1
|
Kim N, Hahn S, Choi YJ, Cho H, Chung H, Jang JE, Lyu CJ, Lee ST, Choi JR, Cheong JW, Shin S. Comprehensive insights into AML relapse: genetic mutations, clonal evolution, and clinical outcomes. Cancer Cell Int 2024; 24:174. [PMID: 38764048 PMCID: PMC11103850 DOI: 10.1186/s12935-024-03368-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 05/10/2024] [Indexed: 05/21/2024] Open
Abstract
INTRODUCTION Acute myeloid leukemia (AML) is a complex hematologic malignancy characterized by uncontrolled proliferation of myeloid precursor cells within bone marrow. Despite advances in understanding of its molecular underpinnings, AML remains a therapeutic challenge due to its high relapse rate and clonal evolution. METHODS In this retrospective study, we analyzed data from 24 AML patients diagnosed at a single institution between January 2017 and August 2023. Comprehensive genetic analyses, including chromosomal karyotyping, next-generation sequencing, and gene fusion assays, were performed on bone marrow samples obtained at initial diagnosis and relapse. Clinical data, treatment regimens, and patient outcomes were also documented. RESULTS Mutations in core genes of FLT3, NPM1, DNMT3A, and IDH2 were frequently discovered in diagnostic sample and remained in relapse sample. FLT3-ITD, TP53, KIT, RUNX1, and WT1 mutation were acquired at relapse in one patient each. Gene fusion assays revealed stable patterns, while chromosomal karyotype analyses indicated a greater diversity of mutations in relapsed patients. Clonal evolution patterns varied, with some cases showing linear or branching evolution and others exhibiting no substantial change in core mutations between diagnosis and relapse. CONCLUSIONS Our study integrates karyotype, gene rearrangements, and gene mutation results to provide a further understanding of AML heterogeneity and evolution. We demonstrate the clinical relevance of specific mutations and clonal evolution patterns, emphasizing the need for personalized therapies and measurable residual disease monitoring in AML management. By bridging the gap between genetics and clinical outcome, we move closer to tailored AML therapies and improved patient prognoses.
Collapse
Affiliation(s)
- Namsoo Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Seungmin Hahn
- Department of Pediatric Hematology-Oncology, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Yu Jeong Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Hyunsoo Cho
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Haerim Chung
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Ji Eun Jang
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Chuhl Joo Lyu
- Department of Pediatric Hematology-Oncology, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
- Dxome Co. Ltd, Seongnam-si, Gyeonggi-do, Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
- Dxome Co. Ltd, Seongnam-si, Gyeonggi-do, Korea
| | - June-Won Cheong
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
| |
Collapse
|
2
|
Nuno K, Azizi A, Koehnke T, Lareau C, Ediriwickrema A, Corces MR, Satpathy AT, Majeti R. Convergent epigenetic evolution drives relapse in acute myeloid leukemia. eLife 2024; 13:e93019. [PMID: 38647535 PMCID: PMC11034943 DOI: 10.7554/elife.93019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Relapse of acute myeloid leukemia (AML) is highly aggressive and often treatment refractory. We analyzed previously published AML relapse cohorts and found that 40% of relapses occur without changes in driver mutations, suggesting that non-genetic mechanisms drive relapse in a large proportion of cases. We therefore characterized epigenetic patterns of AML relapse using 26 matched diagnosis-relapse samples with ATAC-seq. This analysis identified a relapse-specific chromatin accessibility signature for mutationally stable AML, suggesting that AML undergoes epigenetic evolution at relapse independent of mutational changes. Analysis of leukemia stem cell (LSC) chromatin changes at relapse indicated that this leukemic compartment underwent significantly less epigenetic evolution than non-LSCs, while epigenetic changes in non-LSCs reflected overall evolution of the bulk leukemia. Finally, we used single-cell ATAC-seq paired with mitochondrial sequencing (mtscATAC) to map clones from diagnosis into relapse along with their epigenetic features. We found that distinct mitochondrially-defined clones exhibit more similar chromatin accessibility at relapse relative to diagnosis, demonstrating convergent epigenetic evolution in relapsed AML. These results demonstrate that epigenetic evolution is a feature of relapsed AML and that convergent epigenetic evolution can occur following treatment with induction chemotherapy.
Collapse
Affiliation(s)
- Kevin Nuno
- Cancer Biology Graduate Program, Stanford University School of MedicineStanfordUnited States
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Cancer Institute, Stanford University School of MedicineStanfordUnited States
- Department of Medicine, Division of Hematology, Stanford University School of MedicineStanfordUnited States
| | - Armon Azizi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Cancer Institute, Stanford University School of MedicineStanfordUnited States
- Department of Medicine, Division of Hematology, Stanford University School of MedicineStanfordUnited States
- University of California Irvine School of MedicineIrvineUnited States
| | - Thomas Koehnke
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Cancer Institute, Stanford University School of MedicineStanfordUnited States
- Department of Medicine, Division of Hematology, Stanford University School of MedicineStanfordUnited States
| | - Caleb Lareau
- Department of Pathology, Stanford UniversityStanfordUnited States
- Program in Immunology, Stanford UniversityStanfordUnited States
| | - Asiri Ediriwickrema
- Cancer Biology Graduate Program, Stanford University School of MedicineStanfordUnited States
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Cancer Institute, Stanford University School of MedicineStanfordUnited States
- Department of Medicine, Division of Hematology, Stanford University School of MedicineStanfordUnited States
| | - M Ryan Corces
- Cancer Biology Graduate Program, Stanford University School of MedicineStanfordUnited States
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Cancer Institute, Stanford University School of MedicineStanfordUnited States
- Department of Medicine, Division of Hematology, Stanford University School of MedicineStanfordUnited States
- Gladstone Institute of Neurological DiseaseSan FranciscoUnited States
- Gladstone Institute of Data Science and BiotechnologySan FranciscoUnited States
- Department of Neurology, University of California, San FranciscoSan FranciscoUnited States
| | - Ansuman T Satpathy
- Department of Pathology, Stanford UniversityStanfordUnited States
- Program in Immunology, Stanford UniversityStanfordUnited States
- Parker Institute for Cancer Immunotherapy, Stanford UniversityStanfordUnited States
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
| | - Ravindra Majeti
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Cancer Institute, Stanford University School of MedicineStanfordUnited States
- Department of Medicine, Division of Hematology, Stanford University School of MedicineStanfordUnited States
| |
Collapse
|
3
|
Landberg N, Köhnke T, Feng Y, Nakauchi Y, Fan AC, Linde MH, Karigane D, Lim K, Sinha R, Malcovati L, Thomas D, Majeti R. IDH1-mutant preleukemic hematopoietic stem cells can be eliminated by inhibition of oxidative phosphorylation. Blood Cancer Discov 2023; 5:731701. [PMID: 38091010 PMCID: PMC10905513 DOI: 10.1158/2643-3230.bcd-23-0195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/03/2023] [Accepted: 12/06/2023] [Indexed: 01/25/2024] Open
Abstract
Rare preleukemic hematopoietic stem cells (pHSCs) harboring only the initiating mutations can be detected at the time of AML diagnosis. pHSCs are the origin of leukemia and a potential reservoir for relapse. Using primary human samples and gene-editing to model isocitrate dehydrogenase 1 (IDH1) mutant pHSCs, we show epigenetic, transcriptional, and metabolic differences between pHSCs and healthy hematopoietic stem cells (HSCs). We confirm that IDH1 driven clonal hematopoiesis is associated with cytopenia, suggesting an inherent defect to fully reconstitute hematopoiesis. Despite giving rise to multilineage engraftment, IDH1-mutant pHSCs exhibited reduced proliferation, blocked differentiation, downregulation of MHC Class II genes, and reprogramming of oxidative phosphorylation metabolism. Critically, inhibition of oxidative phosphorylation resulted in complete eradication of IDH1-mutant pHSCs but not IDH2-mutant pHSCs or wildtype HSCs. Our results indicate that IDH1-mutant preleukemic clones can be targeted with complex I inhibitors, offering a potential strategy to prevent development and relapse of leukemia.
Collapse
Affiliation(s)
- Niklas Landberg
- Department of Medicine, Division of Hematology, Stanford School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
| | - Thomas Köhnke
- Department of Medicine, Division of Hematology, Stanford School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
| | - Yang Feng
- Department of Medicine, Division of Hematology, Stanford School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
| | - Yusuke Nakauchi
- Department of Medicine, Division of Hematology, Stanford School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
| | - Amy C. Fan
- Department of Medicine, Division of Hematology, Stanford School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
- Immunology Graduate Program, Stanford University, Stanford, California
| | - Miles H. Linde
- Department of Medicine, Division of Hematology, Stanford School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
- Immunology Graduate Program, Stanford University, Stanford, California
| | - Daiki Karigane
- Department of Medicine, Division of Hematology, Stanford School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
| | - Kelly Lim
- Adelaide Medical School, University of Adelaide, Adelaide, Australia
- Precision Medicine, South Australian Health and Medical Research Institute, The University of Adelaide, Adelaide, Australia
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Daniel Thomas
- Adelaide Medical School, University of Adelaide, Adelaide, Australia
- Precision Medicine, South Australian Health and Medical Research Institute, The University of Adelaide, Adelaide, Australia
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Stanford School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
| |
Collapse
|
4
|
Nuno KA, Azizi A, Köhnke T, Lareau CA, Ediwirickrema A, Ryan Corces M, Satpathy AT, Majeti R. Convergent Epigenetic Evolution Drives Relapse in Acute Myeloid Leukemia. bioRxiv 2023:2023.10.10.561642. [PMID: 37873452 PMCID: PMC10592718 DOI: 10.1101/2023.10.10.561642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Relapse of acute myeloid leukemia (AML) is highly aggressive and often treatment refractory. We analyzed previously published AML relapse cohorts and found that 40% of relapses occur without changes in driver mutations, suggesting that non-genetic mechanisms drive relapse in a large proportion of cases. We therefore characterized epigenetic patterns of AML relapse using 26 matched diagnosis-relapse samples with ATAC-seq. This analysis identified a relapse-specific chromatin accessibility signature for mutationally stable AML, suggesting that AML undergoes epigenetic evolution at relapse independent of mutational changes. Analysis of leukemia stem cell (LSC) chromatin changes at relapse indicated that this leukemic compartment underwent significantly less epigenetic evolution than non-LSCs, while epigenetic changes in non-LSCs reflected overall evolution of the bulk leukemia. Finally, we used single-cell ATAC-seq paired with mitochondrial sequencing (mtscATAC) to map clones from diagnosis into relapse along with their epigenetic features. We found that distinct mitochondrially-defined clones exhibit more similar chromatin accessibility at relapse relative to diagnosis, demonstrating convergent epigenetic evolution in relapsed AML. These results demonstrate that epigenetic evolution is a feature of relapsed AML and that convergent epigenetic evolution can occur following treatment with induction chemotherapy.
Collapse
Affiliation(s)
- Kevin A Nuno
- Cancer Biology Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed to this work equally
| | - Armon Azizi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
- University of California Irvine School of Medicine, Irvine, California
- These authors contributed to this work equally
| | - Thomas Köhnke
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
| | - Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
| | - Asiri Ediwirickrema
- Cancer Biology Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Cancer Biology Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, California
- Gladstone Institute of Data Science and Biotechnology, San Francisco, California
- Department of Neurology, University of California San Francisco, San Francisco, California
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Ravindra Majeti
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
| |
Collapse
|
5
|
Rausch J, Ullrich E, Kühn MW. Epigenetic targeting to enhance acute myeloid leukemia-directed immunotherapy. Front Immunol 2023; 14:1269012. [PMID: 37809078 PMCID: PMC10556528 DOI: 10.3389/fimmu.2023.1269012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023] Open
Abstract
AML is a malignant disease of hematopoietic progenitor cells with unsatisfactory treatment outcome, especially in patients that are ineligible for intensive chemotherapy. Immunotherapy, comprising checkpoint inhibition, T-cell engaging antibody constructs, and cellular therapies, has dramatically improved the outcome of patients with solid tumors and lymphatic neoplasms. In AML, these approaches have been far less successful. Discussed reasons are the relatively low mutational burden of AML blasts and the difficulty in defining AML-specific antigens not expressed on hematopoietic progenitor cells. On the other hand, epigenetic dysregulation is an essential driver of leukemogenesis, and non-selective hypomethylating agents (HMAs) are the current backbone of non-intensive treatment. The first clinical trials that evaluated whether HMAs may improve immune checkpoint inhibitors' efficacy showed modest efficacy except for the anti-CD47 antibody that was substantially more efficient against AML when combined with azacitidine. Combining bispecific antibodies or cellular treatments with HMAs is subject to ongoing clinical investigation, and efficacy data are awaited shortly. More selective second-generation inhibitors targeting specific chromatin regulators have demonstrated promising preclinical activity against AML and are currently evaluated in clinical trials. These drugs that commonly cause leukemia cell differentiation potentially sensitize AML to immune-based treatments by co-regulating immune checkpoints, providing a pro-inflammatory environment, and inducing (neo)-antigen expression. Combining selective targeted epigenetic drugs with (cellular) immunotherapy is, therefore, a promising approach to avoid unintended effects and augment efficacy. Future studies will provide detailed information on how these compounds influence specific immune functions that may enable translation into clinical assessment.
