, Japan
| | | | - Katsuya Fujimoto
- Department of Hematology, National Hospital Organization Hokkaido Cancer Center, Sapporo, Japan
| | | | - Hajime Sakai
- Department of Hematology, Teine Keijinkai Hospital, Sapporo, Japan
| | - Takeshi Kondo
- Blood Disorders Center, Aiiku Hospital, Sapporo, Japan
| | - Takanori Teshima
- Department of Hematology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, 0608638, Japan.,Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
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13
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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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14
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Targeting DNA Methylation in Leukemia, Myelodysplastic Syndrome, and Lymphoma: A Potential Diagnostic, Prognostic, and Therapeutic Tool. Int J Mol Sci 2022; 24:ijms24010633. [PMID: 36614080 PMCID: PMC9820560 DOI: 10.3390/ijms24010633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022] Open
Abstract
DNA methylation represents a crucial mechanism of epigenetic regulation in hematologic malignancies. The methylation process is controlled by specific DNA methyl transferases and other regulators, which are often affected by genetic alterations. Global hypomethylation and hypermethylation of tumor suppressor genes are associated with hematologic cancer development and progression. Several epi-drugs have been successfully implicated in the treatment of hematologic malignancies, including the hypomethylating agents (HMAs) decitabine and azacytidine. However, combinations with other treatment modalities and the discovery of new molecules are still the subject of research to increase sensitivity to anti-cancer therapies and improve patient outcomes. In this review, we summarized the main functions of DNA methylation regulators and genetic events leading to changes in methylation landscapes. We provide current knowledge about target genes with aberrant methylation levels in leukemias, myelodysplastic syndromes, and malignant lymphomas. Moreover, we provide an overview of the clinical trials, focused mainly on the combined therapy of HMAs with other treatments and its impact on adverse events, treatment efficacy, and survival rates among hematologic cancer patients. In the era of precision medicine, a transition from genes to their regulation opens up the possibility of an epigenetic-based approach as a diagnostic, prognostic, and therapeutic tool.
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15
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Maksimova VP, Usalka OG, Makus YV, Popova VG, Trapeznikova ES, Khayrieva GI, Sagitova GR, Zhidkova EM, Prus AY, Yakubovskaya MG, Kirsanov KI. Aberrations of DNA methylation in cancer. ADVANCES IN MOLECULAR ONCOLOGY 2022. [DOI: 10.17650/2313-805x-2022-9-4-24-40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA methylation is a chromatin modification that plays an important role in the epigenetic regulation of gene expression. Changes in DNA methylation patterns are characteristic of many malignant neoplasms. DNA methylation is occurred by DNA methyltransferases (DNMTs), while demethylation is mediated by TET family proteins. Mutations and changes in the expression profile of these enzymes lead to DNA hypo- and hypermethylation and have a strong impact on carcinogenesis. In this review, we considered the key aspects of the mechanisms of regulation of DNA methylation and demethylation, and also analyzed the role of DNA methyltransferases and TET family proteins in the pathogenesis of various malignant neoplasms.During the preparation of the review, we used the following biomedical literature information bases: Scopus (504), PubMed (553), Web of Science (1568), eLibrary (190). To obtain full-text documents, the electronic resources of PubMed Central (PMC), Science Direct, Research Gate, CyberLeninka were used. To analyze the mutational profile of epigenetic regulatory enzymes, we used the cBioportal portal (https://www.cbioportal.org / ), data from The AACR Project GENIE Consortium (https://www.mycancergenome.org / ), COSMIC, Clinvar, and The Cancer Genome Atlas (TCGA).
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Affiliation(s)
- V. P. Maksimova
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia
| | - O. G. Usalka
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia; Sechenov First Moscow State Medical University, Ministry of Health of Russia
| | - Yu. V. Makus
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia; Peoples’ Friendship University of Russia
| | - V. G. Popova
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia; Mendeleev University of Chemical Technology of Russia
| | - E. S. Trapeznikova
- Sechenov First Moscow State Medical University, Ministry of Health of Russia
| | - G. I. Khayrieva
- Sechenov First Moscow State Medical University, Ministry of Health of Russia
| | - G. R. Sagitova
- Sechenov First Moscow State Medical University, Ministry of Health of Russia
| | - E. M. Zhidkova
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia
| | - A. Yu. Prus
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia; MIREA – Russian Technological University
| | - M. G. Yakubovskaya
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia
| | - K. I. Kirsanov
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia; Peoples’ Friendship University of Russia
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16
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Aref S, Sallam N, Abd Elaziz S, Salama O, Al Ashwah S, Ayed M. Clinical Implication of DNMT3A and TET2 Genes Mutations in Cytogenetically Normal Acute Myeloid Leukemia. Asian Pac J Cancer Prev 2022; 23:4299-4305. [PMID: 36580013 PMCID: PMC9971478 DOI: 10.31557/apjcp.2022.23.12.4299] [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: 08/03/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Refining risk stratification of cytogenetically normal AML (CN-AML) cases is important for decision making and tailoring of therapy. In this context genetic and epigenetic mutations was considered. Among these epigenetic regulators are DNMT3A & TET2 genes. Therefore, the aim of this study was to determine the prevalence of DNMT3A and TET2 genes mutations and their impact on the outcome of adult AML patients. SUBJECTS AND METHODS The present study is cross sectional study which was conducted on 39 adult CN-AML patients at diagnosis. For all included patients sanger sequencing was done for DNMT3A exon 23 and TET2 exon 3 genes. RESULTS DNMT3A mutations were detected in 8 of 39 patients (20.5%), and in 5 of 39 patients(12.8%) in TET gene. Two CN-AML patients had combined mutations in both genes. All of the mutations detected were missense and only one was frame shift. Mutated TET2 or DNMT3A genes were significantly associated with failure of complete remission (CR) (p <0.001), higher mortality rate, shorter OS (mean=16 versus 22.7 months) and shorter DFS (mean= 9.5 versus 21.4 months) when compared to non-mutated ones. CONCLUSION Mutated TET2 and DNMT3A detection define a subgroup of CN-AML patients with poor outcome.
