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Tien FM, Hou HA. CEBPA mutations in acute myeloid leukemia: implications in risk stratification and treatment. Int J Hematol 2024:10.1007/s12185-024-03773-5. [PMID: 38671183 DOI: 10.1007/s12185-024-03773-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024]
Abstract
Mutations in CCAAT enhancer binding protein α (CEBPA) occur in approximately 10% of patients with de novo acute myeloid leukemia (AML). Emerging evidence supports that in-frame mutations in the basic leucine zipper domain of CEBPA (CEBPAbZIP-inf) confer a survival benefit, and CEBPAbZIP-inf replaced CEBPA double mutations (CEBPAdm) as a unique entity in the 2022 World Health Organization (WHO-2022) classification and International Consensus Classification (ICC). However, challenges remain in daily clinical practice since more than 30% patients with CEBPAbZIP-inf die of AML despite intensive treatment. This review aims to provide a comprehensive summary of the heterogeneities observed in AML with CEBPAdm and CEBPAbZIP-inf, and will discuss the prognostic implications of concurrent mutations and novel mechanistic targets that may inform future drug development. The ultimate goal is to optimize clinical management and to provide precision medicine for this category of patients.
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Affiliation(s)
- Feng-Ming Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
- Division of General Medicine, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
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2
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Xia Z, Wei Z, Li X, Liu Y, Gu X, Huang S, Zhang X, Wang W. C/EBPα aggravates renal fibrosis in CKD through the NOX4-ROS-apoptosis pathway in tubular epithelial cells. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167039. [PMID: 38281712 DOI: 10.1016/j.bbadis.2024.167039] [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: 10/15/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 01/30/2024]
Abstract
BACKGROUND Chronic kidney disease (CKD) is a prevalent renal disorder with various risk factors. Emerging evidence indicates that the transcriptional factor CCAAT/enhancer binding protein alpha (C/EBPα) may be associated with renal fibrosis. However, the precise role of C/EBPα in CKD progression remains unexplored. METHODS We investigated the involvement of C/EBPα in CKD using two distinct mouse models induced by folic acid (FA) and unilateral ureteral obstruction (UUO). Additionally, we used RNA sequencing and KEGG analysis to identify potential downstream pathways governed by C/EBPα. FINDINGS Cebpa knockout significantly shielded mice from renal fibrosis and reduced reactive oxygen species (ROS) levels in both the FA and UUO models. Primary tubular epithelial cells (PTECs) lacking Cebpa exhibited reduced apoptosis and ROS accumulation following treatment with TGF-β. RNA sequencing analysis suggested that apoptosis is among the primary pathways regulated by C/EBPα, and identified NADPH oxidoreductase 4 (NOX4) as a key protein upregulated upon C/EBPα induction (ICCB280). Treatment with l-Theanine, a potential NOX4 inhibitor, mitigated renal fibrosis and inflammation in both the FA and UUO mouse models. INTERPRETATION Our study unveils a role for C/EBPα in suppressing renal fibrosis, mitigating ROS accumulation, and reducing cell apoptosis. Furthermore, we investigate whether these protective effects are mediated by C/EBPα's regulation of NOX4 expression. These findings present a promising therapeutic target for modulating ROS and apoptosis in renal tubular cells, potentially offering an approach to treating CKD and other fibrotic diseases.
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Affiliation(s)
- Ziru Xia
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Zhaonan Wei
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Xin Li
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Yunzi Liu
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Xiangchen Gu
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China; Department of Nephrology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, People's Republic of China
| | - Siyi Huang
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Xiaoyue Zhang
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Weiming Wang
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China; Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.