Collapse
Affiliation(s)
- Johanna Rausch
- Department of Hematology and Medical Oncology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
- German Cancer Consortium (DKTK) Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Evelyn Ullrich
- German Cancer Consortium (DKTK) Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Children’s Hospital, Experimental Immunology, Johann Wolfgang Goethe University, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt, Germany
- University Cancer Center (UCT), Frankfurt, Germany
| | - Michael W.M. Kühn
- Department of Hematology and Medical Oncology, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
- German Cancer Consortium (DKTK) Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
6
|
Tong X, Li M, Jin J, Li Y, Li L, Peng Y, Huang L, Xu B, Meng F, Mao X, Huang L, Huang W, Zhang D. Cladribine- and decitabine-containing conditioning regimen has a low post-transplant relapse rate in patients with relapsed or refractory acute myeloid leukemia and high-risk myelodysplastic syndrome. Int J Cancer 2023; 152:2123-2133. [PMID: 36594582 DOI: 10.1002/ijc.34419] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/24/2022] [Accepted: 12/23/2022] [Indexed: 01/04/2023]
Abstract
To reduce the risk of relapse after allogeneic hematopoietic stem cell transplantation (allo-HSCT), there have been continuing efforts to optimize the conditioning regimens. Our study aimed to analyze the risk factors associated with the relapse of relapsed/refractory (R/R), high-risk acute myeloid leukemia (AML) and high-risk myelodysplastic syndrome (MDS) post-transplant and the efficacy of a new conditioning regimen involving decitabine and cladribine. Clinical data of 125 patients with R/R AML, high-risk AML and high-risk MDS who underwent allo-HSCT were collected. In addition, 35 patients with R/R AML, high-risk AML and high-risk MDS received treatment with a new conditioning regimen including decitabine and cladribine. Cox regression analysis was used to identify risk factors associated with OS, RFS and relapse. Among 125 patients who underwent allo-HSCT, CR before allo-HSCT and matched sibling donors were independent protective factors for OS. DNMT3A abnormality was an independent risk factor for both relapse and RFS. Among 35 patients who received a new conditioning regimen containing decitabine and cladribine, only six patients relapsed and 1-year cumulative incidence of relapse was 11.7%. Moreover, this new regimen showed efficient MRD clearance early after allo-HSCT. The combined decitabine- and cladribine-based conditioning regimen showed a low relapse rate and a high survival without an increased incidence of GVHD or adverse effects and thus has potential for use in allo-HSCT for R/R AML, high-risk AML and high-risk MDS.
Collapse
Affiliation(s)
- Xiwen Tong
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mengyuan Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jie Jin
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yi Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Li Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yizhou Peng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lifang Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bin Xu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fankai Meng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xia Mao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liang Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Donghua Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| |
Collapse
|
7
|
Boila LD, Ghosh S, Bandyopadhyay SK, Jin L, Murison A, Zeng AGX, Shaikh W, Bhowmik S, Muddineni SSNA, Biswas M, Sinha S, Chatterjee SS, Mbong N, Gan OI, Bose A, Chakraborty S, Arruda A, Kennedy JA, Mitchell A, Lechman ER, Banerjee D, Milyavsky M, Minden MD, Dick JE, Sengupta A. KDM6 demethylases integrate DNA repair gene regulation and loss of KDM6A sensitizes human acute myeloid leukemia to PARP and BCL2 inhibition. Leukemia 2023; 37:751-764. [PMID: 36720973 DOI: 10.1038/s41375-023-01833-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 02/01/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous, aggressive malignancy with dismal prognosis and with limited availability of targeted therapies. Epigenetic deregulation contributes to AML pathogenesis. KDM6 proteins are histone-3-lysine-27-demethylases that play context-dependent roles in AML. We inform that KDM6-demethylase function critically regulates DNA-damage-repair-(DDR) gene expression in AML. Mechanistically, KDM6 expression is regulated by genotoxic stress, with deficiency of KDM6A-(UTX) and KDM6B-(JMJD3) impairing DDR transcriptional activation and compromising repair potential. Acquired KDM6A loss-of-function mutations are implicated in chemoresistance, although a significant percentage of relapsed-AML has upregulated KDM6A. Olaparib treatment reduced engraftment of KDM6A-mutant-AML-patient-derived xenografts, highlighting synthetic lethality using Poly-(ADP-ribose)-polymerase-(PARP)-inhibition. Crucially, a higher KDM6A expression is correlated with venetoclax tolerance. Loss of KDM6A increased mitochondrial activity, BCL2 expression, and sensitized AML cells to venetoclax. Additionally, BCL2A1 associates with venetoclax resistance, and KDM6A loss was accompanied with a downregulated BCL2A1. Corroborating these results, dual targeting of PARP and BCL2 was superior to PARP or BCL2 inhibitor monotherapy in inducing AML apoptosis, and primary AML cells carrying KDM6A-domain mutations were even more sensitive to the combination. Together, our study illustrates a mechanistic rationale in support of a novel combination therapy for AML based on subtype-heterogeneity, and establishes KDM6A as a molecular regulator for determining therapeutic efficacy.
Collapse
Affiliation(s)
- Liberalis Debraj Boila
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Subhadeep Ghosh
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Subham K Bandyopadhyay
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Liqing Jin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Wasim Shaikh
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Satyaki Bhowmik
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | | | - Mayukh Biswas
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Irving Cancer Research Center, Columbia University Medical Center, New York, NY, 10032, USA
| | - Sayantani Sinha
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Shankha Subhra Chatterjee
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Nathan Mbong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Anwesha Bose
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Sayan Chakraborty
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India
| | - Andrea Arruda
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.,Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, M5G 2C4, Canada.,Department of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Debasis Banerjee
- Park Clinic, Gorky Terrace and Ramakrishna Mission Seva Pratisthan, Kolkata, 700017, West Bengal, India
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.,Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, M5G 2C4, Canada.,Department of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Amitava Sengupta
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India. .,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India. .,CSIR-IICB-Cancer Biology & Inflammatory Disorder Division, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India.
| |
Collapse
|
8
|
Sperotto A, Bochicchio MT, Simonetti G, Buccisano F, Peccatori J, Piemontese S, Calistri E, Ciotti G, Pierdomenico E, De Marchi R, Ciceri F, Gottardi M. Measurable Residual Disease and Clonal Evolution in Acute Myeloid Leukemia from Diagnosis to Post-Transplant Follow-Up: The Role of Next-Generation Sequencing. Biomedicines 2023; 11. [PMID: 36830896 DOI: 10.3390/biomedicines11020359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
It has now been ascertained that acute myeloid leukemias-as in most type of cancers-are mixtures of various subclones, evolving by acquiring additional somatic mutations over the course of the disease. The complexity of leukemia clone architecture and the phenotypic and/or genotypic drifts that can occur during treatment explain why more than 50% of patients-in hematological remission-could relapse. Moreover, the complexity and heterogeneity of clone architecture represent a hindrance for monitoring measurable residual disease, as not all minimal residual disease monitoring methods are able to detect genetic mutations arising during treatment. Unlike with chemotherapy, which imparts a relatively short duration of selective pressure on acute myeloid leukemia clonal architecture, the immunological effect related to allogeneic hematopoietic stem cell transplant is prolonged over time and must be overcome for relapse to occur. This means that not all molecular abnormalities detected after transplant always imply inevitable relapse. Therefore, transplant represents a critical setting where a measurable residual disease-based strategy, performed during post-transplant follow-up by highly sensitive methods such as next-generation sequencing, could optimize and improve treatment outcome. The purpose of our review is to provide an overview of the role of next-generation sequencing in monitoring both measurable residual disease and clonal evolution in acute myeloid leukemia patients during the entire course of the disease, with special focus on the transplant phase.
Collapse
|
9
|
Ramanan R, Tiong IS, Ivey A, Ong DM, Brown FC, Chua C, Das T, Curtis DJ. Cellular distribution of IDH mutations in AML during morphologic remission. Leuk Res 2023; 124:106993. [PMID: 36459762 DOI: 10.1016/j.leukres.2022.106993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 11/27/2022]
Abstract
Limited information exists about the cellular distribution of mutations which persist in remission in acute myeloid leukemia (AML) (variably considered pre-leukemic mutations). We hypothesized that mutations detectable in all cell compartments may be less pathogenic than those that are myeloid-restricted. Here, we describe the cellular compartments that have IDH mutations in five patients with IDH-mutated AML in morphologic remission. Unlike pre-leukemic clones harboring the more common DNMT3A, TET2 and ASXL1 (DTA) mutations, we show that IDH mutations are myeloid-restricted. This finding provides an explanation for the reports that IDH mutations carry a higher risk for relapse than DTA mutations. Detailed analysis of one case also shows acquisition of additional mutations in distinct cellular compartments, illustrating subclonal complexity associated with therapeutics.
Collapse
|
10
|
Li R, Wang Z, Zhang Y, Guo M, Ni X, Chen J, Chen L, Gao L, Gong S, Tang G, Yang J, Wang J. Cytogenetic evolution predicts a poor prognosis in acute myeloid leukemia patients who relapse after allogeneic hematopoietic stem cell transplantation. Ann Hematol 2023; 102:89-97. [PMID: 36542104 DOI: 10.1007/s00277-022-05061-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 11/13/2022] [Indexed: 12/24/2022]
Abstract
Acute myeloid leukemia (AML) patients relapsing after allogeneic hematopoietic stem cell transplantation (allo-HSCT) have a poor prognosis. Cytogenetic evolution (CGE) has been investigated and found to have an important impact on the prognosis of relapsed leukemia, but its impact on AML patients relapsing after transplantation remains controversial. In this study, we analyzed 34 AML patients relapsing after allo-HSCT, among whom 14 developed additional abnormalities in chromosomal karyotype after leukemia recurrence (CGE group) and 20 patients did not (non-CGE group). We found that the cytogenetic characteristics were much more complex at relapse in the CGE group, and the acquisition of aberrations at relapse most commonly involved chromosome 11. The 6-month post-relapse overall survival (PROS) of the CGE group was significantly lower than that of the non-CGE group (21.4% versus 50.0%, P = 0.004). The CGE group also showed a trend of worse 2-year OS (7.1% versus 28.6%, P = 0.096). In the multivariate analyses, the occurrence of chronic graft-versus-host disease (HR 0.27 [95% CI, 0.11-0.68], P = 0.006) and a reduced-intensity FBA conditioning regimen (HR 0.42 [95% CI, 0.18-0.98], P = 0.045) were found to be two independent factors for a better PROS, whereas CGE (HR 3.16 [95% CI, 1.42-7.05], P = 0.005) was associated with a worse PROS. In conclusion, CGE was associated with a poor prognosis in AML patients who relapsed after allo-HSCT, and the importance of monitoring karyotype changes after transplantation should be noted.
Collapse
|
11
|
Zhou X, Zhang P, Aryal S, Zhang L, Lu R. UTX loss alters therapeutic responses in KMT2A-rearranged acute myeloid leukemia. Leukemia 2023; 37:226-230. [PMID: 36309561 DOI: 10.1038/s41375-022-01741-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 02/01/2023]
Affiliation(s)
- Xinyue Zhou
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
| | - Pengcheng Zhang
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
| | - Sajesan Aryal
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
| | - Lixia Zhang
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA
| | - Rui Lu
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35294, USA.
| |
Collapse
|
12
|
Desai RH, Zandvakili N, Bohlander SK. Dissecting the Genetic and Non-Genetic Heterogeneity of Acute Myeloid Leukemia Using Next-Generation Sequencing and In Vivo Models. Cancers (Basel) 2022; 14:2182. [PMID: 35565315 DOI: 10.3390/cancers14092182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Acute myeloid leukemia (AML) is an extremely aggressive form of blood cancer with high rates of treatment failure. AML arises from the stepwise acquisition of genetic aberrations and is a highly heterogeneous disorder. Recent research has shown that individual AML samples often contain several clones that are defined by a distinct combination of genetic lesions, epigenetic patterns and cell surface marker expression profiles. A better understanding of the clonal dynamics of AML is required to develop novel treatment strategies against this disease. In this review, we discuss the recent developments that have further deepened our understanding of clonal evolution and heterogeneity in AML. Abstract Acute myeloid leukemia (AML) is an extremely aggressive and heterogeneous disorder that results from the transformation of hematopoietic stem cells. Although our understanding of the molecular pathology of AML has greatly improved in the last few decades, the overall and relapse free survival rates among AML patients remain quite poor. This is largely due to evolution of the disease and selection of the fittest, treatment-resistant leukemic clones. There is increasing evidence that most AMLs possess a highly complex clonal architecture and individual leukemias are comprised of genetically, phenotypically and epigenetically distinct clones, which are continually evolving. Advances in sequencing technologies as well as studies using murine AML models have provided further insights into the heterogeneity of leukemias. We will review recent advances in the field of genetic and non-genetic heterogeneity in AML.
