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Ma J, Zhao H, Ge F. Application of m6A regulators to predict transformation from myelodysplastic syndrome to acute myeloid leukemia via machine learning. Medicine (Baltimore) 2024; 103:e38897. [PMID: 38996166 PMCID: PMC11245222 DOI: 10.1097/md.0000000000038897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/14/2024] Open
Abstract
Myelodysplastic syndrome (MDS) frequently transforms into acute myeloid leukemia (AML). Predicting the risk of its transformation will help to make the treatment plan. Levels of expression of N6-methyladenosine (m6A) regulators is difference in patients with AML, MDS, and MDS transformed into AML. Seven machine learning algorithms were established based on all of 26 m6A or main differentially expressed m6A regulator genes, and attempted to establish a risk assessment method to distinguish AML from MDS and predict the transformation of MDS into AML. In collective of m6A regulators sets, support vector machine (SVM) and neural network (NNK) model best distinguished AML or MDS from control, with area under the ROC curve (AUROC) 0.966 and 0.785 respectively. The SVM model best distinguished MDS from AML, with AUROC 0.943, sensitivity 0.862, specificity 0.864, and accuracy 0.864. In differentially expressed gene sets, SVM and logistic regression (LR) model best distinguished AML or MDS from control, with AUROC 0.945 and 0.801 respectively. The random forest (RF) model best distinguished between MDS and AML, with AUROC 0.928, sensitivity 0.725, specificity 0.898, and accuracy 0.818. For predictive capacity of MDS transformed into AML, SVM model showed the best predicted in collective m6A regulators sets, with AUROC 0.781 and accuracy 0.740. The LR model showed the best predicted in differential expression m6A regulators sets, with AUROC 0.820 and accuracy 0.760. All results suggested that machine learning model established by m6A regulators can be used to distinguished AML or MDS from control, distinguished AML from MDS and predicted the transformation of MDS into AML.
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Affiliation(s)
- Jichun Ma
- Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | | | - Fang Ge
- Yantai Harbour Hospital, Yantai, Shandong, China
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2
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Zhao Y, Chaw JK, Liu L, Chaw SH, Ang MC, Ting TT. Systematic literature review on reinforcement learning in non-communicable disease interventions. Artif Intell Med 2024; 154:102901. [PMID: 38838400 DOI: 10.1016/j.artmed.2024.102901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 02/21/2024] [Accepted: 06/02/2024] [Indexed: 06/07/2024]
Abstract
There is evidence that reducing modifiable risk factors and strengthening medical and health interventions can reduce early mortality and economic losses from non-communicable diseases (NCDs). Machine learning (ML) algorithms have been successfully applied to preventing and controlling NCDs. Reinforcement learning (RL) is the most promising of these approaches because of its ability to dynamically adapt interventions to NCD disease progression and its commitment to achieving long-term intervention goals. This paper reviews the preferred algorithms, data sources, design details, and obstacles to clinical application in existing studies to facilitate the early application of RL algorithms in clinical practice research for NCD interventions. We screened 40 relevant papers for quantitative and qualitative analysis using the PRISMA review flow diagram. The results show that researchers tend to use Deep Q-Network (DQN) and Actor-Critic as well as their improved or hybrid algorithms to train and validate RL models on retrospective datasets. Often, the patient's physical condition is the main defining parameter of the state space, while interventions are the main defining parameter of the action space. Mostly, changes in the patient's physical condition are used as a basis for immediate rewards to the agent. Various attempts have been made to address the challenges to clinical application, and several approaches have been proposed from existing research. However, as there is currently no universally accepted solution, the use of RL algorithms in clinical practice for NCD interventions necessitates more comprehensive responses to the issues addressed in this paper, which are safety, interpretability, training efficiency, and the technical aspect of exploitation and exploration in RL algorithms.