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3
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Tien FM, Yao CY, Tsai XCH, Lo MY, Chen CY, Lee WH, Lin CC, Kuo YY, Peng YL, Tseng MH, Wu YS, Liu MC, Lin LI, Chuang MK, Ko BS, Yao M, Tang JL, Chou WC, Hou HA, Tien HF. Dysregulated immune and metabolic pathways are associated with poor survival in adult acute myeloid leukemia with CEBPA bZIP in-frame mutations. Blood Cancer J 2024; 14:15. [PMID: 38253683 PMCID: PMC10803338 DOI: 10.1038/s41408-023-00975-8] [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: 04/04/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Acute myeloid leukemia (AML) with CEBPA bZIP in-frame mutations (CEBPAbZIP-inf) is classified within the favorable-risk group by the 2022 European LeukemiaNet (ELN-2022). However, heterogeneous clinical outcomes are still observed in these patients. In this study, we aimed to investigate the mutation profiles and transcriptomic patterns associated with poor outcomes in patients with CEBPAbZIP-inf. One hundred and thirteen CEBPAbZIP-inf patients were identified in a cohort of 887 AML patients homogeneously treated with intensive chemotherapy. Concurrent WT1 or DNMT3A mutations significantly predicted worse survival in AML patients with CEBPAbZIP-inf. RNA-sequencing analysis revealed an enrichment of interferon (IFN) signaling and metabolic pathways in those with a shorter event-free survival (EFS). CEBPAbZIP-inf patients with a shorter EFS had higher expression of IFN-stimulated genes (IRF2, IRF5, OAS2, and IFI35). Genes in mitochondrial complexes I (NDUFA12 and NDUFB6) and V (ATP5PB and ATP5IF1) were overexpressed and were associated with poorer survival, and the results were independently validated in the TARGET AML cohort. In conclusion, concurrent WT1 or DNMT3A mutations and a dysregulated immune and metabolic state were correlated with poor survival in patients with CEBPAbZIP-inf, and upfront allogeneic transplantation may be indicated for better long-term disease control.
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Affiliation(s)
- Feng-Ming Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chi-Yuan Yao
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Xavier Cheng-Hong Tsai
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Min-Yen Lo
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital Yunlin Branch, Yunlin, Taiwan
| | - Chien-Yuan Chen
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Wan-Hsuan Lee
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Hsin-Chu Branch, Hsin-Chu, Taiwan
| | - Chien-Chin Lin
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yuan-Yeh Kuo
- Tai-Chen Cell Therapy Center, National Taiwan University, Taipei, Taiwan
| | - Yen-Ling Peng
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Mei-Hsuan Tseng
- Tai-Chen Cell Therapy Center, National Taiwan University, Taipei, Taiwan
| | - Yu-Sin Wu
- Department of Nursing, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Ming-Chih Liu
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Liang-In Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Kai Chuang
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Bor-Sheng Ko
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Hematological Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Ming Yao
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Jih-Luh Tang
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Tai-Chen Cell Therapy Center, National Taiwan University, Taipei, Taiwan
- Department of Hematological Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Wen-Chien Chou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, Far-Eastern Memorial Hospital, New Taipei City, Taiwan
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4
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Garcia-Cuellar MP, Akan S, Slany RK. A C/ebpα isoform specific differentiation program in immortalized myelocytes. Leukemia 2023; 37:1850-1859. [PMID: 37532789 PMCID: PMC10457184 DOI: 10.1038/s41375-023-01989-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023]
Abstract
The transcription factor CCAAT-enhancer binding factor alpha (C/ebpα) is a master controller of myeloid differentiation that is expressed as long (p42) and short (p30) isoform. Mutations within the CEBPA gene selectively deleting p42 are frequent in human acute myeloid leukemia. Here we investigated the individual genomics and transcriptomics of p42 and p30. Both proteins bound to identical sites across the genome. For most targets, they induced a highly similar transcriptional response with the exception of a few isoform specific genes. Amongst those we identified early growth response 1 (Egr1) and tribbles1 (Trib1) as key targets selectively induced by p42 that are also underrepresented in CEBPA-mutated AML. Egr1 executed a program of myeloid differentiation and growth arrest. Oppositely, Trib1 established a negative feedback loop through activation of Erk1/2 kinase thus placing differentiation under control of signaling. Unexpectedly, differentiation elicited either by removal of an oncogenic input or by G-CSF did not peruse C/ebpα as mediator but rather directly affected the cell cycle core by upregulation of p21/p27 inhibitors. This points to functions downstream of C/ebpα as intersection point where transforming and differentiation stimuli converge and this finding offers a new perspective for therapeutic intervention.
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Affiliation(s)
| | - Selin Akan
- Department of Genetics, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Robert K Slany
- Department of Genetics, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany.