Collapse
|
13
|
Kamath-loeb AS, Shen J, Schmitt MW, Kohrn BF, Loeb KR, Estey EH, Dai J, Chien S, Loeb LA, Becker PS. Accurate Detection of Subclonal Variants in Paired Diagnosis-Relapse Acute Myeloid Leukemia Samples by Next Generation Duplex Sequencing. Leuk Res 2022. [PMID: 35303493 PMCID: PMC9014797 DOI: 10.1016/j.leukres.2022.106822] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/22/2022] [Accepted: 03/07/2022] [Indexed: 11/22/2022]
Abstract
Mutations characterize diverse human cancers; there is a positive correlation between elevated mutation frequency and tumor progression. One exception is acute myeloid leukemia (AML), which has few clonal single nucleotide mutations. We used highly sensitive and accurate Duplex Sequencing (DS) to show now that AML, in addition, has an extensive repertoire of variants with low allele frequencies, < 1%, which is below the accurate detection limit of most other sequencing methodologies. The subclonal variants are unique to each individual and change in composition, frequency, and sequence context from diagnosis to relapse. Their functional significance is apparent by the observation that many are known variants and cluster within functionally important protein domains. Subclones provide a reservoir of variants that could expand and contribute to the development of drug resistance and relapse. In accord, we accurately identified subclonal variants in AML driver genes NRAS and RUNX1 at allele frequencies between 0.1% and 0.3% at diagnosis, which expanded to comprise a major fraction (14-53%) of the blast population at relapse. Early and accurate detection of subclonal variants with low allele frequency thus offers the opportunity for early intervention, prior to detection of clinical relapse, to improve disease outcome and enhance patient survival.
Collapse
|
14
|
Chen S, Zhao Y, Liu S, Zhang J, Assaraf YG, Cui W, Wang L. Epigenetic enzyme mutations as mediators of anti-cancer drug resistance. Drug Resist Updat 2022. [DOI: 10.1016/j.drup.2022.100821] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
15
|
El Hussein S, DiNardo CD, Takahashi K, Khoury JD, Fang H, Furudate K, Lyapichev KA, Garces S, Kanagal-Shamanna R, Ok CY, Patel KP, Routbort MJ, Ravandi F, Medeiros LJ, Wang SA, Loghavi S. Acquired WT1 mutations contribute to relapse of NPM1-mutated acute myeloid leukemia following allogeneic hematopoietic stem cell transplant. Bone Marrow Transplant 2022. [PMID: 34992253 DOI: 10.1038/s41409-021-01538-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/08/2021] [Accepted: 11/19/2021] [Indexed: 11/08/2022]
Abstract
The role of WT1 protein in hematopoiesis and leukemogenesisis incompletely elucidated. WT1 overexpression is common in acute myeloid leukemia (AML); however, WT1 mutations occur in only about 10% of cases, with increasing incidence in the setting of relapse. In this study, we investigated the clinical and molecular characteristics of WT1 mutations in NPM1-mutated AML, to enhance our understanding of the biology and potential therapeutic implications of WT1 mutations. Our study cohort included 67 patients with NPM1 mutated AML and a median follow-up of 13.7 months. WT1 mutations were identified in 7% (n = 5) of patients at the time of initial diagnosis. WT1 mutant clones were presumed to be present as co-dominant clones in 3/5 and in subclonal populations in 2/5 cases based on variant allelic frequency (VAF) when compared with NPM1 mutation VAF. All WT1 mutations became undetectable at time of MRD-negative (NPM1-wild type) remission. None of these patients experienced relapse at the time of last follow-up (median, 15 months; range, 4.5-20.2 months). A total of 15/67 (22%) patients relapsed; among these patient, four (27%) relapsed with WT1 mutant AML. Three of four patients had undergone allogeneic hematopoietic stem cell transplantation (HSCT). None of these patients had detectable WT1 mutations at the time of initial diagnosis. WT1 mutations were presumed clonal in two cases and subclonal in the other two cases, based on VAF. Our results indicate that WT1 mutations contribute to relapse in NPM1 mutated AML, especially in the setting of HSCT. These findings suggest that emerging WT1 mutations may serve as a conduit for relapse in NPM1-mutated AML, and that sequential molecular profiling to evaluate potential emergent WT1 mutations during surveillance and particularly at relapse likely has prognostic value in patients with NPM1 mutated AML.
Collapse
|
16
|
Kerbs P, Vosberg S, Krebs S, Graf A, Blum H, Swoboda A, Batcha AMN, Mansmann U, Metzler D, Heckman CA, Herold T, Greif PA. Fusion gene detection by RNA-sequencing complements diagnostics of acute myeloid leukemia and identifies recurring NRIP1-MIR99AHG rearrangements. Haematologica 2022; 107:100-111. [PMID: 34134471 PMCID: PMC8719081 DOI: 10.3324/haematol.2021.278436] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/03/2021] [Indexed: 12/04/2022] Open
Abstract
Identification of fusion genes in clinical routine is mostly based on cytogenetics and targeted molecular genetics, such as metaphase karyotyping, fluorescence in situ hybridization and reverse-transcriptase polymerase chain reaction. However, sequencing technologies are becoming more important in clinical routine as processing time and costs per sample decrease. To evaluate the performance of fusion gene detection by RNAsequencing compared to standard diagnostic techniques, we analyzed 806 RNA-sequencing samples from patients with acute myeloid leukemia using two state-of-the-art software tools, namely Arriba and FusionCatcher. RNA-sequencing detected 90% of fusion events that were reported by routine with high evidence, while samples in which RNA-sequencing failed to detect fusion genes had overall lower and inhomogeneous sequence coverage. Based on properties of known and unknown fusion events, we developed a workflow with integrated filtering strategies for the identification of robust fusion gene candidates by RNA-sequencing. Thereby, we detected known recurrent fusion events in 26 cases that were not reported by routine and found discrepancies in evidence for known fusion events between routine and RNA-sequencing in three cases. Moreover, we identified 157 fusion genes as novel robust candidates and comparison to entries from ChimerDB or Mitelman Database showed novel recurrence of fusion genes in 14 cases. Finally, we detected the novel recurrent fusion gene NRIP1- MIR99AHG resulting from inv(21)(q11.2;q21.1) in nine patients (1.1%) and LTN1-MX1 resulting from inv(21)(q21.3;q22.3) in two patients (0.25%). We demonstrated that NRIP1-MIR99AHG results in overexpression of the 3' region of MIR99AHG and the disruption of the tricistronic miRNA cluster miR-99a/let-7c/miR-125b-2. Interestingly, upregulation of MIR99AHG and deregulation of the miRNA cluster, residing in the MIR99AHG locus, are known mechanisms of leukemogenesis in acute megakaryoblastic leukemia. Our findings demonstrate that RNA-sequencing has a strong potential to improve the systematic detection of fusion genes in clinical applications and provides a valuable tool for fusion discovery.
Collapse
Affiliation(s)
- Paul Kerbs
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Vosberg
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Anja Swoboda
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Aarif M N Batcha
- Department of Medical Data Processing, Biometry and Epidemiology, LMU Munich, Munich, Germany
| | - Ulrich Mansmann
- Department of Medical Data Processing, Biometry and Epidemiology, LMU Munich, Munich, Germany
| | - Dirk Metzler
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp A Greif
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
17
|
Wang Q, Mazor T, Harbig TA, Cerami E, Gehlenborg N. ThreadStates: State-based Visual Analysis of Disease Progression. IEEE Trans Vis Comput Graph 2022; 28:238-247. [PMID: 34587068 DOI: 10.1109/tvcg.2021.3114840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A growing number of longitudinal cohort studies are generating data with extensive patient observations across multiple timepoints. Such data offers promising opportunities to better understand the progression of diseases. However, these observations are usually treated as general events in existing visual analysis tools. As a result, their capabilities in modeling disease progression are not fully utilized. To fill this gap, we designed and implemented ThreadStates, an interactive visual analytics tool for the exploration of longitudinal patient cohort data. The focus of ThreadStates is to identify the states of disease progression by learning from observation data in a human-in-the-loop manner. We propose a novel Glyph Matrix design and combine it with a scatter plot to enable seamless identification, observation, and refinement of states. The disease progression patterns are then revealed in terms of state transitions using Sankey-based visualizations. We employ sequence clustering techniques to find patient groups with distinctive progression patterns, and to reveal the association between disease progression and patient-level features. The design and development were driven by a requirement analysis and iteratively refined based on feedback from domain experts over the course of a 10-month design study. Case studies and expert interviews demonstrate that ThreadStates can successively summarize disease states, reveal disease progression, and compare patient groups.
Collapse
|
18
|
Abstract
Cancer therapy is moving beyond traditional chemotherapy to include epigenetic approaches. KDM6 demethylases are dynamic regulation of gene expression by histone demethylation in response to diverse stimuli, and thus their dysregulation has been observed in various cancers. In this review, we first briefly introduce structural features of KDM6 subfamily, and then discuss the regulation of KDM6, which involves the coordinated control between cellular metabolism (intrinsic regulators) and tumor microenvironment (extrinsic stimuli). We further describe the aberrant functions of KDM6 in human cancers, acting as either a tumor suppressor or an oncoprotein in a context-dependent manner. Finally, we propose potential therapy of KDM6 enzymes based on their structural features, epigenetics, and immunomodulatory mechanisms, providing novel insights for prevention and treatment of cancers.
Collapse
Affiliation(s)
- Chunyan Hua
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | | | - Shuting Li
- Wenzhou Medical University, Wenzhou, China
| | | | - Jiahong Fu
- Wenzhou Medical University, Wenzhou, China
| | - Weijian Sun
- Department of Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wenqian Wang
- Department of Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
19
|
Staehle HF, Pahl HL, Jutzi JS. The Cross Marks the Spot: The Emerging Role of JmjC Domain-Containing Proteins in Myeloid Malignancies. Biomolecules 2021; 11:biom11121911. [PMID: 34944554 PMCID: PMC8699298 DOI: 10.3390/biom11121911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022] Open
Abstract
Histone methylation tightly regulates chromatin accessibility, transcription, proliferation, and cell differentiation, and its perturbation contributes to oncogenic reprogramming of cells. In particular, many myeloid malignancies show evidence of epigenetic dysregulation. Jumonji C (JmjC) domain-containing proteins comprise a large and diverse group of histone demethylases (KDMs), which remove methyl groups from lysines in histone tails and other proteins. Cumulating evidence suggests an emerging role for these demethylases in myeloid malignancies, rendering them attractive targets for drug interventions. In this review, we summarize the known functions of Jumonji C (JmjC) domain-containing proteins in myeloid malignancies. We highlight challenges in understanding the context-dependent mechanisms of these proteins and explore potential future pharmacological targeting.
Collapse
Affiliation(s)
- Hans Felix Staehle
- Division of Molecular Hematology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany; (H.F.S.); (H.L.P.)
| | - Heike Luise Pahl
- Division of Molecular Hematology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany; (H.F.S.); (H.L.P.)
| | - Jonas Samuel Jutzi
- Division of Molecular Hematology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany; (H.F.S.); (H.L.P.)
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02115, MA, USA
- Correspondence:
| |
Collapse
|
20
|
Benard BA, Leak LB, Azizi A, Thomas D, Gentles AJ, Majeti R. Clonal architecture predicts clinical outcomes and drug sensitivity in acute myeloid leukemia. Nat Commun 2021; 12:7244. [PMID: 34903734 PMCID: PMC8669028 DOI: 10.1038/s41467-021-27472-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/17/2021] [Indexed: 12/17/2022] Open
Abstract
The impact of clonal heterogeneity on disease behavior or drug response in acute myeloid leukemia remains poorly understood. Using a cohort of 2,829 patients, we identify features of clonality associated with clinical features and drug sensitivities. High variant allele frequency for 7 mutations (including NRAS and TET2) associate with dismal prognosis; elevated GATA2 variant allele frequency correlates with better outcomes. Clinical features such as white blood cell count and blast percentage correlate with the subclonal abundance of mutations such as TP53 and IDH1. Furthermore, patients with cohesin mutations occurring before NPM1, or transcription factor mutations occurring before splicing factor mutations, show shorter survival. Surprisingly, a branched pattern of clonal evolution is associated with superior clinical outcomes. Finally, several mutations (including NRAS and IDH1) predict drug sensitivity based on their subclonal abundance. Together, these results demonstrate the importance of assessing clonal heterogeneity with implications for prognosis and actionable biomarkers for therapy.