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Affiliation(s)
- Salah Aref
- Hematology Unit, Clinical Pathology Department, Mansoura University, Egypt. ,For Correspondence:
| | - Nahed Sallam
- Hematology Unit, Clinical Pathology Department, Mansoura University, Egypt.
| | - Sherin Abd Elaziz
- Hematology Unit, Clinical Pathology Department, Mansoura University, Egypt.
| | - Osama Salama
- Hematology Unit, Clinical Pathology Department, Mansoura University, Egypt.
| | - Shaimaa Al Ashwah
- Hematology Unit, Mansoura University, Oncology Center, Mansoura University, Egypt.
| | - Mohamed Ayed
- Hematology Unit, Clinical Pathology Department, Mansoura University, Egypt.
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17
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Nie L, Zhang Y, You Y, Lin C, Li Q, Deng W, Ma J, Luo W, He H. The signature based on seven genomic instability-related genes could predict the prognosis of acute myeloid leukemia patients. HEMATOLOGY (AMSTERDAM, NETHERLANDS) 2022; 27:840-848. [PMID: 35924822 DOI: 10.1080/16078454.2022.2107970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is the most common acute blood malignancy in adults. The complicated and dynamic genomic instability (GI) is the most prominent feature of AML. Our study aimed to explore the prognostic value of GI-related genes in AML patients. METHODS The mRNA data and mutation data were downloaded from the TCGA and GEO databases. Differential expression analyses were completed in limma package. GO and KEGG functional enrichment was conducted using clusterProfiler function of R. Univariate Cox and LASSO Cox regression analyses were performed to screen key genes for Risk score model construction. Nomogram was built with rms package. RESULTS We identified 114 DEGs between high TMB patients and low TMB AML patients, which were significantly enriched in 429 GO terms and 13 KEGG pathways. Based on the univariate Cox and LASSO Cox regression analyses, seven optimal genes were finally applied for Risk score model construction, including SELE, LGALS1, ITGAX, TMEM200A, SLC25A21, S100A4 and CRIP1. The Risk score could reliably predict the prognosis of AML patients. Age and Risk score were both independent prognostic indicators for AML, and the Nomogram based on them could also reliably predict the OS of AML patients. CONCLUSIONS A prognostic signature based on seven GI-related genes and a predictive Nomogram for AML patients are finally successfully constructed.
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Affiliation(s)
- Lirong Nie
- Department of Hematology, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Yuming Zhang
- Department of Hematology, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Yuchan You
- Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Changmei Lin
- Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Qinghua Li
- Department of Hematology, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Wenbo Deng
- Department of Hematology, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Jingzhi Ma
- Department of Hematology, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Wenying Luo
- Department of Clinical Laboratory, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Honghua He
- Department of Hematology, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
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18
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Identification of three novel DNMT3A mutations with compromising methylation capacity in human acute myeloid leukaemia. Mol Biol Rep 2022; 49:11685-11693. [PMID: 36175738 DOI: 10.1007/s11033-022-07977-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/21/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Acute myeloid leukaemia (AML) is a complex and heterogeneous hematopoietic stem and progenitor cell malignancy characterised by the accumulation of immature blast cells in the bone marrow, blood, and other organs linked to environmental, genetic, and epigenetic factors. Somatic mutations in the gene DNA (cytosine-5)-methyltransferase 3A (DNMT3A; NM_022552.4) are common in AML patients. METHODS In this study, we used Sanger sequencing to detect the mutations in the DNMT3A gene in 61 Iraqi AML patients, Hence, the protein function and stability within alterations were identified and analyzed using a variety of computational tools with the goal of determining how these changes affect total protein stability, and then the capacity of methylation was analyzed by methylation specific PCR MSP status at CpG islands. RESULTS Three novel mutations in exon 23 of DNMT3A were identified in 14 patients (22.9%; V877I, N879delA, and L888Q). The V877I and L888Q substitutions are caused by heterozygous C2629G > A and C2663T > A mutations, respectively, while frameshift mutation C2635delA caused protein truncation with stop codon N879T*. Methylation was detected in the DNMT3A promoter region in 9 patients carrying DNMT3A mutations (64.28%) by MSP, and we found significant correlations between DNMT3A mutations and promoter methylation (p = 8.52 × 105). In addition, we found a significant overrepresentation of DNMT3A methylation status in patients ≥ 50 years old (p = 0.025). CONCLUSION Our findings highlight the importance of studying the effects of DNMT3A methylation alteration in Iraqi populations beyond R882 substitutions in the leukemogenic pathway so that patient treatment can be tailored to prevent therapeutic resistance and relapse.