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5
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Pessoa FMCDP, Machado CB, Barreto IV, Sampaio GF, Oliveira DDS, Ribeiro RM, Lopes GS, de Moraes MEA, de Moraes Filho MO, de Souza LEB, Khayat AS, Moreira-Nunes CA. Association between Immunophenotypic Parameters and Molecular Alterations in Acute Myeloid Leukemia. Biomedicines 2023; 11:1098. [PMID: 37189716 PMCID: PMC10135936 DOI: 10.3390/biomedicines11041098] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Acute myeloid leukemia (AML) is a hematologic malignancy that occurs due to alterations such as genetic mutations, chromosomal translocations, or changes in molecular levels. These alterations can accumulate in stem cells and hematopoietic progenitors, leading to the development of AML, which has a prevalence of 80% of acute leukemias in the adult population. Recurrent cytogenetic abnormalities, in addition to mediating leukemogenesis onset, participate in its evolution and can be used as established diagnostic and prognostic markers. Most of these mutations confer resistance to the traditionally used treatments and, therefore, the aberrant protein products are also considered therapeutic targets. The surface antigens of a cell are characterized through immunophenotyping, which has the ability to identify and differentiate the degrees of maturation and the lineage of the target cell, whether benign or malignant. With this, we seek to establish a relationship according to the molecular aberrations and immunophenotypic alterations that cells with AML present.
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Affiliation(s)
- Flávia Melo Cunha de Pinho Pessoa
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Caio Bezerra Machado
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Igor Valentim Barreto
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Giulia Freire Sampaio
- Unichristus University Center, Faculty of Biomedicine, Fortaleza 60430-275, CE, Brazil
| | | | | | - Germison Silva Lopes
- Department of Hematology, César Cals General Hospital, Fortaleza 60015-152, CE, Brazil
| | - Maria Elisabete Amaral de Moraes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Manoel Odorico de Moraes Filho
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Lucas Eduardo Botelho de Souza
- Center for Cell-Based Therapy, Regional Blood Center of Ribeirão Preto, University of São Paulo, São Paulo 14040-900, SP, Brazil
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
- Unichristus University Center, Faculty of Biomedicine, Fortaleza 60430-275, CE, Brazil
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
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6
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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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7
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Genomic Alterations, Gene Expression Profiles and Functional Enrichment of Normal-Karyotype Acute Myeloid Leukaemia Based on Targeted Next-Generation Sequencing. Cancers (Basel) 2023; 15:cancers15051386. [PMID: 36900179 PMCID: PMC10000176 DOI: 10.3390/cancers15051386] [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: 01/10/2023] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023] Open
Abstract
Characterising genomic variants is paramount in understanding the pathogenesis and heterogeneity of normal-karyotype acute myeloid leukaemia (AML-NK). In this study, clinically significant genomic biomarkers were ascertained using targeted DNA sequencing and RNA sequencing on eight AML-NK patients' samples collected at disease presentation and after complete remission. In silico and Sanger sequencing validations were performed to validate variants of interest, and they were followed by the performance of functional and pathway enrichment analyses for overrepresentation analysis of genes with somatic variants. Somatic variants involving 26 genes were identified and classified as follows: 18/42 (42.9%) as pathogenic, 4/42 (9.5%) as likely pathogenic, 4/42 (9.5%) as variants of unknown significance, 7/42 (16.7%) as likely benign and 9/42 (21.4%) as benign. Nine novel somatic variants were discovered, of which three were likely pathogenic, in the CEBPA gene with significant association with its upregulation. Transcription misregulation in cancer tops the affected pathways involving upstream genes (CEBPA and RUNX1) that were deregulated in most patients during disease presentation and were closely related to the most enriched molecular function gene ontology category, DNA-binding transcription activator activity RNA polymerase II-specific (GO:0001228). In summary, this study elucidated putative variants and their gene expression profiles along with functional and pathway enrichment in AML-NK patients.
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8
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Li MM, Awasthi S, Ghosh S, Bisht D, Coban Akdemir ZH, Sheynkman GM, Sahni N, Yi SS. Gain-of-Function Variomics and Multi-omics Network Biology for Precision Medicine. Methods Mol Biol 2023; 2660:357-372. [PMID: 37191809 PMCID: PMC10476052 DOI: 10.1007/978-1-0716-3163-8_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Traditionally, disease causal mutations were thought to disrupt gene function. However, it becomes more clear that many deleterious mutations could exhibit a "gain-of-function" (GOF) behavior. Systematic investigation of such mutations has been lacking and largely overlooked. Advances in next-generation sequencing have identified thousands of genomic variants that perturb the normal functions of proteins, further contributing to diverse phenotypic consequences in disease. Elucidating the functional pathways rewired by GOF mutations will be crucial for prioritizing disease-causing variants and their resultant therapeutic liabilities. In distinct cell types (with varying genotypes), precise signal transduction controls cell decision, including gene regulation and phenotypic output. When signal transduction goes awry due to GOF mutations, it would give rise to various disease types. Quantitative and molecular understanding of network perturbations by GOF mutations may provide explanations for 'missing heritability" in previous genome-wide association studies. We envision that it will be instrumental to push current paradigm toward a thorough functional and quantitative modeling of all GOF mutations and their mechanistic molecular events involved in disease development and progression. Many fundamental questions pertaining to genotype-phenotype relationships remain unresolved. For example, which GOF mutations are key for gene regulation and cellular decisions? What are the GOF mechanisms at various regulation levels? How do interaction networks undergo rewiring upon GOF mutations? Is it possible to leverage GOF mutations to reprogram signal transduction in cells, aiming to cure disease? To begin to address these questions, we will cover a wide range of topics regarding GOF disease mutations and their characterization by multi-omic networks. We highlight the fundamental function of GOF mutations and discuss the potential mechanistic effects in the context of signaling networks. We also discuss advances in bioinformatic and computational resources, which will dramatically help with studies on the functional and phenotypic consequences of GOF mutations.