Collapse
Affiliation(s)
- Brooks A Benard
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University, Stanford, CA, USA
| | - Logan B Leak
- Cancer Biology Program, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Armon Azizi
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
| | - Daniel Thomas
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Andrew J Gentles
- Department of Medicine (Biomedical Informatics/Quantitative Sciences unit), Stanford University, Stanford, CA, USA
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA.
| |
Collapse
|
21
|
Duchmann M, Laplane L, Itzykson R. Clonal Architecture and Evolutionary Dynamics in Acute Myeloid Leukemias. Cancers (Basel) 2021; 13:4887. [PMID: 34638371 PMCID: PMC8507870 DOI: 10.3390/cancers13194887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/19/2022] Open
Abstract
Acute myeloid leukemias (AML) results from the accumulation of genetic and epigenetic alterations, often in the context of an aging hematopoietic environment. The development of high-throughput sequencing-and more recently, of single-cell technologies-has shed light on the intratumoral diversity of leukemic cells. Taking AML as a model disease, we review the multiple sources of genetic, epigenetic, and functional heterogeneity of leukemic cells and discuss the definition of a leukemic clone extending its definition beyond genetics. After introducing the two dimensions contributing to clonal diversity, namely, richness (number of leukemic clones) and evenness (distribution of clone sizes), we discuss the mechanisms at the origin of clonal emergence (mutation rate, number of generations, and effective size of the leukemic population) and the causes of clonal dynamics. We discuss the possible role of neutral drift, but also of cell-intrinsic and -extrinsic influences on clonal fitness. After reviewing available data on the prognostic role of genetic and epigenetic diversity of leukemic cells on patients' outcome, we discuss how a better understanding of AML as an evolutionary process could lead to the design of novel therapeutic strategies in this disease.
Collapse
Affiliation(s)
- Matthieu Duchmann
- Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Université de Paris, 75010 Paris, France;
- Laboratoire d’Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 75010 Paris, France
| | - Lucie Laplane
- Institut d’Histoire et Philosophie des Sciences et des Techniques UMR 8590, CNRS, Université Paris 1 Panthéon-Sorbonne, 75010 Paris, France;
- Gustave Roussy Cancer Center, UMR1287, 94805 Villejuif, France
| | - Raphael Itzykson
- Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Université de Paris, 75010 Paris, France;
- Département Hématologie et Immunologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 75010 Paris, France
| |
Collapse
|
22
|
Mat Yusoff Y, Ahid F, Abu Seman Z, Abdullah J, Kamaluddin NR, Esa E, Zakaria Z. Comprehensive analysis of mutations and clonal evolution patterns in a cohort of patients with cytogenetically normal acute myeloid leukemia. Mol Cytogenet 2021; 14:45. [PMID: 34560908 PMCID: PMC8464159 DOI: 10.1186/s13039-021-00561-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
Background Relapsed acute myeloid leukemia (AML) is associated with the acquisition of additional somatic mutations which are thought to drive phenotypic adaptability, clonal selection and evolution of leukemic clones during treatment. We performed high throughput exome sequencing of matched presentation and relapsed samples from 6 cytogenetically normal AML (CN-AML) patients treated with standard remission induction chemotherapy in order to contribute with the investigation of the mutational landscape of CN-AML and clonal evolution during AML treatment. Result A total of 24 and 32 somatic variants were identified in presentation and relapse samples respectively with an average of 4.0 variants per patient at presentation and 5.3 variants per patient at relapse, with SNVs being more frequent than indels at both disease stages. All patients have somatic variants in at least one gene that is frequently mutated in AML at both disease presentation and relapse, with most of these variants are classic AML and recurrent hotspot mutations including NPM1 p.W288fs, FLT3-ITD, NRAS p.G12D and IDH2 p.R140Q. In addition, we found two distinct clonal evolution patterns of relapse: (1) a leukemic clone at disease presentation acquires additional mutations and evolves into the relapse clone after the chemotherapy; (2) a leukemic clone at disease presentation persists at relapse without the addition of novel somatic mutations. Conclusions The findings of this study suggest that the relapse-initiating clones may pre-exist prior to therapy, which harbor or acquire mutations that confer selective advantage during chemotherapy, resulting in clonal expansion and eventually leading to relapse.
Collapse
Affiliation(s)
- Yuslina Mat Yusoff
- Hematology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170, Shah Alam, Selangor, Malaysia
| | - Fadly Ahid
- Centre for Medical Laboratory Technology Studies, Faculty of Health Sciences, Universiti Teknologi MARA, 42300, Puncak Alam, Selangor, Malaysia.
| | - Zahidah Abu Seman
- Hematology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170, Shah Alam, Selangor, Malaysia
| | - Julia Abdullah
- Hematology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170, Shah Alam, Selangor, Malaysia
| | - Nor Rizan Kamaluddin
- Hematology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170, Shah Alam, Selangor, Malaysia
| | - Ezalia Esa
- Hematology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170, Shah Alam, Selangor, Malaysia
| | - Zubaidah Zakaria
- Hematology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170, Shah Alam, Selangor, Malaysia
| |
Collapse
|
23
|
Dinh KN, Jaksik R, Corey SJ, Kimmel M. Predicting Time to Relapse in Acute Myeloid Leukemia through Stochastic Modeling of Minimal Residual Disease Based on Clonality Data. Comput Syst Oncol 2021; 1. [PMID: 34541576 DOI: 10.1002/cso2.1026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Event-free and overall survival remain poor for patients with acute myeloid leukemia. Chemoresistant clones contributing to relapse arise from minimal residual disease (MRD) or newly-acquired mutations. However, the dynamics of clones comprising MRD is poorly understood. We developed a predictive stochastic model, based on a multitype age-dependent Markov branching process, to describe how random events in MRD contribute to the heterogeneity in treatment response. We employed training and validation sets of patients who underwent whole genome sequencing and for whom mutant clone frequencies at diagnosis and relapse were available. The disease evolution and treatment outcome are subject to stochastic fluctuations. Estimates of malignant clone growth rates, obtained by model fitting, are consistent with published data. Using the estimates from the training set, we developed a function linking MRD and time of relapse, with MRD inferred from the model fits to clone frequencies and other data. An independent validation set confirmed our model. In a third data set, we fitted the model to data at diagnosis and remission and predicted the time to relapse. As a conclusion, given bone marrow genome at diagnosis and MRD at or past remission, the model can predict time to relapse, and help guide treatment decisions to mitigate relapse.
Collapse
Affiliation(s)
- Khanh N Dinh
- Irving Institute of Cancer Dynamics, Columbia University, New York, NY, USA
| | - Roman Jaksik
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Seth J Corey
- Departments of Pediatric Hematology/Oncology and Stem Cell Transplantation and Cancer Biology, Cleveland Clinic, Cleveland, OH, USA
| | - Marek Kimmel
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland.,Department of Statistics, Rice University, Houston, TX, USA
| |
Collapse
|
24
|
Stiehl T, Marciniak-Czochra A. Computational Reconstruction of Clonal Hierarchies From Bulk Sequencing Data of Acute Myeloid Leukemia Samples. Front Physiol 2021; 12:596194. [PMID: 34497529 PMCID: PMC8419336 DOI: 10.3389/fphys.2021.596194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Acute myeloid leukemia is an aggressive cancer of the blood forming system. The malignant cell population is composed of multiple clones that evolve over time. Clonal data reflect the mechanisms governing treatment response and relapse. Single cell sequencing provides most direct insights into the clonal composition of the leukemic cells, however it is still not routinely available in clinical practice. In this work we develop a computational algorithm that allows identifying all clonal hierarchies that are compatible with bulk variant allele frequencies measured in a patient sample. The clonal hierarchies represent descendance relations between the different clones and reveal the order in which mutations have been acquired. The proposed computational approach is tested using single cell sequencing data that allow comparing the outcome of the algorithm with the true structure of the clonal hierarchy. We investigate which problems occur during reconstruction of clonal hierarchies from bulk sequencing data. Our results suggest that in many cases only a small number of possible hierarchies fits the bulk data. This implies that bulk sequencing data can be used to obtain insights in clonal evolution.
Collapse
Affiliation(s)
- Thomas Stiehl
- Institute for Computational Biomedicine – Disease Modeling, RWTH Aachen University, Aachen, Germany
- Institute of Applied Mathematics, Interdisciplinary Center for Scientific Computing and Bioquant Center, Heidelberg University, Heidelberg, Germany
| | - Anna Marciniak-Czochra
- Institute of Applied Mathematics, Interdisciplinary Center for Scientific Computing and Bioquant Center, Heidelberg University, Heidelberg, Germany
| |
Collapse
|
25
|
Song A, Altabbakh O, Sallman DA, Padron E, Talati C, Hussaini MO. Acquisition of IDH2 mutations in relapsed/refractory AML is associated with worse patient outcomes. Eur J Haematol 2021; 107:609-616. [PMID: 34407254 DOI: 10.1111/ejh.13698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVES The presence of targeted therapy, Enasidenib, for IDH2-mutated AML underscores the importance of understanding the clonal dynamics of IDH2 mutations, which has not been elucidated. In the largest study of IDH2 clonal dynamics, we detail the IDH2-evolutionary patterns and their clinical significance. METHODS We analyzed ~6000 patients with NGS results to identify 120 AML patients with IDH2 mutations and longitudinal NGS testing. IDH2 mutation status was recorded at diagnosis, remission, relapse, and persistent disease. RESULTS One hundred and five patients were IDH2-positive at the initial diagnosis, and 15 acquired the mutation later. Of those 15 patients, 7 patients gained the mutation during persistent disease, 6 during relapse, and 2 at remission. Twenty-one patients (18%) who were IDH2-positive in a prior test remained IDH2-positive in remission. Twenty-four patients with IDH2-positive AML were IDH2-positive at relapse. IDH2-positive at diagnosis had better survival than IDH2 mutation acquired later in disease (P = .024). Patients who were IDH2-negative in remission had significantly improved survival (P = .002). Also, loss-of-IDH2 mutation with persistent disease had better OS (P = .035). CONCLUSIONS There are 70% that clear IDH2 in disease remission. 12% gain IDH2 mutation later, usually in the setting of refractory/relapsed AML. These patients fared worse. Longitudinal IDH2 testing may be helpful in prognostic stratification.
Collapse
Affiliation(s)
- Amy Song
- New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | | | - David A Sallman
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Eric Padron
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Chetasi Talati
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | |
Collapse
|
26
|
Stratmann S, Yones SA, Mayrhofer M, Norgren N, Skaftason A, Sun J, Smolinska K, Komorowski J, Herlin MK, Sundström C, Eriksson A, Höglund M, Palle J, Abrahamsson J, Jahnukainen K, Munthe-Kaas MC, Zeller B, Tamm KP, Cavelier L, Holmfeldt L. Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets. Blood Adv 2021; 5:900-12. [PMID: 33560403 DOI: 10.1182/bloodadvances.2020003709] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/04/2021] [Indexed: 11/20/2022] Open
Abstract
Relapse is the leading cause of death of adult and pediatric patients with acute myeloid leukemia (AML). Numerous studies have helped to elucidate the complex mutational landscape at diagnosis of AML, leading to improved risk stratification and new therapeutic options. However, multi-whole-genome studies of adult and pediatric AML at relapse are necessary for further advances. To this end, we performed whole-genome and whole-exome sequencing analyses of longitudinal diagnosis, relapse, and/or primary resistant specimens from 48 adult and 25 pediatric patients with AML. We identified mutations recurrently gained at relapse in ARID1A and CSF1R, both of which represent potentially actionable therapeutic alternatives. Further, we report specific differences in the mutational spectrum between adult vs pediatric relapsed AML, with MGA and H3F3A p.Lys28Met mutations recurrently found at relapse in adults, whereas internal tandem duplications in UBTF were identified solely in children. Finally, our study revealed recurrent mutations in IKZF1, KANSL1, and NIPBL at relapse. All of the mentioned genes have either never been reported at diagnosis in de novo AML or have been reported at low frequency, suggesting important roles for these alterations predominantly in disease progression and/or resistance to therapy. Our findings shed further light on the complexity of relapsed AML and identified previously unappreciated alterations that may lead to improved outcomes through personalized medicine.