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19
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Chen Y, Li J, Xu L, Găman MA, Zou Z. The genesis and evolution of acute myeloid leukemia stem cells in the microenvironment: From biology to therapeutic targeting. Cell Death Dis 2022; 8:397. [PMID: 36163119 PMCID: PMC9513079 DOI: 10.1038/s41420-022-01193-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/09/2022]
Abstract
Acute myeloid leukemia (AML) is a hematological malignancy characterized by cytogenetic and genomic alterations. Up to now, combination chemotherapy remains the standard treatment for leukemia. However, many individuals diagnosed with AML develop chemotherapeutic resistance and relapse. Recently, it has been pointed out that leukemic stem cells (LSCs) are the fundamental cause of drug resistance and AML relapse. LSCs only account for a small subpopulation of all leukemic cells, but possess stem cell properties, including a self-renewal capacity and a multi-directional differentiation potential. LSCs reside in a mostly quiescent state and are insensitive to chemotherapeutic agents. When LSCs reside in a bone marrow microenvironment (BMM) favorable to their survival, they engage into a steady, continuous clonal evolution to better adapt to the action of chemotherapy. Most chemotherapeutic drugs can only eliminate LSC-derived clones, reducing the number of leukemic cells in the BM to a normal range in order to achieve complete remission (CR). LSCs hidden in the BM niche can hardly be targeted or eradicated, leading to drug resistance and AML relapse. Understanding the relationship between LSCs, the BMM, and the generation and evolution laws of LSCs can facilitate the development of effective therapeutic targets and increase the efficiency of LSCs elimination in AML.
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Affiliation(s)
- Yongfeng Chen
- Department of Basic Medical Sciences, Medical College of Taizhou University, Taizhou, Zhejiang, 318000, China.
| | - Jing Li
- Department of Histology and Embryology, North Sichuan Medical College, Nanchong, Sichuan, 637000, China
| | - Linglong Xu
- Department of Hematology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, 318000, China
| | - Mihnea-Alexandru Găman
- Faculty of Medicine, "Carol Davila" University of Medicine and Pharmacy, 050474, Bucharest, Romania. .,Department of Hematology, Centre of Hematology and Bone Marrow Transplantation, Fundeni Clinical Institute, Bucharest, Romania.
| | - Zhenyou Zou
- Brain Hospital of Guangxi Zhuang Autonomous Region, Liuzhou, Guangxi, 545005, China.
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20
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Florez MA, Tran BT, Wathan TK, DeGregori J, Pietras EM, King KY. Clonal hematopoiesis: Mutation-specific adaptation to environmental change. Cell Stem Cell 2022; 29:882-904. [PMID: 35659875 PMCID: PMC9202417 DOI: 10.1016/j.stem.2022.05.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) describes a widespread expansion of genetically variant hematopoietic cells that increases exponentially with age and is associated with increased risks of cancers, cardiovascular disease, and other maladies. Here, we discuss how environmental contexts associated with CHIP, such as old age, infections, chemotherapy, or cigarette smoking, alter tissue microenvironments to facilitate the selection and expansion of specific CHIP mutant clones. Further, we consider major remaining gaps in knowledge, including intrinsic effects, clone size thresholds, and factors affecting clonal competition, that will determine future application of this field in transplant and preventive medicine.
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Affiliation(s)
- Marcus A Florez
- Medical Scientist Training Program and Program in Translational Biology and Molecular Medicine, Graduate School of Biomedical Sciences, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA; Division of Infectious Disease, Department of Pediatrics, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA
| | - Brandon T Tran
- Graduate School of Biomedical Sciences, Program in Cancer and Cell Biology, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA; Division of Infectious Disease, Department of Pediatrics, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA
| | - Trisha K Wathan
- Division of Infectious Disease, Department of Pediatrics, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Microbiology and Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Eric M Pietras
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Microbiology and Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katherine Y King
- Medical Scientist Training Program and Program in Translational Biology and Molecular Medicine, Graduate School of Biomedical Sciences, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Program in Cancer and Cell Biology, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA; Division of Infectious Disease, Department of Pediatrics, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA.