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Affiliation(s)
- Mark M Li
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Sharad Awasthi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sumanta Ghosh
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Deepa Bisht
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zeynep H Coban Akdemir
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, USA
- Center for Public Health Genomics, and UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Quantitative and Computational Biosciences Program, Baylor College of Medicine, Houston, TX, USA.
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA.
- Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, USA.
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, USA.
- Interdisciplinary Life Sciences Graduate Programs (ILSGP), College of Natural Sciences, The University of Texas at Austin, Austin, TX, USA.
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9
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Weinberg OK, Porwit A, Orazi A, Hasserjian RP, Foucar K, Duncavage EJ, Arber DA. The International Consensus Classification of acute myeloid leukemia. Virchows Arch 2023; 482:27-37. [PMID: 36264379 DOI: 10.1007/s00428-022-03430-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/05/2022] [Accepted: 10/15/2022] [Indexed: 01/24/2023]
Abstract
Acute myeloid leukemias (AMLs) are overlapping hematological neoplasms associated with rapid onset, progressive, and frequently chemo-resistant disease. At diagnosis, classification and risk stratification are critical for treatment decisions. A group with expertise in the clinical, pathologic, and genetic aspects of these disorders developed the International Consensus Classification (ICC) of acute leukemias. One of the major changes includes elimination of AML with myelodysplasia-related changes group, while creating new categories of AML with myelodysplasia-related cytogenetic abnormalities, AML with myelodysplasia-related gene mutations, and AML with mutated TP53. Most of recurrent genetic abnormalities, including mutations in NPM1, that define specific subtypes of AML have a lower requirement of ≥ 10% blasts in the bone marrow or blood, and a new category of MDS/AML is created for other case types with 10-19% blasts. Prior therapy, antecedent myeloid neoplasms or underlying germline genetic disorders predisposing to the development of AML are now recommended as qualifiers to the initial diagnosis of AML. With these changes, classification of AML is updated to include evolving genetic, clinical, and morphologic findings.
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Affiliation(s)
- Olga K Weinberg
- Department of Pathology, University of Texas Southwestern Medical Center, BioCenter, 2230 Inwood Rd, Dallas, TX, EB03.220G75235, USA.
| | - Anna Porwit
- Division of Oncology and Pathology, Department of Clinical Sciences, Faculty of Medicine, Lund University, Lund, Sweden
| | - Attilio Orazi
- Department of Pathology, Texas Tech University Health Sciences Center, El Paso, El Paso, TX, USA
| | | | - Kathryn Foucar
- Department of Pathology, University of New Mexico, Albuquerque, NM, USA
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Daniel A Arber
- Department of Pathology, University of Chicago, Chicago, IL, USA
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10
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Wagner N, Wagner KD. Peroxisome Proliferator-Activated Receptors and the Hallmarks of Cancer. Cells 2022; 11:cells11152432. [PMID: 35954274 PMCID: PMC9368267 DOI: 10.3390/cells11152432] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/02/2022] [Accepted: 08/04/2022] [Indexed: 12/11/2022] Open
Abstract
Peroxisome proliferator-activated receptors (PPARs) function as nuclear transcription factors upon the binding of physiological or pharmacological ligands and heterodimerization with retinoic X receptors. Physiological ligands include fatty acids and fatty-acid-derived compounds with low specificity for the different PPAR subtypes (alpha, beta/delta, and gamma). For each of the PPAR subtypes, specific pharmacological agonists and antagonists, as well as pan-agonists, are available. In agreement with their natural ligands, PPARs are mainly focused on as targets for the treatment of metabolic syndrome and its associated complications. Nevertheless, many publications are available that implicate PPARs in malignancies. In several instances, they are controversial for very similar models. Thus, to better predict the potential use of PPAR modulators for personalized medicine in therapies against malignancies, it seems necessary and timely to review the three PPARs in relation to the didactic concept of cancer hallmark capabilities. We previously described the functions of PPAR beta/delta with respect to the cancer hallmarks and reviewed the implications of all PPARs in angiogenesis. Thus, the current review updates our knowledge on PPAR beta and the hallmarks of cancer and extends the concept to PPAR alpha and PPAR gamma.