Collapse
|
27
|
Simoes C, Paiva B, Martínez-Cuadrón D, Bergua JM, Vives S, Algarra L, Tormo M, Martinez P, Serrano J, Herrera P, Ramos F, Salamero O, Lavilla E, Gil C, Lopez JL, Vidriales MB, Labrador J, Falantes JF, Sayas MJ, Ayala R, Martinez-Lopez J, Villar S, Calasanz MJ, Prosper F, San-Miguel JF, Sanz MÁ, Montesinos P. Measurable residual disease in elderly acute myeloid leukemia: results from the PETHEMA-FLUGAZA phase 3 clinical trial. Blood Adv 2021; 5:760-70. [PMID: 33560390 DOI: 10.1182/bloodadvances.2020003195] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/02/2020] [Indexed: 02/06/2023] Open
Abstract
The value of measurable residual disease (MRD) in elderly patients with acute myeloid leukemia (AML) is inconsistent between those treated with intensive vs hypomethylating drugs, and unknown after semi-intensive therapy. We investigated the role of MRD in refining complete remission (CR) and treatment duration in the phase 3 FLUGAZA clinical trial, which randomized 283 elderly AML patients to induction and consolidation with fludarabine plus cytarabine (FLUGA) vs 5-azacitidine. After consolidation, patients continued treatment if MRD was ≥0.01% or stopped if MRD was <0.01%, as assessed by multidimensional flow cytometry (MFC). On multivariate analysis including genetic risk and treatment arm, MRD status in patients achieving CR (N = 72) was the only independent prognostic factor for relapse-free survival (RFS) (HR, 3.45; P = .002). Achieving undetectable MRD significantly improved RFS of patients with adverse genetics (HR, 0.32; P = .013). Longer overall survival was observed in patients with undetectable MRD after induction though not after consolidation. Although leukemic cells from most patients displayed phenotypic aberrancies vs their normal counterpart (N = 259 of 265), CD34 progenitors from cases with undetectable MRD by MFC carried extensive genetic abnormalities identified by whole-exome sequencing. Interestingly, the number of genetic alterations significantly increased from diagnosis to MRD stages in patients treated with FLUGA vs 5-azacitidine (2.2-fold vs 1.1-fold; P = .001). This study supports MRD assessment to refine CR after semi-intensive therapy or hypomethylating agents, but unveils that improved sensitivity is warranted to individualize treatment and prolong survival of elderly AML patients achieving undetectable MRD.
Collapse
|
28
|
Wang M, Wang R, Wang H, Chen C, Qin J, Gao X, Yu L. Difference in gene mutation profile in patients with refractory/relapsed versus newly diagnosed acute myeloid leukemia based on targeted next-generation sequencing. Leuk Lymphoma 2021; 62:2416-2427. [PMID: 33913388 DOI: 10.1080/10428194.2021.1919661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
We have reported the genetic mutation profile in previously untreated acute myeloid leukemia (AML) patients using a targeted NGS screening method. In this study, we evaluated the characteristics and prognostic significance of gene mutations in refractory/relapsed (R/R) AML patients by comparing their gene mutation spectrum to those newly diagnosed. The frequencies of tumor suppressor mutations were increased, while the mutation frequencies of nucleophosmin and spliceosome complex were decreased in relapsed AML. The frequency of FLT3-ITD mutation was increased, while that of CEBPA biallelic mutation decreased in refractory AML. Activated signaling mutations predicted a lower complete remission rate. FLT3-ITD mutation predicted an inferior overall survival after relapse. DNMT3A mutation predicted an inferior relapse-free survival in R/R AML. These findings may shed light on the molecular mechanism study of leukemia refractory or relapse and provide new guidance for the dynamic risk assessment of AML.
Collapse
Affiliation(s)
- Mengzhen Wang
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Ruiqi Wang
- School of Medicine, Nankai University, Tianjin, China
| | - Hong Wang
- School of Medicine, Nankai University, Tianjin, China
| | - Chongjian Chen
- Annoroad Gene Technology Co, Beijing Economic-Technological Development Area, Beijing, China
| | - Jiayue Qin
- Annoroad Gene Technology Co, Beijing Economic-Technological Development Area, Beijing, China
| | - Xiaoning Gao
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Li Yu
- Department of Hematology, Chinese PLA General Hospital, Beijing, China.,Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
| |
Collapse
|
29
|
Kempf JM, Weser S, Bartoschek MD, Metzeler KH, Vick B, Herold T, Völse K, Mattes R, Scholz M, Wange LE, Festini M, Ugur E, Roas M, Weigert O, Bultmann S, Leonhardt H, Schotta G, Hiddemann W, Jeremias I, Spiekermann K. Loss-of-function mutations in the histone methyltransferase EZH2 promote chemotherapy resistance in AML. Sci Rep 2021; 11:5838. [PMID: 33712646 DOI: 10.1038/s41598-021-84708-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/15/2021] [Indexed: 12/25/2022] Open
Abstract
Chemotherapy resistance is the main impediment in the treatment of acute myeloid leukaemia (AML). Despite rapid advances, the various mechanisms inducing resistance development remain to be defined in detail. Here we report that loss-of-function mutations (LOF) in the histone methyltransferase EZH2 have the potential to confer resistance against the chemotherapeutic agent cytarabine. We identify seven distinct EZH2 mutations leading to loss of H3K27 trimethylation via multiple mechanisms. Analysis of matched diagnosis and relapse samples reveal a heterogenous regulation of EZH2 and a loss of EZH2 in 50% of patients. We confirm that loss of EZH2 induces resistance against cytarabine in the cell lines HEK293T and K562 as well as in a patient-derived xenograft model. Proteomics and transcriptomics analysis reveal that resistance is conferred by upregulation of multiple direct and indirect EZH2 target genes that are involved in apoptosis evasion, augmentation of proliferation and alteration of transmembrane transporter function. Our data indicate that loss of EZH2 results in upregulation of its target genes, providing the cell with a selective growth advantage, which mediates chemotherapy resistance.
Collapse
|
30
|
Giacopelli B, Wang M, Cleary A, Wu YZ, Schultz AR, Schmutz M, Blachly JS, Eisfeld AK, Mundy-Bosse B, Vosberg S, Greif PA, Claus R, Bullinger L, Garzon R, Coombes KR, Bloomfield CD, Druker BJ, Tyner JW, Byrd JC, Oakes CC. DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia. Genome Res 2021; 31:747-761. [PMID: 33707228 PMCID: PMC8092005 DOI: 10.1101/gr.269233.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/09/2021] [Indexed: 02/06/2023]
Abstract
Acute myeloid leukemia (AML) is a molecularly complex disease characterized by heterogeneous tumor genetic profiles and involving numerous pathogenic mechanisms and pathways. Integration of molecular data types across multiple patient cohorts may advance current genetic approaches for improved subclassification and understanding of the biology of the disease. Here, we analyzed genome-wide DNA methylation in 649 AML patients using Illumina arrays and identified a configuration of 13 subtypes (termed “epitypes”) using unbiased clustering. Integration of genetic data revealed that most epitypes were associated with a certain recurrent mutation (or combination) in a majority of patients, yet other epitypes were largely independent. Epitypes showed developmental blockage at discrete stages of myeloid differentiation, revealing epitypes that retain arrested hematopoietic stem-cell-like phenotypes. Detailed analyses of DNA methylation patterns identified unique patterns of aberrant hyper- and hypomethylation among epitypes, with variable involvement of transcription factors influencing promoter, enhancer, and repressed regions. Patients in epitypes with stem-cell-like methylation features showed inferior overall survival along with up-regulated stem cell gene expression signatures. We further identified a DNA methylation signature involving STAT motifs associated with FLT3-ITD mutations. Finally, DNA methylation signatures were stable at relapse for the large majority of patients, and rare epitype switching accompanied loss of the dominant epitype mutations and reversion to stem-cell-like methylation patterns. These results show that DNA methylation-based classification integrates important molecular features of AML to reveal the diverse pathogenic and biological aspects of the disease.
Collapse
Affiliation(s)
- Brian Giacopelli
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Min Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ada Cleary
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Yue-Zhong Wu
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Anna Reister Schultz
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Maximilian Schmutz
- Hematology and Oncology, Medical Faculty, University of Augsburg, 86159 Augsburg, Germany
| | - James S Blachly
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ann-Kathrin Eisfeld
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Bethany Mundy-Bosse
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Sebastian Vosberg
- Department of Medicine III, University Hospital, LMU Munich, 80539 Munich, Germany.,Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Munich, Germany
| | - Philipp A Greif
- Department of Medicine III, University Hospital, LMU Munich, 80539 Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rainer Claus
- Department of Medicine II, Stem Cell Transplantation Unit, Klinikum Augsburg, Ludwig-Maximilians University Munich, 86156 Munich, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumorimmunology, Charité-Universitätsmedizin, 13353 Berlin, Germany
| | - Ramiro Garzon
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Kevin R Coombes
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Clara D Bloomfield
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - John C Byrd
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Christopher C Oakes
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| |
Collapse
|
31
|
Feusier JE, Arunachalam S, Tashi T, Baker MJ, VanSant-Webb C, Ferdig A, Welm BE, Rodriguez-Flores JL, Ours C, Jorde LB, Prchal JT, Mason CC. Large-Scale Identification of Clonal Hematopoiesis and Mutations Recurrent in Blood Cancers. Blood Cancer Discov 2021; 2:226-237. [PMID: 34027416 DOI: 10.1158/2643-3230.bcd-20-0094] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by detectable hematopoietic-associated gene mutations in a person without evidence of hematologic malignancy. We sought to identify additional cancer-presenting mutations useable for CHIP detection by performing a data mining analysis of 48 somatic mutation studies reporting mutations at diagnoses of 7,430 adult and pediatric patients with hematologic malignancies. Following extraction of 20,141 protein-altering mutations, we identified 434 significantly recurrent mutation hotspots, 364 of which occurred at loci confidently assessable for CHIP. We then performed an additional large-scale analysis of whole exome sequencing data from 4,538 persons belonging to three non-cancer cohorts for clonal mutations. We found the combined cohort prevalence of CHIP with mutations identical to those reported at blood cancer mutation hotspots to be 1.8%, and that some of these CHIP mutations occurred in children. Our findings may help to improve CHIP detection and pre-cancer surveillance for both children and adults.
Collapse
Affiliation(s)
- Julie E Feusier
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Utah, Salt Lake City, UT, USA.,Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Sasi Arunachalam
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Utah, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Tsewang Tashi
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA.,VA Medical Center, Salt Lake City, UT, USA
| | - Monika J Baker
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Utah, Salt Lake City, UT, USA
| | - Chad VanSant-Webb
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Utah, Salt Lake City, UT, USA
| | - Amber Ferdig
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Utah, Salt Lake City, UT, USA
| | - Bryan E Welm
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Surgery, University of Utah, Salt Lake City, UT, USA
| | | | - Christopher Ours
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Utah, Salt Lake City, UT, USA
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Josef T Prchal
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA.,VA Medical Center, Salt Lake City, UT, USA
| | - Clinton C Mason
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Utah, Salt Lake City, UT, USA
| |
Collapse
|
32
|
Rapaport F, Neelamraju Y, Baslan T, Hassane D, Gruszczynska A, Robert de Massy M, Farnoud N, Haddox S, Lee T, Medina-Martinez J, Sheridan C, Thurmond A, Becker M, Bekiranov S, Carroll M, Moses Murdock H, Valk PJM, Bullinger L, D'Andrea R, Lowe SW, Neuberg D, Levine RL, Melnick A, Garrett-Bakelman FE. Genomic and evolutionary portraits of disease relapse in acute myeloid leukemia. Leukemia 2021; 35:2688-2692. [PMID: 33580203 PMCID: PMC8357838 DOI: 10.1038/s41375-021-01153-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/23/2020] [Accepted: 01/22/2021] [Indexed: 11/12/2022]
Affiliation(s)
- Franck Rapaport
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Center for Clinical and Translational Science, The Rockefeller University, New York, NY, USA.,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Duane Hassane
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Agata Gruszczynska
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Marc Robert de Massy
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Noushin Farnoud
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel Haddox
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Tak Lee
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Juan Medina-Martinez
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caroline Sheridan
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Alexis Thurmond
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Michael Becker
- Department of Medicine, University of Rochester, Rochester, NY, USA
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Heardly Moses Murdock
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Lars Bullinger
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany.,Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine Berlin, Berlin, Germany
| | - Richard D'Andrea
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Donna Neuberg
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Ross L Levine
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ari Melnick
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Francine E Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA. .,Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA. .,Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA. .,University of Virginia Cancer Center, Charlottesville, VA, USA.
| |
Collapse
|
33
|
Rapaport F, Boisson B, Gregor A, Béziat V, Boisson-Dupuis S, Bustamante J, Jouanguy E, Puel A, Rosain J, Zhang Q, Zhang SY, Gleeson JG, Quintana-Murci L, Casanova JL, Abel L, Patin E. Negative selection on human genes underlying inborn errors depends on disease outcome and both the mode and mechanism of inheritance. Proc Natl Acad Sci U S A 2021; 118:e2001248118. [PMID: 33408250 PMCID: PMC7826345 DOI: 10.1073/pnas.2001248118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genetic variants underlying life-threatening diseases, being unlikely to be transmitted to the next generation, are gradually and selectively eliminated from the population through negative selection. We study the determinants of this evolutionary process in human genes underlying monogenic diseases by comparing various negative selection scores and an integrative approach, CoNeS, at 366 loci underlying inborn errors of immunity (IEI). We find that genes underlying autosomal dominant (AD) or X-linked IEI have stronger negative selection scores than those underlying autosomal recessive (AR) IEI, whose scores are not different from those of genes not known to be disease causing. Nevertheless, genes underlying AR IEI that are lethal before reproductive maturity with complete penetrance have stronger negative selection scores than other genes underlying AR IEI. We also show that genes underlying AD IEI by loss of function have stronger negative selection scores than genes underlying AD IEI by gain of function, while genes underlying AD IEI by haploinsufficiency are under stronger negative selection than other genes underlying AD IEI. These results are replicated in 1,140 genes underlying inborn errors of neurodevelopment. Finally, we propose a supervised classifier, SCoNeS, which predicts better than state-of-the-art approaches whether a gene is more likely to underlie an AD or AR disease. The clinical outcomes of monogenic inborn errors, together with their mode and mechanisms of inheritance, determine the levels of negative selection at their corresponding loci. Integrating scores of negative selection may facilitate the prioritization of candidate genes and variants in patients suspected to carry an inborn error.