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21
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Gray JS, Wani SA, Campbell MJ. Epigenomic alterations in cancer: mechanisms and therapeutic potential. Clin Sci (Lond) 2022; 136:473-492. [PMID: 35383835 DOI: 10.1042/cs20210449] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/11/2022] [Accepted: 03/21/2022] [Indexed: 11/17/2022]
Abstract
The human cell requires ways to specify its transcriptome without altering the essential sequence of DNA; this is achieved through mechanisms which govern the epigenetic state of DNA and epitranscriptomic state of RNA. These alterations can be found as modified histone proteins, cytosine DNA methylation, non-coding RNAs, and mRNA modifications, such as N6-methyladenosine (m6A). The different aspects of epigenomic and epitranscriptomic modifications require protein complexes to write, read, and erase these chemical alterations. Reflecting these important roles, many of these reader/writer/eraser proteins are either frequently mutated or differentially expressed in cancer. The disruption of epigenetic regulation in the cell can both contribute to cancer initiation and progression, and increase the likelihood of developing resistance to chemotherapies. Development of therapeutics to target proteins involved in epigenomic/epitranscriptomic modifications has been intensive, but further refinement is necessary to achieve ideal treatment outcomes without too many off-target effects for cancer patients. Therefore, further integration of clinical outcomes combined with large-scale genomic analyses is imperative for furthering understanding of epigenomic mechanisms in cancer.
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Affiliation(s)
- Jaimie S Gray
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Sajad A Wani
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Moray J Campbell
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
- Biomedical Informatics Shared Resource, The Ohio State University, Columbus, OH 43210, U.S.A
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22
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Prognostic impact of DNMT3A mutation in acute myeloid leukemia with mutated NPM1. Blood Adv 2022; 6:882-890. [PMID: 34516636 PMCID: PMC8945292 DOI: 10.1182/bloodadvances.2020004136] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/07/2021] [Indexed: 11/20/2022] Open
Abstract
The negative prognostic impact of internal tandem duplication of FLT3 (FLT3-ITD) in patients with acute myeloid leukemia with mutated NPM1 (AML-NPM1) is restricted to those with a higher FLT3-ITD allelic ratio (FLT3high; ≥0.5) and considered negligible in those with a wild-type (FLT3WT)/low ITD ratio (FLT3low). Because the comutation of DNMT3A (DNMT3Amut) has been suggested to negatively influence prognosis in AML-NPM1, we analyzed the impact of DNMT3Amut in FLT3-ITD subsets (absent, low, and high ratios). A total of 164 patients diagnosed with AML-NPM1 included in 2 consecutive CETLAM protocols and with DNMT3A and FLT3 status available were studied. Overall, DNMT3Amut status did not have a prognostic impact, with comparable overall survival (P = .2). Prognostic stratification established by FLT3-ITD (FLT3WT = FLT3low > FLT3high) was independent of DNMT3Amut status. Measurable residual disease (MRD) based on NPM1 quantitative polymerase chain reaction was available for 94 patients. DNMT3Amut was associated with a higher number of mutated NPM1 transcripts after induction (P = .012) and first consolidation (C1; P < .001). All DNMT3Amut patients were MRD+ after C1 (P < .001) and exhibited significant MRD persistence after C2 and C3 (MRD+ vs MRD-; P = .027 and P = .001, respectively). Finally, DNMT3Amut patients exhibited a trend toward greater risk of molecular relapse (P = .054). In conclusion, DNMT3Amut did not modify the overall prognosis exerted by FLT3-ITD in AML-NPM1 despite delayed MRD clearance, possibly because of MRD-driven preemptive intervention.
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Yao K, Liu H, Yu S, Zhu H, Pan J. Resistance to mutant IDH inhibitors in acute myeloid leukemia: Molecular mechanisms and therapeutic strategies. Cancer Lett 2022; 533:215603. [DOI: 10.1016/j.canlet.2022.215603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/02/2022]
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Mishra S, Liu J, Chai L, Tenen DG. Diverse functions of long noncoding RNAs in acute myeloid leukemia: emerging roles in pathophysiology, prognosis, and treatment resistance. Curr Opin Hematol 2022; 29:34-43. [PMID: 34854833 PMCID: PMC8647777 DOI: 10.1097/moh.0000000000000692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE OF REVIEW Advancements in the next-generation sequencing technologies have identified rare transcripts of long noncoding RNAs (lncRNAs) in the genome of cancers, including in acute myeloid leukemia (AML). The purpose of this review is to highlight the contribution of lncRNAs in AML pathogenesis, prognosis, and chemoresistance. RECENT FINDINGS Several studies have recently reported that deregulated lncRNAs are novel key players in the development of AML and are associated with AML pathophysiology and may serve as prognostic indicators. A few aberrantly expressed lncRNAs that correlated with the recurrent genetic mutations in AML such as NPM1 and RUNX1 have recently been characterized. Moreover, a few lncRNAs in MLL-rearranged leukemia have been described. Additionally, the involvement of lncRNAs in AML chemoresistance has been postulated. SUMMARY Investigating the functional roles of the noncoding regions including lncRNAs, may provide novel insights into the pathophysiology, refine the prognostic schema, and provide novel therapeutic treatment strategies in AML.