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Affiliation(s)
- Yanfeng Zhao
- Institute of Visual Informatics, National University of Malaysia, Bangi, Selangor, Malaysia
| | - Jun Kit Chaw
- Institute of Visual Informatics, National University of Malaysia, Bangi, Selangor, Malaysia.
| | - Lin Liu
- Henan Vocational University of Science and Technology, Zhoukou, Henan, China
| | - Sook Hui Chaw
- Department of Anaesthesiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Mei Choo Ang
- Institute of Visual Informatics, National University of Malaysia, Bangi, Selangor, Malaysia
| | - Tin Tin Ting
- Faculty of Data Science and Information Technology, INTI International University, Nilai, Negeri Sembilan, Malaysia
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3
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Travaglini S, Marinoni M, Visconte V, Guarnera L. Therapy-Related Myeloid Neoplasm: Biology and Mechanistic Aspects of Malignant Progression. Biomedicines 2024; 12:1054. [PMID: 38791019 PMCID: PMC11118122 DOI: 10.3390/biomedicines12051054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Therapy-related myeloid neoplasms (t-MN) arise after a documented history of chemo/radiotherapy as treatment for an unrelated condition and account for 10-20% of myelodysplastic syndromes and acute myeloid leukemia. T-MN are characterized by a specific genetic signature, aggressive features and dismal prognosis. The nomenclature and the subsets of these conditions have changed frequently over time, and despite the fact that, in the last classification, they lost their autonomous entity status and became disease qualifiers, the recognition of this feature remains of major importance. Furthermore, in recent years, extensive studies focusing on clonal hematopoiesis and germline variants shed light on the mechanisms of positive pressure underpinning the rise of driver gene mutations in t-MN. In this manuscript, we aim to review the evolution of defining criteria and characteristics of t-MN from a clinical and biological perspective, the advances in mechanistic aspects of malignant progression and the challenges in prevention and management.
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Affiliation(s)
- Serena Travaglini
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Massimiliano Marinoni
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Valeria Visconte
- Department of Translational Hematology & Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Luca Guarnera
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
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4
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Sackstein P, Williams A, Zemel R, Marks JA, Renteria AS, Rivero G. Transplant Eligible and Ineligible Elderly Patients with AML-A Genomic Approach and Next Generation Questions. Biomedicines 2024; 12:975. [PMID: 38790937 PMCID: PMC11117792 DOI: 10.3390/biomedicines12050975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/26/2024] Open
Abstract
The management of elderly patients diagnosed with acute myelogenous leukemia (AML) is complicated by high relapse risk and comorbidities that often preclude access to allogeneic hematopoietic cellular transplantation (allo-HCT). In recent years, fast-paced FDA drug approval has reshaped the therapeutic landscape, with modest, albeit promising improvement in survival. Still, AML outcomes in elderly patients remain unacceptably unfavorable highlighting the need for better understanding of disease biology and tailored strategies. In this review, we discuss recent modifications suggested by European Leukemia Network 2022 (ELN-2022) risk stratification and review recent aging cell biology advances with the discussion of four AML cases. While an older age, >60 years, does not constitute an absolute contraindication for allo-HCT, the careful patient selection based on a detailed and multidisciplinary risk stratification cannot be overemphasized.
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Affiliation(s)
- Paul Sackstein
- Lombardi Cancer Institute, School of Medicine, Georgetown University, Washington, DC 20007, USA; (P.S.); (R.Z.); (J.A.M.)
| | - Alexis Williams
- Department of Medicine, New York University, New York, NY 10016, USA;
| | - Rachel Zemel
- Lombardi Cancer Institute, School of Medicine, Georgetown University, Washington, DC 20007, USA; (P.S.); (R.Z.); (J.A.M.)
| | - Jennifer A. Marks
- Lombardi Cancer Institute, School of Medicine, Georgetown University, Washington, DC 20007, USA; (P.S.); (R.Z.); (J.A.M.)
| | - Anne S. Renteria
- Lombardi Cancer Institute, School of Medicine, Georgetown University, Washington, DC 20007, USA; (P.S.); (R.Z.); (J.A.M.)
| | - Gustavo Rivero
- Lombardi Cancer Institute, School of Medicine, Georgetown University, Washington, DC 20007, USA; (P.S.); (R.Z.); (J.A.M.)