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Affiliation(s)
- Nicole Wagner
- Correspondence: (N.W.); (K.-D.W.); Tel.: +33-489-153-713 (K.-D.W.)
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11
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Molina B, Chavez J, Grainger S. Zebrafish models of acute leukemias: Current models and future directions. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2021; 10:e400. [PMID: 33340278 PMCID: PMC8213871 DOI: 10.1002/wdev.400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022]
Abstract
Acute myeloid leukemias (AML) and acute lymphoid leukemias (ALL) are heterogenous diseases encompassing a wide array of genetic mutations with both loss and gain of function phenotypes. Ultimately, these both result in the clonal overgrowth of blast cells in the bone marrow, peripheral blood, and other tissues. As a consequence of this, normal hematopoietic stem cell function is severely hampered. Technologies allowing for the early detection of genetic alterations and understanding of these varied molecular pathologies have helped to advance our treatment regimens toward personalized targeted therapies. In spite of this, both AML and ALL continue to be a major cause of morbidity and mortality worldwide, in part because molecular therapies for the plethora of genetic abnormalities have not been developed. This underscores the current need for better model systems for therapy development. This article reviews the current zebrafish models of AML and ALL and discusses how novel gene editing tools can be implemented to generate better models of acute leukemias. This article is categorized under: Adult Stem Cells, Tissue Renewal, and Regeneration > Stem Cells and Disease Technologies > Perturbing Genes and Generating Modified Animals.
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Affiliation(s)
- Brandon Molina
- Biology Department, San Diego State University, San Diego, California, USA
| | - Jasmine Chavez
- Biology Department, San Diego State University, San Diego, California, USA
| | - Stephanie Grainger
- Biology Department, San Diego State University, San Diego, California, USA
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12
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Heyes E, Schmidt L, Manhart G, Eder T, Proietti L, Grebien F. Identification of gene targets of mutant C/EBPα reveals a critical role for MSI2 in CEBPA-mutated AML. Leukemia 2021; 35:2526-2538. [PMID: 33623142 PMCID: PMC7611617 DOI: 10.1038/s41375-021-01169-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 01/12/2021] [Accepted: 01/28/2021] [Indexed: 01/31/2023]
Abstract
Mutations in the gene encoding the transcription factor CCAAT/enhancer-binding protein alpha (C/EBPα) occur in 10-15% of acute myeloid leukemia (AML). Frameshifts in the CEBPA N-terminus resulting in exclusive expression of a truncated p30 isoform represent the most prevalent type of CEBPA mutations in AML. C/EBPα p30 interacts with the epigenetic machinery, but it is incompletely understood how p30-induced changes cause leukemogenesis. We hypothesized that critical effector genes in CEBPA-mutated AML are dependent on p30-mediated dysregulation of the epigenome. We mapped p30-associated regulatory elements (REs) by ATAC-seq and ChIP-seq in a myeloid progenitor cell model for p30-driven AML that enables inducible RNAi-mediated knockdown of p30. Concomitant p30-dependent changes in gene expression were measured by RNA-seq. Integrative analysis identified 117 p30-dependent REs associated with 33 strongly down-regulated genes upon p30-knockdown. CRISPR/Cas9-mediated mutational disruption of these genes revealed the RNA-binding protein MSI2 as a critical p30-target. MSI2 knockout in p30-driven murine AML cells and in the CEBPA-mutated human AML cell line KO-52 caused proliferation arrest and terminal myeloid differentiation, and delayed leukemia onset in vivo. In summary, this work presents a comprehensive dataset of p30-dependent effects on epigenetic regulation and gene expression and identifies MSI2 as an effector of the C/EBPα p30 oncoprotein.
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Affiliation(s)
- Elizabeth Heyes
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Luisa Schmidt
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Gabriele Manhart
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Thomas Eder
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Ludovica Proietti
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Florian Grebien
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria.