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Affiliation(s)
- Srishti Mishra
- Cancer Science Institute, National University of Singapore, Singapore, Singapore
| | - Jun Liu
- Department of Pathology, Brigham & Women's Hospital
| | - Li Chai
- Department of Pathology, Brigham & Women's Hospital
| | - Daniel G Tenen
- Cancer Science Institute, National University of Singapore, Singapore, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, USA
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Oncogenic Mutations and Gene Fusions in CD30-Positive Lymphoproliferations and Clonally Related Mycosis Fungoides Occurring in the Same Patients. JID INNOVATIONS 2021; 1:100034. [PMID: 34909731 PMCID: PMC8659398 DOI: 10.1016/j.xjidi.2021.100034] [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: 12/21/2020] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 11/27/2022] Open
Abstract
The emergence of a common progenitor cell has been postulated for the association of CD30-positive lymphoproliferative disease (LPD) and mycosis fungoides (MF) within the same patient. Up to now, no comprehensive analysis has yet addressed the genetic profiles of such concurrent lymphoma subtypes. We aimed to delineate the molecular alterations of clonally related CD30-positive LPD and MF occurring in the same two patients. We analyzed the molecular profile of 16 samples of two patients suffering both from CD30-positive LPD and MF being obtained over a time course of at least 5 years. To detect oncogenic mutations, we applied targeted sequencing technologies with a hybrid capture-based DNA library preparation approach, and for the identification of fusion transcripts, an anchored multiplex PCR enrichment kit was used. In all samples of CD30-positive LPD and MF, oncogenic fusions afflicting the Jak/signal transducer and activator of transcription signaling pathway were present, namely NPM1‒TYK2 in patient 1 and ILF3‒JAK2 in patient 2. Additional signal transducer and activator of transcription 5A gene STAT5A mutations exclusively occurred in lesions of CD30-positive LPD in one patient. CD30-positive LPD and MF may share genetic events when occurring within the same patients. Constitutive activation of the Jak/signal transducer and activator of transcription signaling pathway may play a central role in the molecular pathogenesis of both entities.
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Yu DD, Zhang J. Update on recurrent mutations in angioimmunoblastic T-cell lymphoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2021; 14:1108-1118. [PMID: 35027991 PMCID: PMC8748014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/26/2021] [Indexed: 06/14/2023]
Abstract
Angioimmunoblastic T-cell lymphoma (AITL) is a subtype of peripheral T cell lymphoma (PTCL), defined by genetic alterations that induce abnormal immune activity and inflammatory disorders. Through recent discoveries using genomic studies, the identification of various recurrent mutations has provided greater insight and changed our understanding of the molecular genetics of the disease. By acknowledging these recurrent mutations and their affected pathways, the diagnosis, prognosis, treatment, and survival of AITL can be improved. In this review, we summarize the known recurrent mutations present in the molecular pathogenesis of AITL by emphasizing the effects of mutations on signaling pathways and genes, as well as the multistep process of AITL development.
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Affiliation(s)
| | - Jianzhong Zhang
- Department of Pathology, Strategic Support Force Medical CenterBeijing, China
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Mensah IK, Norvil AB, AlAbdi L, McGovern S, Petell CJ, He M, Gowher H. Misregulation of the expression and activity of DNA methyltransferases in cancer. NAR Cancer 2021; 3:zcab045. [PMID: 34870206 PMCID: PMC8634572 DOI: 10.1093/narcan/zcab045] [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: 09/20/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
In mammals, DNA methyltransferases DNMT1 and DNMT3's (A, B and L) deposit and maintain DNA methylation in dividing and nondividing cells. Although these enzymes have an unremarkable DNA sequence specificity (CpG), their regional specificity is regulated by interactions with various protein factors, chromatin modifiers, and post-translational modifications of histones. Changes in the DNMT expression or interacting partners affect DNA methylation patterns. Consequently, the acquired gene expression may increase the proliferative potential of cells, often concomitant with loss of cell identity as found in cancer. Aberrant DNA methylation, including hypermethylation and hypomethylation at various genomic regions, therefore, is a hallmark of most cancers. Additionally, somatic mutations in DNMTs that affect catalytic activity were mapped in Acute Myeloid Leukemia cancer cells. Despite being very effective in some cancers, the clinically approved DNMT inhibitors lack specificity, which could result in a wide range of deleterious effects. Elucidating distinct molecular mechanisms of DNMTs will facilitate the discovery of alternative cancer therapeutic targets. This review is focused on: (i) the structure and characteristics of DNMTs, (ii) the prevalence of mutations and abnormal expression of DNMTs in cancer, (iii) factors that mediate their abnormal expression and (iv) the effect of anomalous DNMT-complexes in cancer.
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Affiliation(s)
- Isaiah K Mensah
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sarah McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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Hindley A, Catherwood MA, McMullin MF, Mills KI. Significance of NPM1 Gene Mutations in AML. Int J Mol Sci 2021; 22:ijms221810040. [PMID: 34576201 PMCID: PMC8467861 DOI: 10.3390/ijms221810040] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
The aim of this literature review is to examine the significance of the nucleophosmin 1 (NPM1) gene in acute myeloid leukaemia (AML). This will include analysis of the structure and normal cellular function of NPM1, the type of mutations commonly witnessed in NPM1, and the mechanism by which this influences the development and progression of AML. The importance of NPM1 mutation on prognosis and the treatment options available to patients will also be reviewed along with current guidelines recommending the rapid return of NPM1 mutational screening results and the importance of employing a suitable laboratory assay to achieve this. Finally, future developments in the field including research into new therapies targeting NPM1 mutated AML are considered.