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Song GY, Kim HJ, Kim T, Ahn SY, Jung SH, Kim M, Yang DH, Lee JJ, Kim MY, Cheong JW, Jung CW, Jang JH, Kim HJ, Moon JH, Sohn SK, Won JH, Park SK, Kim SH, Choi CK, Kim HJ, Ahn JS, Kim DDH. Validation of the 2022 European LeukemiaNet risk stratification for acute myeloid leukemia. Sci Rep 2024; 14:8517. [PMID: 38609396 PMCID: PMC11014905 DOI: 10.1038/s41598-024-57295-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 03/16/2024] [Indexed: 04/14/2024] Open
Abstract
This study aimed to validate the 2022 European LeukemiaNet (ELN) risk stratification for acute myeloid leukemia (AML). A total of 624 newly diagnosed AML patients from 1998 to 2014 were included in the analysis. Genetic profiling was conducted using targeted deep sequencing of 45 genes based on recurrent driver mutations. In total, 134 (21.5%) patients had their risk classification reassessed according to the 2022 ELN risk stratification. Among those initially classified as having a favorable risk in 2017 (n = 218), 31 and 3 patients were reclassified as having intermediate risk or adverse risk, respectively. Among the three subgroups, the 2022 ELN favorable-risk group showed significantly longer survival outcomes than the other groups. Within the 2017 ELN intermediate-risk group (n = 298), 21 and 46 patients were reclassified as having favorable risk or adverse risk, respectively, and each group showed significant stratifications in survival outcomes. Some patients initially classified as having adverse risk in 2017 were reclassified into the intermediate-risk group (33 of 108 patients), but no prognostic improvements were observed in this group. A multivariable analysis identified the 2022 ELN risk stratification, age, and receiving allogeneic hematopoietic cell transplantation as significant prognostic factors for survival. The 2022 ELN risk stratification enables more precise decisions for proceeding with allogeneic hematopoietic cell transplantation for AML patients.
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Affiliation(s)
- Ga-Young Song
- Department of Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Gwangju, Jeollanam-Do, Republic of Korea
| | - Hyeon-Jong Kim
- Department of Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Gwangju, Jeollanam-Do, Republic of Korea
| | - TaeHyung Kim
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Seo-Yeon Ahn
- Department of Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Gwangju, Jeollanam-Do, Republic of Korea
| | - Sung-Hoon Jung
- Department of Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Gwangju, Jeollanam-Do, Republic of Korea
| | - Mihee Kim
- Department of Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Gwangju, Jeollanam-Do, Republic of Korea
| | - Deok-Hwan Yang
- Department of Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Gwangju, Jeollanam-Do, Republic of Korea
| | - Je-Jung Lee
- Department of Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Gwangju, Jeollanam-Do, Republic of Korea
| | - Mi Yeon Kim
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Gwangju, Jeollanam-Do, Republic of Korea
| | - June-Won Cheong
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Chul Won Jung
- Division of Hematology-Oncology, Samsung Medical Center, Seoul, South Korea
| | - Jun Ho Jang
- Division of Hematology-Oncology, Samsung Medical Center, Seoul, South Korea
| | - Hee- Je Kim
- Department of Hematology, The Catholic University of Korea, Seoul, South Korea
| | - Joon Ho Moon
- Department of Hematology-Oncology, School of Medicine, Kyungpook National University Hospital, Kyungpook National University, Daegu, South Korea
| | - Sang Kyun Sohn
- Department of Hematology-Oncology, School of Medicine, Kyungpook National University Hospital, Kyungpook National University, Daegu, South Korea
| | - Jong-Ho Won
- Division of Hematology & Oncology, Department of Internal Medicine, Soonchunhyang University College of Medicine, Soonchunhyang University Hospital, Seoul, South Korea
| | - Seong Kyu Park
- Division of Hematology & Oncology, Department of Internal Medicine, Soonchunhyang University College of Medicine, Soonchunhyang University Hospital, Seoul, South Korea
| | - Sung-Hyun Kim
- Department of Hematology-Oncology, Dong-A University College of Medicine, Busan, South Korea
| | - Chang Kyun Choi
- Division of Cancer Registration and Surveillance, National Cancer Control Institute, National Cancer Canter, Goyang, South Korea
| | - Hyeoung-Joon Kim
- Department of Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Gwangju, Jeollanam-Do, Republic of Korea
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Gwangju, Jeollanam-Do, Republic of Korea
| | - Jae-Sook Ahn
- Department of Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Gwangju, Jeollanam-Do, Republic of Korea.
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Gwangju, Jeollanam-Do, Republic of Korea.
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Chonnam National University, 322 Seoyang-Ro, Hwasun-Eup, Hwasun-Gun, Jeollanam-Do, 58128, Republic of Korea.
| | - Dennis Dong Hwan Kim
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada.