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13
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Mendoza H, Podoltsev NA, Siddon AJ. Laboratory evaluation and prognostication among adults and children with CEBPA-mutant acute myeloid leukemia. Int J Lab Hematol 2021; 43 Suppl 1:86-95. [PMID: 34288448 DOI: 10.1111/ijlh.13517] [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: 01/28/2021] [Accepted: 02/25/2021] [Indexed: 02/02/2023]
Abstract
CEBPA-mutant acute myeloid leukemia (AML) encompasses clinically and biologically distinct subtypes of AML in both adults and children. CEBPA-mutant AML may occur with monoallelic (moCEBPA) or biallelic (biCEBPA) mutations, which can be somatic or germline, with each entity impacting prognosis in unique ways. BiCEBPA AML is broadly associated with a favorable prognosis, but differences in the type and location of CEBPA mutations as well as the presence of additional leukemogenic mutations can lead to heterogeneity in survival. Concurrent FLT3-ITD mutations have a well-documented negative effect on survival in adult biCEBPA AML, whereas support for a negative prognostic effect of mutations in TET2, DNMT3A, WT1, CSF3R, ASXL1, and KIT is mixed. NPM1 and GATA2 mutations may have a positive prognostic impact. MoCEBPA AML has similar survival outcomes compared to AML with wild-type CEBPA, and risk stratification is determined by other cytogenetic and molecular findings. Germline CEBPA mutations may lead to familial biCEBPA AML after acquisition of second somatic CEBPA mutation, with variable penetrance and age. BiCEBPA AML in children is likely a favorable-risk diagnosis as it is in adults, but the role of a single CEBPA mutation and the impact of concurrent leukemogenic mutations are not clear in this population. Laboratory evaluation of the CEBPA gene includes PCR-based fragment-length analysis, Sanger sequencing, and next-generation sequencing. Phenotypic analysis using multiparameter flow cytometry can also provide additional data in evaluating CEBPA, helping to assess for the likelihood of mutation presence.
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Affiliation(s)
- Hadrian Mendoza
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Nikolai A Podoltsev
- Hematology Section, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Alexa J Siddon
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.,Department of Pathology, Yale School of Medicine, New Haven, CT, USA
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Kang Y, Chen X, Fang F, Zhang L, Wang J, Tian C, Guo W, Xu J, Ren H, Muyey DM, Tan Y, Xu Z, Wang H. The clinical characteristics and prognosis of cytogenetically normal AML with single mutations of CEBPA. Int J Lab Hematol 2021; 43:1424-1431. [PMID: 34216417 DOI: 10.1111/ijlh.13612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/19/2021] [Accepted: 05/10/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION CEBPA mutation is a common mutation in normal karyotype AML. CEBPAdm AML has been recognized as a separate entity, but there is still controversy to the prognosis of CEBPAsm patients. METHODS A total of 151 newly diagnosed cytogenetically normal AML patients treated at the Second Hospital Center of Shanxi Medical University from February 2017 to December 2019 were the subjects of the study. According to the number of mutations in the CEBPA gene, the patients were divided into three groups, CEBPAsm, CEBPAdm, and CEBPAwt patients. The clinical characteristics, gene mutations, response, and prognosis were retrospectively compared among the three groups. RESULTS CEBPAsm patients had lower hemoglobin values compared to CEBPAdm (P = .049). There was no statistical difference between the CEBPAsm cases and the CEBPAdm cases in the mutation types and the distribution of mutation regions (P > .050). Compared with CEBPAdm, cases with CEBPAsm were more likely associated with multiple other gene mutations (P = .023). Patients with CEBPAdm had a higher CR, ORR, and OS than those CEBPAwt (P < .050). CEBPAsm patients had a similar OS with CEBPAdm and CEBPAwt patients (P = .281). These CEBPAsm patients with VAF<30% had lower OS than the patients with VAF≥30%. FLT3-ITD mutations could reduce CEBPAsm patients' OS (P = .019). CONCLUSION Our data first highlighted the impact of CEBPAsm VAF on OS, and the results showed the lower the VAF was, the shorter the OS tended to. The VAF of CEBPAsm could provide specific significance in some extent for the prognosis of patients.
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Affiliation(s)
- Yefang Kang
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Xiuhua Chen
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Fang Fang
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Lingli Zhang
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Jiaxuan Wang
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Chuchu Tian
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Wenzheng Guo
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Jing Xu
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Huanying Ren
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Daniel Muteb Muyey
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Yanhong Tan
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Zhifang Xu
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Hongwei Wang
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
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