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Affiliation(s)
- Andrew Hindley
- Clinical Haematology, Belfast City Hospital, Belfast BT9 7AB, UK;
- Correspondence:
| | | | - Mary Frances McMullin
- Centre for Medical Education, Queen’s University Belfast, Belfast BT7 1NN, UK;
- Northern Ireland and Belfast Health and Social Care Trust, Belfast BT9 7AB, UK
| | - Ken I. Mills
- Patrick G Johnston Center for Cancer Research, Queens University Belfast, Belfast BT9 7AE, UK;
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Li Y, Wan H, Jing Y. Molecular Characterization and Clinical Treatment of Acute Myeloid Leukemia (AML) and Myelodysplastic Syndromes (MDS) Patients With TP53 Mutation. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2021; 21:841-851. [PMID: 34376372 DOI: 10.1016/j.clml.2021.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND Mutations in TP53 in myeloid neoplasms patients have been associated with poor prognosis. Effective treatments to these patients remain unclear. PATIENTS AND METHODS In this study, we retrospectively analyzed diagnostic and outcomes of 31 Acute Myeloid leukemia (AML) and 9 Myelodysplastic syndromes (MDS) patients with TP53 mutation at our hospital from September 2015 to October 2020. RESULTS A total of 42 variants (28 unique variants) in the coding region of TP53 gene were identified, and most were missense mutation (34 of 42, 81%). The median overall survival (OS) was 8 months for the AML patients (1-32 months) and 7 months for the MDS patients (3-27 months). There were 35 and 13 patients underwent frontline chemical therapy and Allo-HSCT, respectively. The overall response rate was 45.3% (16/35) for the frontline treatment. There was no significant difference between intensive and low-intensity regimens on either response to the frontline treatment (P = .255) or overall survival (P = .078). Patients, who achieved complete or partial remission at the frontline treatment, presented a higher survival than patients in non-remission, no matter transplant or not. CONCLUSION This study corroborates that improving the response to the first-line treatment could prolong the survival of myeloid neoplasms patients with TP53 mutation. Allo-HSCT could be a curative option for patients with TP53 mutation, when in complete remission during the first-line treatment.
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Affiliation(s)
- Yanfen Li
- Department of Hematology, the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Hua Wan
- Beijing USCI Medical Laboratory, Beijing, China
| | - Yu Jing
- Department of Hematology, the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
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Gene Transcription as a Therapeutic Target in Leukemia. Int J Mol Sci 2021; 22:ijms22147340. [PMID: 34298959 PMCID: PMC8304797 DOI: 10.3390/ijms22147340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 12/11/2022] Open
Abstract
Blood malignancies often arise from undifferentiated hematopoietic stem cells or partially differentiated stem-like cells. A tight balance of multipotency and differentiation, cell division, and quiescence underlying normal hematopoiesis requires a special program governed by the transcriptional machinery. Acquisition of drug resistance by tumor cells also involves reprogramming of their transcriptional landscape. Limiting tumor cell plasticity by disabling reprogramming of the gene transcription is a promising strategy for improvement of treatment outcomes. Herein, we review the molecular mechanisms of action of transcription-targeted drugs in hematological malignancies (largely in leukemia) with particular respect to the results of clinical trials.
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Sampath S, Misra P, Yadav SK, Sharma S, Somasundaram V. A study on DNA methylation status in promoter region of p15 gene in patients of acute myeloid leukemia and myelodysplastic syndrome. Med J Armed Forces India 2021; 77:337-342. [PMID: 34305288 PMCID: PMC8282539 DOI: 10.1016/j.mjafi.2021.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 04/22/2021] [Indexed: 10/21/2022] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) are a spectrum of hematological malignancies with a multistep process of accumulated genetic and epigenetic alterations. DNA methylation is most extensively studied epigenetic alteration in malignancies. Recent research studies in the field have brought out translational implications of promoter methylation of tumor suppressor gene p15 in tumors. Therefore, we studied the role of DNA Methylation of p15 gene in AML and MDS. METHODS The study was carried out in 41 consecutive AML/MDS cases reporting to hematological OPD of a tertiary care center along with 25 age and sex-matched healthy controls. The methylation status in the promoter region of the p15 gene was assessed by methylation-specific PCR (MSP) from blood samples after ethical approval and informed consent of the patients and controls. The association of methylation status was studied with clinical presentations, AML subtypes, and cytogenetics using Chi-square test/Fisher's exact test tools. RESULTS A total of 41 cases included in the study comprised 33 cases of AML and 08 cases of MDS with an age range between 06 months and 82 years. Of the 41 cases, 29 revealed promoter methylation of the p15 gene, which compared to healthy controls was found statistically significant (p < 0.001). The methylation status did not significantly correlate with AML subtypes or the cytogenetic abnormalities detected in cases. CONCLUSION The outcome of the study indicates p15 promoter DNA methylation in cases of AML and MDS may identify those individuals who might benefit from the targeted therapeutic approaches.