Collapse
Affiliation(s)
- Franck Rapaport
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065;
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Anne Gregor
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Vivien Béziat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
- Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
- Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Joseph G Gleeson
- Howard Hughes Medical Institute, La Jolla, CA 92093
- Rady Children's Institute of Genomic Medicine, Department of Neurosciences, University of California San Diego, La Jolla, CA 92093
- Laboratory for Pediatric Brain Disease, The Rockefeller University, New York, NY 10065
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, 75015 Paris, France
- Chair of Human Genomics and Evolution, Collège de France, 75231 Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065;
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
- Howard Hughes Medical Institute, New York, NY 10065
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, 75015 Paris, France
| |
Collapse
|
34
|
Das AB, Smith-Díaz CC, Vissers MCM. Emerging epigenetic therapeutics for myeloid leukemia: modulating demethylase activity with ascorbate. Haematologica 2021; 106:14-25. [PMID: 33099992 PMCID: PMC7776339 DOI: 10.3324/haematol.2020.259283] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/17/2020] [Indexed: 12/23/2022] Open
Abstract
The past decade has seen a proliferation of drugs that target epigenetic pathways. Many of these drugs were developed to treat acute myeloid leukemia, a condition in which dysregulation of the epigenetic landscape is well established. While these drugs have shown promise, critical issues persist. Specifically, patients with the same mutations respond quite differently to treatment. This is true even with highly specific drugs that are designed to target the underlying oncogenic driver mutations. Furthermore, patients who do respond may eventually develop resistance. There is now evidence that epigenetic heterogeneity contributes, in part, to these issues. Cancer cells also have a remarkable capacity to ‘rewire’ themselves at the epigenetic level in response to drug treatment, and thereby maintain expression of key oncogenes. This epigenetic plasticity is a promising new target for drug development. It is therefore important to consider combination therapy in cases in which both driver mutations and epigenetic plasticity are targeted. Using ascorbate as an example of an emerging epigenetic therapeutic, we review the evidence for its potential use in both of these modes. We provide an overview of 2-oxoglutarate dependent dioxygenases with DNA, histone and RNA demethylase activity, focusing on those which require ascorbate as a cofactor. We also evaluate their role in the development and maintenance of acute myeloid leukemia. Using this information, we highlight situations in which the use of ascorbate to restore 2-oxoglutarate dependent dioxygenase activity could prove beneficial, in contrast to contexts in which targeted inhibition of specific enzymes might be preferred. Finally, we discuss how these insights could be incorporated into the rational design of future clinical trials.
Collapse
Affiliation(s)
- Andrew B Das
- Department of Pathology and Biomedical Science, University of Otago, Christchurch.
| | - Carlos C Smith-Díaz
- Department of Pathology and Biomedical Science, University of Otago, Christchurch
| | - Margreet C M Vissers
- Department of Pathology and Biomedical Science, University of Otago, Christchurch
| |
Collapse
|
35
|
Stiehl T. Using mathematical models to improve risk-scoring in acute myeloid leukemia. Chaos 2020; 30:123150. [PMID: 33380018 DOI: 10.1063/5.0023830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Acute myeloid leukemia (AML) is an aggressive cancer of the blood forming (hematopoietic) system. Due to the high patient variability of disease dynamics, risk-scoring is an important part of its clinical management. AML is characterized by impaired blood cell formation and the accumulation of so-called leukemic blasts in the bone marrow of patients. Recently, it has been proposed to use counts of blood-producing (hematopoietic) stem cells (HSCs) as a biomarker for patient prognosis. In this work, we use a non-linear mathematical model to provide mechanistic evidence for the suitability of HSC counts as a prognostic marker. Using model analysis and computer simulations, we compare different risk-scores involving HSC quantification. We propose and validate a simple approach to improve risk prediction based on HSC and blast counts measured at the time of diagnosis.
Collapse
Affiliation(s)
- Thomas Stiehl
- Institute of Applied Mathematics, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| |
Collapse
|
36
|
Flach J, Shumilov E, Porret N, Shakhanova I, Legros M, Kronig MN, Joncourt R, Bacher U, Pabst T. Experiences with Next-Generation Sequencing in Relapsed Acute Myeloid Leukemia: A Patient Case Series. Mediterr J Hematol Infect Dis 2020; 12:e2020068. [PMID: 32952979 DOI: 10.4084/MJHID.2020.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 08/16/2020] [Indexed: 12/04/2022] Open
|
37
|
Ishida H, Iguchi A, Aoe M, Nishiuchi R, Matsubara T, Keino D, Sanada M, Shimada A. Panel-based next-generation sequencing facilitates the characterization of childhood acute myeloid leukemia in clinical settings. Biomed Rep 2020; 13:46. [PMID: 32934818 PMCID: PMC7469563 DOI: 10.3892/br.2020.1353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 07/10/2020] [Indexed: 12/20/2022] Open
Abstract
Acute myeloid leukemia (AML) accounts for ~20% of pediatric leukemia cases. The prognosis of pediatric AML has been improved in recent decades, but it trails that of most other types of pediatric cancer, with mortality rates of 30-40%. Consequently, newer more targeted drugs are required for incorporation into treatment plans. These newer drugs selectively target AML cells with specific gene alterations. However, there are significant differences in genetic alterations between adult and pediatric patients with AML. In the present study, inexpensive and rapid next-generation sequencing (NGS) of >150 cancer-related genes was performed for matched diagnostic, remission and relapse (if any) samples from 27 pediatric patients with AML. In this analysis, seven genes were recurrently mutated. KRAS was mutated in seven patients, NRAS was mutated in three patients, and KIT, GATA1, WT1, PTPN11, JAK3 and FLT3 were each mutated in two patients. Among patients with relapsed AML, six harbored KRAS mutations at diagnosis; however, four of these patients lost these mutations at relapse. Additionally, two genetic alterations (FLT3-ITD and TP53 alterations) were detected among patients who eventually relapsed, and these mutations are reported to be adverse prognostic factors for adult patients with AML. This panel-based, targeted sequencing approach may be useful in determining the genetic background of pediatric AML and improving the prediction of treatment response and detection of potentially targetable gene alterations. RAS pathway mutations were highly unstable at relapse; therefore, these mutations should be chosen as a target with caution. Incorporating this panel-based NGS approach into the clinical setting may allow for a patient-oriented strategy of precision treatment for childhood AML.
Collapse
Affiliation(s)
- Hisashi Ishida
- Department of Pediatrics/Pediatric Hematology and Oncology, Okayama University Hospital, Okayama 700-8558, Japan
| | - Akihiro Iguchi
- Department of Pediatrics, Hokkaido University Hospital, Sapporo, Hokkaido 060-8648, Japan
| | - Michinori Aoe
- Division of Medical Support, Okayama University Hospital, Okayama 700-8558, Japan
| | - Ritsuo Nishiuchi
- Department of Pediatrics, Kochi Health Sciences Center, Kochi 781-8555, Japan
| | - Takehiro Matsubara
- Division of Biobank, Center for Comprehensive Genomic Medicine, Okayama University Hospital, Okayama 700-8558, Japan
| | - Dai Keino
- Department of Pediatrics, St. Marianna University School of Medicine Hospital, Kawasaki, Kanagawa 216-8511, Japan
| | - Masashi Sanada
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Akira Shimada
- Department of Pediatrics/Pediatric Hematology and Oncology, Okayama University Hospital, Okayama 700-8558, Japan
| |
Collapse
|
38
|
Yuasa M, Yamamoto H, Mitsuki T, Kageyama K, Kaji D, Taya Y, Nishida A, Ishiwata K, Takagi S, Yamamoto G, Asano-Mori Y, Wake A, Koike Y, Makino S, Uchida N, Taniguchi S. Prognostic Impact of Cytogenetic Evolution on the Outcome of Allogeneic Stem Cell Transplantation in Patients with Acute Myeloid Leukemia in Nonremission: A Single-Institute Analysis of 212 Recipients. Biol Blood Marrow Transplant 2020; 26:2262-2270. [PMID: 32871257 DOI: 10.1016/j.bbmt.2020.08.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 08/16/2020] [Accepted: 08/22/2020] [Indexed: 12/16/2022]
Abstract
Recent progress in genetic analysis technology has helped researchers understand the pathogenesis of acute myeloid leukemia (AML). Considering this progress, AML karyotype is still one of the most significant prognostic factors that provides risk-adapted treatment approaches. Karyotype changes during treatment have been observed at times, but their prognostic impact is sparse, especially on allogeneic stem cell transplantation (allo-SCT). Here, we retrospectively investigated the effect of chromosomal changes between diagnosis and pretransplantation on the prognosis of allo-SCT by analyzing the outcomes of 212 consecutive patients who underwent allo-SCT for the first time at Toranomon Hospital, Tokyo, Japan, between 2008 and 2018. Cytogenetic abnormalities at diagnosis and pretransplantation were categorized based on the 2017 European Leukemia Net risk stratification. Genetic abnormalities such as FLT3-ITD and NPM1 were not considered in this study due to lack of genetic information in most patients. We defined cytogenetic evolution as chromosomal changes classified from lower category to higher category. Seventeen patients (8%) had cytogenetic evolution between diagnosis and pretransplantation, and they showed a significantly worse relapse rate than those who were categorized in the intermediate group based on the karyotype at diagnosis (3-year confidence interval [CI] of relapse, 57.4% versus 24.9%; P < .01). In multivariate analysis, cytogenetic evolution before allo-SCT had a significant impact on the CI of relapse (hazard ratio [HR], 3.89; CI, 1.75 to 8.67; P < .01), as well as the high score of the hematopoietic cell transplantation-specific comorbidity index (HR, 0.54; CI, 0.31 to 0.94; P = .03), but had no significant impact on overall survival or nonrelapse mortality. These results indicate that cytogenetic evolution has a significant impact after allo-SCT and should be considered during AML treatment.
Collapse
Affiliation(s)
| | | | - Takashi Mitsuki
- Department of Hematology, Toranomon Hospital Kajigaya, Kanagawa, Japan
| | - Kosei Kageyama
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
| | - Daisuke Kaji
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
| | - Yuki Taya
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
| | - Aya Nishida
- Department of Hematology, Toranomon Hospital Kajigaya, Kanagawa, Japan
| | - Kazuya Ishiwata
- Department of Hematology, Toranomon Hospital Kajigaya, Kanagawa, Japan
| | | | - Go Yamamoto
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
| | | | - Atsushi Wake
- Department of Hematology, Toranomon Hospital Kajigaya, Kanagawa, Japan
| | - Yukako Koike
- Department of Clinical Laboratory, Toranomon Hospital, Tokyo, Japan
| | - Shigeyoshi Makino
- Department of Transfusion Medicine, Toranomon Hospital, Tokyo, Japan
| | - Naoyuki Uchida
- Department of Hematology, Toranomon Hospital, Tokyo, Japan.
| | - Shuichi Taniguchi
- Department of Hematology, Toranomon Hospital, Tokyo, Japan; Okinaka Memorial Institute for Medical Research, Tokyo, Japan
| |
Collapse
|
39
|
Stiehl T, Wang W, Lutz C, Marciniak-Czochra A. Mathematical Modeling Provides Evidence for Niche Competition in Human AML and Serves as a Tool to Improve Risk Stratification. Cancer Res 2020; 80:3983-3992. [PMID: 32651258 DOI: 10.1158/0008-5472.can-20-0283] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/10/2020] [Accepted: 07/07/2020] [Indexed: 11/16/2022]
Abstract
Acute myeloid leukemia (AML) is a stem cell-driven malignant disease. There is evidence that leukemic stem cells (LSC) interact with stem cell niches and outcompete hematopoietic stem cells (HSC). The impact of this interaction on the clinical course of the disease remains poorly understood. We developed and validated a mathematical model of stem cell competition in the human HSC niche. Model simulations predicted how processes in the stem cell niche affect the speed of disease progression. Combining the mathematical model with data of individual patients, we quantified the selective pressure LSCs exert on HSCs and demonstrated the model's prognostic significance. A novel model-based risk-stratification approach allowed extraction of prognostic information from counts of healthy and malignant cells at the time of diagnosis. This model's feasibility was demonstrable based on a cohort of patients with ALDH-rare AML and shows that the model-based risk stratification is an independent predictor of disease-free and overall survival. This proof-of-concept study shows how model-based interpretation of patient data can improve prognostic scoring and contribute to personalized medicine. SIGNIFICANCE: Combining a novel mathematical model of the human hematopoietic stem cell niche with individual patient data enables quantification of properties of leukemic stem cells and improves risk stratification in acute myeloid leukemia.
Collapse
Affiliation(s)
- Thomas Stiehl
- Institute of Applied Mathematics and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.
| | - Wenwen Wang
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Christoph Lutz
- Department of Medicine V, Heidelberg University, Heidelberg, Germany
| | - Anna Marciniak-Czochra
- Institute of Applied Mathematics, Interdisciplinary Center for Scientific Computing (IWR) and Bioquant Center, Heidelberg University, Heidelberg, Germany
| |
Collapse
|
40
|
Wang X, Feng Y, Zhang P, Chen H, Bai J, Wang F, He A. miR-582-5p serves as an antioncogenic biomarker in intermediate risk AML with normal cytogenetics and could inhibit proliferation and induce apoptosis of leukemia cells. Cell Biol Int 2020; 44:2021-2030. [PMID: 32543749 DOI: 10.1002/cbin.11408] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 06/05/2020] [Accepted: 06/13/2020] [Indexed: 12/21/2022]
Abstract
Numerous studies confirmed that aberrant microRNA (miRNA) expression contributes to cancer development and progression. We carried out this study to explore the expression profile of miRNAs in intermediate risk acute myeloid leukemia (AML) and locate certain miRNAs as biomarkers. We profiled differentially expressed miRNAs by performing miRNA sequencing analysis in the patients' samples. Bioinformatic analysis showed the most significantly expressed genes mostly involved in cellular component organization, cell differentiation, and cell development. Reverse-transcription polymerase chain reaction validated the expression of miR-582-5p in different groups of AML samples. It was confirmed that miR-582-5p was downregulated in newly diagnosed AML and relapse/refractory AML compared with CR AML or controls. Among intermediate risk AML patients with normal cytogenetics, a lower level of miR-582-5p is correlated with an unfavorable outcome, and a shorter overall survival. Gain- and loss-of-function experiments revealed that miR-582-5p could inhibit proliferation, suppress migration, and invasion ability and induce apoptosis of leukemia cells. Furthermore, overexpression of miR-582-5p can increase sensitivity of cells to Ara-C. In conclusion, miR-582-5p can serve as an antioncogenic biomarker in intermediate risk AML with normal cytogenetics for risk classification and outcome prediction. These results showed a novel role for miR-582-5p in predicting the prognosis and promoting the tumor growth of AML.
Collapse
Affiliation(s)
- Xiaman Wang
- Department of Hematology, Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yuandong Feng
- Department of Hematology, Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Peihua Zhang
- Department of Hematology, Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hongli Chen
- Department of Hematology, Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ju Bai
- Department of Hematology, Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Fangxia Wang
- Department of Hematology, Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Aili He
- Department of Hematology, Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Hematology Department, National-Local Joint Engineering Research Center of Biodiagnostics and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
41
|
Cerrano M, Duchmann M, Kim R, Vasseur L, Hirsch P, Thomas X, Quentin S, Pasanisi J, Passet M, Rabian F, Rahmé R, Lengliné E, Raffoux E, Dhédin N, Sébert M, Maarek O, Raimbault A, Celli-Lebras K, Adès L, Fenaux P, Boissel N, Delhommeau F, Soulier J, Dombret H, Clappier E, Sujobert P, Itzykson R. Clonal dominance is an adverse prognostic factor in acute myeloid leukemia treated with intensive chemotherapy. Leukemia 2021; 35:712-23. [PMID: 32581253 DOI: 10.1038/s41375-020-0932-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023]
Abstract
Intra-tumor heterogeneity portends poor outcome in many cancers. In AML, a higher number of drivers worsens prognosis. The Shannon Index is a robust metric of clonal heterogeneity that accounts for the number of clones, but also their relative abundance. We show that a Shannon Index can be estimated from bulk sequencing, which is correlated (ρ = 0.76) with clonal diversity from single-colony genotyping. In a discovery cohort of 292 patients with sequencing of 43 genes, a higher number of drivers (HR = 1.18, P = 0.028) and a lower Shannon Index (HR = 0.68, P = 0.048), the latter reflecting clonal dominance, are independently associated with worse OS independently of European LeukemiaNet 2017 risk. These findings are validated in an independent cohort of 1184 patients with 111-gene sequencing (number of drivers HR = 1.16, P = 1 × 10-5, Shannon Index HR = 0.81, P = 0.007). By re-interrogating paired diagnosis/relapse exomes from 50 cytogenetically normal AMLs, we find clonal dominance at diagnosis to be correlated with the gain of a significantly higher number of mutations at relapse (P = 6 × 10-6), hence with clonal sweeping. Our results suggest that clonal dominance at diagnosis is associated with the presence of a leukemic phenotype allowing rapid expansion of new clones and driving relapse after chemotherapy.
Collapse
|
42
|
Rengifo LY, Michaux L, Maertens J, Tousseyn T, Lenaerts L, Vermeesch JR, Vandenberghe P, Dewaele B. Noninvasive prenatal testing detected acute myeloid leukemia in paucisymptomatic pregnant patient. Clin Case Rep 2020; 8:1924-1927. [PMID: 33088520 PMCID: PMC7562837 DOI: 10.1002/ccr3.3027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/18/2020] [Accepted: 05/23/2020] [Indexed: 12/03/2022] Open
Abstract
To the authors' best knowledge, this is the first report of acute myeloid leukemia (AML) detected by noninvasive prenatal testing. This was an aggressive case that otherwise would have been difficult to characterize due to disadvantages of "gold‐standard" techniques.
Collapse
Affiliation(s)
| | - Lucienne Michaux
- Center for Human Genetics University Hospitals Leuven Leuven Belgium
| | - Johan Maertens
- Department of Microbiology and Immunology KU Leuven Leuven Belgium.,Department of Hematology University Hospitals Leuven Leuven Belgium
| | - Thomas Tousseyn
- Department of Pathology University Hospitals Leuven Leuven Belgium
| | | | | | - Peter Vandenberghe
- Center for Human Genetics University Hospitals Leuven Leuven Belgium.,Department of Hematology University Hospitals Leuven Leuven Belgium
| | - Barbara Dewaele
- Center for Human Genetics University Hospitals Leuven Leuven Belgium
| |
Collapse
|
43
|
Flach J, Shumilov E, Wiedemann G, Porret N, Shakhanova I, Bürki S, Legros M, Joncourt R, Pabst T, Bacher U. Clinical potential of introducing next-generation sequencing in patients at relapse of acute myeloid leukemia. Hematol Oncol 2020; 38:425-431. [PMID: 32306411 DOI: 10.1002/hon.2739] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/02/2020] [Accepted: 04/14/2020] [Indexed: 12/19/2022]
Abstract
Relapse of acute myeloid leukemia (AML) remains a major determinant of outcome. A number of molecularly directed treatment options have recently emerged making comprehensive diagnostics an important pillar of clinical decision making at relapse. Acknowledging the high degree of individual genetic variability at AML relapse, next-generation sequencing (NGS) has opened the opportunity for assessing the unique clonal hierarchy of individual AML patients. Knowledge on the genetic makeup of AML is reflected in patient customized treatment strategies thereby providing improved outcomes. For example, the emergence of druggable mutations at relapse enable the use of novel targeted therapies, including FLT3 inhibitors or the recently approved IDH1/2 inhibitors ivosidenib and enasidenib, respectively. Consequently, some patients may undergo novel bridging approaches for reinduction before allogeneic stem cell transplantation, or the identification of an adverse prognostic marker may initiate early donor search. In this review, we summarize the current knowledge of NGS in identifying clonal stability, clonal evolution, and clonal devolution in the context of AML relapse. In light of recent improvements in AML treatment options, NGS-based molecular diagnostics emerges as the basis for molecularly directed treatment decisions in patients at relapse.
Collapse
Affiliation(s)
- Johanna Flach
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Mannheim, Germany
| | - Evgenii Shumilov
- Department of Hematology and Medical Oncology, University Medicine Göttingen (UMG), Göttingen, Germany
| | - Gertrud Wiedemann
- University Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, Bern, Switzerland.,Center of Laboratory Medicine (ZLM)/University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Naomi Porret
- University Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, Bern, Switzerland.,Center of Laboratory Medicine (ZLM)/University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Inna Shakhanova
- Department of Nephrology and Rheumatology, University Medicine Göttingen (UMG), Göttingen, Germany
| | - Susanne Bürki
- Department of Medical Oncology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Myriam Legros
- Center of Laboratory Medicine (ZLM)/University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Raphael Joncourt
- University Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, Bern, Switzerland.,Center of Laboratory Medicine (ZLM)/University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Thomas Pabst
- Department of Medical Oncology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Ulrike Bacher
- University Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, Bern, Switzerland.,Center of Laboratory Medicine (ZLM)/University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| |
Collapse
|
44
|
Aasebø E, Berven FS, Bartaula-Brevik S, Stokowy T, Hovland R, Vaudel M, Døskeland SO, McCormack E, Batth TS, Olsen JV, Bruserud Ø, Selheim F, Hernandez-Valladares M. Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia. Cancers (Basel) 2020; 12:cancers12030709. [PMID: 32192169 PMCID: PMC7140113 DOI: 10.3390/cancers12030709] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/05/2020] [Accepted: 03/13/2020] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is a hematological cancer that mainly affects the elderly. Although complete remission (CR) is achieved for the majority of the patients after induction and consolidation therapies, nearly two-thirds relapse within a short interval. Understanding biological factors that determine relapse has become of major clinical interest in AML. We utilized liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify the protein changes and protein phosphorylation events associated with AML relapse in primary cells from 41 AML patients at time of diagnosis. Patients were defined as relapse-free if they had not relapsed within a five-year clinical follow-up after AML diagnosis. Relapse was associated with increased expression of RNA processing proteins and decreased expression of V-ATPase proteins. We also observed an increase in phosphorylation events catalyzed by cyclin-dependent kinases (CDKs) and casein kinase 2 (CSK2). The biological relevance of the proteome findings was supported by cell proliferation assays using inhibitors of V-ATPase (bafilomycin), CSK2 (CX-4945), CDK4/6 (abemaciclib) and CDK2/7/9 (SNS-032). While bafilomycin preferentially inhibited the cells from relapse patients, the kinase inhibitors were less efficient in these cells. This suggests that therapy against the upregulated kinases could also target the factors inducing their upregulation rather than their activity. This study, therefore, presents markers that could help predict AML relapse and direct therapeutic strategies.
Collapse
Affiliation(s)
- Elise Aasebø
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
| | - Frode S. Berven
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Sushma Bartaula-Brevik
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- Department for Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway;
| | - Randi Hovland
- Department for Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway;
- Department of Biological Sciences, University of Bergen, 5006 Bergen, Norway
| | - Marc Vaudel
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | | | - Emmet McCormack
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway;
| | - Tanveer S. Batth
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; (T.S.B.); (J.V.O.)
| | - Jesper V. Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; (T.S.B.); (J.V.O.)
| | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | - Frode Selheim
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Maria Hernandez-Valladares
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- Correspondence: ; Tel.: +47-5558-6368
| |
Collapse
|
45
|
Sandén C, Lilljebjörn H, Orsmark Pietras C, Henningsson R, Saba KH, Landberg N, Thorsson H, von Palffy S, Peña-Martinez P, Högberg C, Rissler M, Gisselsson D, Lazarevic V, Juliusson G, Ågerstam H, Fioretos T. Clonal competition within complex evolutionary hierarchies shapes AML over time. Nat Commun 2020; 11:579. [PMID: 32024830 DOI: 10.1038/s41467-019-14106-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022] Open
Abstract
Clonal heterogeneity and evolution has major implications for disease progression and relapse in acute myeloid leukemia (AML). To model clonal dynamics in vivo, we serially transplanted 23 AML cases to immunodeficient mice and followed clonal composition for up to 15 months by whole-exome sequencing of 84 xenografts across two generations. We demonstrate vast changes in clonality that both progress and reverse over time, and define five patterns of clonal dynamics: Monoclonal, Stable, Loss, Expansion and Burst. We also show that subclonal expansion in vivo correlates with a more adverse prognosis. Furthermore, clonal expansion enabled detection of very rare clones with AML driver mutations that were undetectable by sequencing at diagnosis, demonstrating that the vast majority of AML cases harbor multiple clones already at diagnosis. Finally, the rise and fall of related clones enabled deconstruction of the complex evolutionary hierarchies of the clones that compete to shape AML over time. Clonal evolution and heterogeneity has strong implications for treatment response in acute myeloid leukemia. Here, the authors use patient derived in vivo modelling to highlight the complex clonal and evolutionary dynamics underpinning acute myeloid leukemia progression.