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Affiliation(s)
- Sangeetha Sampath
- Professor (Biochemistry), Command Hospital (Air Force), Bengaluru, India
| | - Pratibha Misra
- Professor & Head, Department of Biochemistry, Armed Forces Medical College, Pune, India
| | | | - Sanjeevan Sharma
- Senior Advisor (Medicine & Hematology), Command Hospital (Central Command), Lucknow, India
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Making it or breaking it: DNA methylation and genome integrity. Essays Biochem 2021; 64:687-703. [PMID: 32808652 DOI: 10.1042/ebc20200009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 12/11/2022]
Abstract
Cells encounter a multitude of external and internal stress-causing agents that can ultimately lead to DNA damage, mutations and disease. A cascade of signaling events counters these challenges to DNA, which is termed as the DNA damage response (DDR). The DDR preserves genome integrity by engaging appropriate repair pathways, while also coordinating cell cycle and/or apoptotic responses. Although many of the protein components in the DDR are identified, how chemical modifications to DNA impact the DDR is poorly understood. This review focuses on our current understanding of DNA methylation in maintaining genome integrity in mammalian cells. DNA methylation is a reversible epigenetic mark, which has been implicated in DNA damage signaling, repair and replication. Sites of DNA methylation can trigger mutations, which are drivers of human diseases including cancer. Indeed, alterations in DNA methylation are associated with increased susceptibility to tumorigenesis but whether this occurs through effects on the DDR, transcriptional responses or both is not entirely clear. Here, we also highlight epigenetic drugs currently in use as therapeutics that target DNA methylation pathways and discuss their effects in the context of the DDR. Finally, we pose unanswered questions regarding the interplay between DNA methylation, transcription and the DDR, positing the potential coordinated efforts of these pathways in genome integrity. While the impact of DNA methylation on gene regulation is widely understood, how this modification contributes to genome instability and mutations, either directly or indirectly, and the potential therapeutic opportunities in targeting DNA methylation pathways in cancer remain active areas of investigation.
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Papuc SM, Erbescu A, Cisleanu D, Ozunu D, Enache C, Dumitru I, Lupoaia Andrus E, Gaman M, Popov VM, Dobre M, Stanca O, Angelescu S, Berbec N, Colita A, Vladareanu AM, Bumbea H, Arghir A. Delineation of Molecular Lesions in Acute Myeloid Leukemia Patients at Diagnosis: Integrated Next Generation Sequencing and Cytogenomic Studies. Genes (Basel) 2021; 12:genes12060846. [PMID: 34070898 PMCID: PMC8229708 DOI: 10.3390/genes12060846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/19/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disorder characterized by a wide range of genetic defects. Cytogenetics, molecular and genomic technologies have proved to be helpful for deciphering the mutational landscape of AML and impacted clinical practice. Forty-eight new AML patients were investigated with an integrated approach, including classical and molecular cytogenetics, array-based comparative genomic hybridization and targeted next generation sequencing (NGS). Various genetic defects were identified in all the patients using our strategy. Targeted NGS revealed known pathogenic mutations as well as rare or unreported variants with deleterious predictions. The mutational screening of the normal karyotype (NK) group identified clinically relevant variants in 86.2% of the patients; in the abnormal cytogenetics group, the mutation detection rate was 87.5%. Overall, the highest mutation prevalence was observed for the NPM1 gene, followed by DNMT3A, FLT3 and NRAS. An unexpected co-occurrence of KMT2A translocation and DNMT3A-R882 was identified; alterations of these genes, which are involved in epigenetic regulation, are considered to be mutually exclusive. A microarray analysis detected CNVs in 25% of the NK AML patients. In patients with complex karyotypes, the microarray analysis made a significant contribution toward the accurate characterization of chromosomal defects. In summary, our results show that the integration of multiple investigative strategies increases the detection yield of genetic defects with potential clinical relevance.
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Affiliation(s)
- Sorina Mihaela Papuc
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Alina Erbescu
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Diana Cisleanu
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Diana Ozunu
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Cristina Enache
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Ion Dumitru
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Elena Lupoaia Andrus
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Mihaela Gaman
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | | | - Maria Dobre
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Oana Stanca
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Silvana Angelescu
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Nicoleta Berbec
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Andrei Colita
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Ana-Maria Vladareanu
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Horia Bumbea
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Aurora Arghir
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
- Correspondence: ; Tel.: +40-2-1319-2732-207; Fax: +40-2-1319-4528
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Doucette K, Karp J, Lai C. Advances in therapeutic options for newly diagnosed, high-risk AML patients. Ther Adv Hematol 2021; 12:20406207211001138. [PMID: 33995985 PMCID: PMC8111550 DOI: 10.1177/20406207211001138] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 12/18/2022] Open
Abstract
Acute myeloid leukemia (AML) is an aggressive malignancy characterized by clonal proliferation of neoplastic immature precursor cells. AML impacts older adults and has a poor prognosis. Despite recent advances in treatment, AML is complex, with both genetic and epigenetic aberrations in the malignant clone and elaborate interactions with its microenvironment. We are now able to stratify patients on the basis of specific clinical and molecular features in order to optimize individual treatment strategies. However, our understanding of the complex nature of these molecular abnormalities continues to expand the defining characteristics of high-risk mutations. In this review, we focus on genetic and microenvironmental factors in adverse risk AML that play critical roles in leukemogenesis, including those not described in an European LeukemiaNet adverse risk group, and describe therapies that are currently in the clinical arena, either approved or under development.