Collapse
|
46
|
Vosberg S, Greif PA. Clonal evolution of acute myeloid leukemia from diagnosis to relapse. Genes Chromosomes Cancer 2019; 58:839-849. [PMID: 31478278 PMCID: PMC6852285 DOI: 10.1002/gcc.22806] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 12/13/2022] Open
Abstract
Based on the individual genetic profile, acute myeloid leukemia (AML) patients are classified into clinically meaningful molecular subtypes. However, the mutational profile within these groups is highly heterogeneous and multiple AML subclones may exist in a single patient in parallel. Distinct alterations of single cells may be key factors in providing the fitness to survive in this highly competitive environment. Although the majority of AML patients initially respond to induction chemotherapy and achieve a complete remission, most patients will eventually relapse. These points toward an evolutionary process transforming treatment-sensitive cells into treatment-resistant cells. As described by Charles Darwin, evolution by natural selection is the selection of individuals that are optimally adapted to their environment, based on the random acquisition of heritable changes. By changing their mutational profile, AML cell populations are able to adapt to the new environment defined by chemotherapy treatment, ultimately leading to cell survival and regrowth. In this review, we will summarize the current knowledge about clonal evolution in AML, describe different models of clonal evolution, and provide the methodological background that allows the detection of clonal evolution in individual AML patients. During the last years, numerous studies have focused on delineating the molecular patterns that are associated with AML relapse, each focusing on a particular genetic subgroup of AML. Finally, we will review the results of these studies in the light of Darwinian evolution and discuss open questions regarding the molecular background of relapse development.
Collapse
Affiliation(s)
- Sebastian Vosberg
- Department of Medicine IIIUniversity Hospital, LMU MunichMunichGermany
- Experimental Leukemia and Lymphoma Research (ELLF)University Hospital, LMU MunichMunichGermany
- German Cancer Consortium (DKTK)HeidelbergGermany
- German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Philipp A. Greif
- Department of Medicine IIIUniversity Hospital, LMU MunichMunichGermany
- Experimental Leukemia and Lymphoma Research (ELLF)University Hospital, LMU MunichMunichGermany
- German Cancer Consortium (DKTK)HeidelbergGermany
- German Cancer Research Center (DKFZ)HeidelbergGermany
| |
Collapse
|
47
|
Rechkoblit O, Johnson RE, Buku A, Prakash L, Prakash S, Aggarwal AK. Structural insights into mutagenicity of anticancer nucleoside analog cytarabine during replication by DNA polymerase η. Sci Rep 2019; 9:16400. [PMID: 31704958 DOI: 10.1038/s41598-019-52703-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/22/2019] [Indexed: 01/08/2023] Open
Abstract
Cytarabine (AraC) is the mainstay chemotherapy for acute myeloid leukemia (AML). Whereas initial treatment with AraC is usually successful, most AML patients tend to relapse, and AraC treatment-induced mutagenesis may contribute to the development of chemo-resistant leukemic clones. We show here that whereas the high-fidelity replicative polymerase Polδ is blocked in the replication of AraC, the lower-fidelity translesion DNA synthesis (TLS) polymerase Polη is proficient, inserting both correct and incorrect nucleotides opposite a template AraC base. Furthermore, we present high-resolution crystal structures of human Polη with a template AraC residue positioned opposite correct (G) and incorrect (A) incoming deoxynucleotides. We show that Polη can accommodate local perturbation caused by the AraC via specific hydrogen bonding and maintain a reaction-ready active site alignment for insertion of both correct and incorrect incoming nucleotides. Taken together, the structures provide a novel basis for the ability of Polη to promote AraC induced mutagenesis in relapsed AML patients.
Collapse
|
48
|
Yoon JH, Roy Choudhury J, Prakash L, Prakash S. Translesion synthesis DNA polymerases η, ι, and ν promote mutagenic replication through the anticancer nucleoside cytarabine. J Biol Chem 2019; 294:19048-19054. [PMID: 31685662 DOI: 10.1074/jbc.ra119.011381] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/30/2019] [Indexed: 11/06/2022] Open
Abstract
Cytarabine (AraC) is the mainstay for the treatment of acute myeloid leukemia. Although complete remission is observed in a large proportion of patients, relapse occurs in almost all the cases. The chemotherapeutic action of AraC derives from its ability to inhibit DNA synthesis by the replicative polymerases (Pols); the replicative Pols can insert AraCTP at the 3' terminus of the nascent DNA strand, but they are blocked at extending synthesis from AraC. By extending synthesis from the 3'-terminal AraC and by replicating through AraC that becomes incorporated into DNA, translesion synthesis (TLS) DNA Pols could reduce the effectiveness of AraC in chemotherapy. Here we identify the TLS Pols required for replicating through the AraC templating residue and determine their error-proneness. We provide evidence that TLS makes a consequential contribution to the replication of AraC-damaged DNA; that TLS through AraC is conducted by three different pathways dependent upon Polη, Polι, and Polν, respectively; and that TLS by all these Pols incurs considerable mutagenesis. The prominent role of TLS in promoting proficient and mutagenic replication through AraC suggests that TLS inhibition in acute myeloid leukemia patients would increase the effectiveness of AraC chemotherapy; and by reducing mutation formation, TLS inhibition may dampen the emergence of drug-resistant tumors and thereby the high incidence of relapse in AraC-treated patients.
Collapse
Affiliation(s)
- Jung-Hoon Yoon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555
| | - Jayati Roy Choudhury
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555
| | - Louise Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555
| | - Satya Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555
| |
Collapse
|
49
|
Montesinos P, Bergua J, Infante J, Esteve J, Guimaraes JE, Sierra J, Sanz MÁ. Update on management and progress of novel therapeutics for R/R AML: an Iberian expert panel consensus. Ann Hematol 2019; 98:2467-2483. [PMID: 31667544 DOI: 10.1007/s00277-019-03820-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 10/08/2019] [Indexed: 12/19/2022]
Abstract
A significant proportion of adult patients with acute myeloid leukemia (AML) fail to achieve complete remission or will relapse later on after achieving it. Prognosis for relapsed or refractory (R/R) AML patients remains discouraging, with the main curative option still relying on hematopoietic stem cell transplant (HSCT) for those who are eligible. Beyond morphological bone marrow and peripheral blood assessment, evaluation of patient performance status and comorbidities, as well as genetic/molecular characterization, is crucial to make an accurate diagnosis and prognosis, which will be useful to select the most appropriate treatment. Emerging strategies are mainly focusing on the development of immune- and molecular-based approaches. Novel targeted therapies are generally well tolerated, potentially allowing them to be administered alone or in combination with classical chemotherapy agents. Enrolment in clinical trials should be considered first option for R/R AML patients, either as a bridge to HSCT or to benefit from novel therapies that eventually may prolong survival and improve quality of life. An Iberian expert panel has reviewed the recent advances in the management of R/R AML with the aim to develop updated evidence and expert opinion-based recommendations.
Collapse
Affiliation(s)
- Pau Montesinos
- Hematology Department, Hospital Universitari I Politècnic La Fe, Av. Fernando Abril Martorell, 106, 46026, Valencia, Spain. .,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain.
| | - Juan Bergua
- Division of Hematology/Oncology, Hospital San Pedro Alcántara, Cáceres, Spain
| | - Joana Infante
- Serviço de Hematologia e Transplantação de Medula Óssea, Hospital de Santa Maria, Centro Hospitalar de Lisboa Norte, Lisbon, Portugal
| | - Jordi Esteve
- Department of Hematology, IDIBAPS, Hospital Clinic, Barcelona, Spain
| | - José Eduardo Guimaraes
- Serviço de Hematologia Clínica, Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Jordi Sierra
- Hematology Department, Hospital de la Santa Creu i Sant Pau, IIB Sant Pau and Jose Carreras Leukemia Research Institutes, Autonomous University of Barcelona, Barcelona, Spain
| | - Miguel Ángel Sanz
- Hematology Department, Hospital Universitari I Politècnic La Fe, Av. Fernando Abril Martorell, 106, 46026, Valencia, Spain
| |
Collapse
|
50
|
Olarte I, García A, Ramos C, Arratia B, Centeno F, Paredes J, Rozen E, Kassack J, Collazo J, Martínez A. Detection Of Mutations In The Isocitrate Dehydrogenase Genes (IDH1/IDH2) Using castPCR TM In Patients With AML And Their Clinical Impact In Mexico City. Onco Targets Ther 2019; 12:8023-8031. [PMID: 31632056 PMCID: PMC6781602 DOI: 10.2147/ott.s219703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/01/2019] [Indexed: 12/15/2022] Open
Abstract
Objective Approximately 40–50% of patients with acute myeloid leukaemia (AML) have been reported to present with a normal karyotype and a variable disease-free period, most likely due to the molecular heterogeneity presented by these patients. A variety of mutations have been identified at the molecular level, such as those in the IDH1/2 gene, which causes a gain of function of the isocitrate dehydrogenase enzyme, generating high levels of the (R)-2-hydroxyglutarate oncometabolite, which competitively inhibits dioxygenase enzymes. Therefore, the objective of this study was to evaluate the incidence of IDH1/2 gene mutations in AML patients and their impact on survival. Materials and methods A total of 101 patients with a diagnosis of AML were included; mononuclear cells were obtained for DNA extraction and purification. Mutations were detected using TaqMan™ competitive allele-specific probes (castPCR™). Overall survival curves were plotted using IBM SPSS Statistics 23 software. Results The frequency of IDH gene mutations was 19.8%. For the IDH1 gene, 13.8% of the mutations identified included R132H, V178I, G105G and R132C. The frequency of mutations of the IDH2 gene was 5.9%; the variants included R172K and R140Q. The mean survival time in patients without IDH1 gene mutations was 173.15 days (120.20–226.10), while the mean survival time for patients with mutations was 54.95 days (9.7–100.18), p = 0.001. Conclusion The frequency of IDH1 and IDH2 gene mutations in the sample was similar to that reported in other studies. The analysis of these mutations in AML patients is of great importance as a prognostic factor due to their impact on survival and their use as potential therapeutic targets or as targets of inhibitors of IDH1(Ivosidenib, Tibsovo) and IDH2 (Enasidenib, Idhifa).
Collapse
Affiliation(s)
- Irma Olarte
- Department of Molecular Biology, Hematology Service, Hospital General de México, "Dr. Eduardo Liceaga", Mexico City, Mexico
| | - Anel García
- Department of Molecular Biology, Hematology Service, Hospital General de México, "Dr. Eduardo Liceaga", Mexico City, Mexico
| | - Christian Ramos
- Department of Medical Hematology, Hospital General de México, "Dr. Eduardo Liceaga", Mexico City, Mexico
| | - Brenda Arratia
- Department of Molecular Biology, Hematology Service, Hospital General de México, "Dr. Eduardo Liceaga", Mexico City, Mexico
| | - Federico Centeno
- Department Immunogenomics and Metabolic Disease, Instituto Nacional de Medicina Genómic, SS, Mexico City, Mexico
| | - Johanna Paredes
- Department of Molecular Biology, Hematology Service, Hospital General de México, "Dr. Eduardo Liceaga", Mexico City, Mexico
| | - Etta Rozen
- Department of Medical Hematology, Hospital General de México, "Dr. Eduardo Liceaga", Mexico City, Mexico
| | - Juan Kassack
- Department of Medical Hematology, Hospital General de México, "Dr. Eduardo Liceaga", Mexico City, Mexico
| | - Juan Collazo
- Department of Medical Hematology, Hospital General de México, "Dr. Eduardo Liceaga", Mexico City, Mexico
| | - Adolfo Martínez
- Department of Molecular Biology, Hematology Service, Hospital General de México, "Dr. Eduardo Liceaga", Mexico City, Mexico
| |
Collapse
|