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Affiliation(s)
- Kimberley Doucette
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - Judith Karp
- Johns Hopkins University Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Catherine Lai
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, 3800 Reservoir Road, NW, Washington, DC 20007, USA
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Moncada A, Pancrazzi A. Lab tests for MPN. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 366:187-220. [PMID: 35153004 DOI: 10.1016/bs.ircmb.2021.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Molecular laboratory investigations for myeloproliferative neoplasm (MPN) can ideally be divided into two distincts groups, those for the detection of the BCR-ABL rearrangement (suspect of chronic myeloid leukemia) and those for the variants determination of the driver genes of the negative Philadelphia forms (MPN Ph neg). The BCR-ABL detection is based on RT-Polymerase Chain Reaction techniques and more recently on droplet digital PCR (ddPCR). For this type of analysis, combined with chromosome banding analysis (CBA) and Fluorescent in situ hybridization (FISH), it is essential to quantify BCR-ABL mutated copies by standard curve method. The investigation on driver genes for MPN Ph neg forms includes activity for erythroid forms such as Polycythemia Vera (test JAK2V617F and JAK2 exon 12), for non-erythroid forms such as essential thrombocythemia and myelofibrosis (test JAK2V617F, CALR exon 9, MPL exon 10), for "atypical" ones such as mastocytosis (cKIT D816V test) and for hypereosinophilic syndrome (FIP1L1-PDGFRalpha test). It's crucial to assign prognosis value through calculating allelic burden of JAK2 V617F variant and determining CALR esone 9 variants (type1/1like, type2/2like and atypical ones). A fundamental innovation for investigating triple negative cases for JAK2, CALR, MPL and for providing prognostic score is the use of Next Generation Sequencing panels containing high molecular risk genes as ASXL1, EZH2, TET2, IDH1/IDH2, SRSF2. This technique allows to detect additional or subclonal mutations which are usually acquired in varying sized sub-clones of hematopoietic progenitors. These additional variants have a prognostic significance and should be indagated to exclude false negative cases.
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Affiliation(s)
- Alice Moncada
- Laboratory Medicine Department, Molecular and Clinical Pathology Sector, Azienda USL Toscana Sudest, Ospedale San Donato, Arezzo, Italy
| | - Alessandro Pancrazzi
- Laboratory Medicine Department, Molecular and Clinical Pathology Sector, Azienda USL Toscana Sudest, Ospedale San Donato, Arezzo, Italy.
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Pettersson L, Holmgren B, Juliusson G, Lazarevic VL, Ehinger M. Mutational spectrum of de novo NPM1-mutated acute myeloid leukemia patients older than 75 years. Leuk Lymphoma 2021; 62:1958-1966. [PMID: 33711909 DOI: 10.1080/10428194.2021.1894650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AML with mutated NPM1 occurs in all age groups. Yet, the mutational pattern is not extensively studied in the very old, which may hamper appropriate risk assessment. Herein we examined 22 cases of NPM1-mutated de novo AML in patients older than 75, with a median age of 84. All diagnostic samples were sequenced aiming for coverage of the most relevant AML-associated mutations. For comparison with younger patients, we used already published data on several cohorts. A total of 76 mutations including 50 different variants were identified in 16 recurrently mutated AML genes. Compared with younger patients, a significant enrichment of TET2 and SRSF2 was observed, together with a reduced frequency of DNMT3A mutations. Our results indicate that the mutational pattern may be different in the very old as compared to younger patients with NPM1-mutated AML.HighlightsThe mutational spectrum of NPM1-mutated AML in patients above 75 years displays distinct features.A significant enrichment of TET2 and SRSF2 mutations together with a reduced frequency of DNMT3A mutations was observed in the elderly.NPM1 mutation is a secondary event in the development of AML in the very old.
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Affiliation(s)
- Louise Pettersson
- Department of Clinical Sciences, Division of Pathology, Lund University, Skane University Hospital, Lund, Sweden.,Department of Pathology, Halland Hospital Halmstad, Region Halland, Halmstad, Sweden
| | - Benjamin Holmgren
- Department of Pathology, Halland Hospital Halmstad, Region Halland, Halmstad, Sweden
| | - Gunnar Juliusson
- Department of Hematology, Oncology and Radiation Physics, Lund University, Skane University Hospital, Lund, Sweden.,Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Vladimir Lj Lazarevic
- Department of Hematology, Oncology and Radiation Physics, Lund University, Skane University Hospital, Lund, Sweden
| | - Mats Ehinger
- Department of Clinical Sciences, Division of Pathology, Lund University, Skane University Hospital, Lund, Sweden
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