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Zhang B, Liu H, Wu F, Ding Y, Wu J, Lu L, Bajpai AK, Sang M, Wang X. Identification of hub genes and potential molecular mechanisms related to drug sensitivity in acute myeloid leukemia based on machine learning. Front Pharmacol 2024; 15:1359832. [PMID: 38650628 PMCID: PMC11033397 DOI: 10.3389/fphar.2024.1359832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/21/2024] [Indexed: 04/25/2024] Open
Abstract
Background: Acute myeloid leukemia (AML) is the most common form of leukemia among adults and is characterized by uncontrolled proliferation and clonal expansion of hematopoietic cells. There has been a significant improvement in the treatment of younger patients, however, prognosis in the elderly AML patients remains poor. Methods: We used computational methods and machine learning (ML) techniques to identify and explore the differential high-risk genes (DHRGs) in AML. The DHRGs were explored through multiple in silico approaches including genomic and functional analysis, survival analysis, immune infiltration, miRNA co-expression and stemness features analyses to reveal their prognostic importance in AML. Furthermore, using different ML algorithms, prognostic models were constructed and validated using the DHRGs. At the end molecular docking studies were performed to identify potential drug candidates targeting the selected DHRGs. Results: We identified a total of 80 DHRGs by comparing the differentially expressed genes derived between AML patients and normal controls and high-risk AML genes identified by Cox regression. Genetic and epigenetic alteration analyses of the DHRGs revealed a significant association of their copy number variations and methylation status with overall survival (OS) of AML patients. Out of the 137 models constructed using different ML algorithms, the combination of Ridge and plsRcox maintained the highest mean C-index and was used to build the final model. When AML patients were classified into low- and high-risk groups based on DHRGs, the low-risk group had significantly longer OS in the AML training and validation cohorts. Furthermore, immune infiltration, miRNA coexpression, stemness feature and hallmark pathway analyses revealed significant differences in the prognosis of the low- and high-risk AML groups. Drug sensitivity and molecular docking studies revealed top 5 drugs, including carboplatin and austocystin-D that may significantly affect the DHRGs in AML. Conclusion: The findings from the current study identified a set of high-risk genes that may be used as prognostic and therapeutic markers for AML patients. In addition, significant use of the ML algorithms in constructing and validating the prognostic models in AML was demonstrated. Although our study used extensive bioinformatics and machine learning methods to identify the hub genes in AML, their experimental validations using knock-out/-in methods would strengthen our findings.
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Affiliation(s)
- Boyu Zhang
- Department of Hematology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Haiyan Liu
- Department of Hematology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Fengxia Wu
- Department of Hematology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Yuhong Ding
- Department of Hematology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Jiarun Wu
- Department of Hematology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Lu Lu
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Akhilesh K. Bajpai
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Mengmeng Sang
- Department of Hematology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Xinfeng Wang
- Department of Hematology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
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Guarnera L, Visconte V. Using machine learning to unravel the intricacy of acute myeloid leukemia. Haematologica 2024; 109:1025-1026. [PMID: 37822260 PMCID: PMC10985428 DOI: 10.3324/haematol.2023.284085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023] Open
Abstract
Not available.
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Affiliation(s)
- Luca Guarnera
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland OH, 44114, USA; Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland OH, 44114.
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Park S, Kim TY, Cho BS, Kwag D, Lee JM, Kim M, Kim Y, Koo J, Raman A, Kim TK, Kim HJ. Prognostic value of European LeukemiaNet 2022 criteria and genomic clusters using machine learning in older adults with acute myeloid leukemia. Haematologica 2024; 109:1095-1106. [PMID: 37706344 PMCID: PMC10985444 DOI: 10.3324/haematol.2023.283606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
This study aimed to validate the new European Leukemia Net (ELN) 2022 criteria for genetic risk stratification in older adults with acute myeloid leukemia (AML) and to determine the most likely set of clusters of similar cytogenetic and mutation properties correlated with survival outcomes in three treatment groups: intensive chemotherapy (IC), hypomethylating agents (HMA) alone, and HMA plus venetoclax (HMA/VEN). The study included 279 patients (aged ≥60 years) who received IC (N=131), HMA (N=76), and HMA/VEN (N=72) between July 2017 and October 2021. No significant differences were observed in survival among the groups according to ELN 2022 risk stratification. Unsupervised hierarchical clustering analysis identified nine genomic clusters (C1-9) with varying survival outcomes depending on treatment type. For example, C4 (predominant for core binding factor-AML) displayed a favorable prognosis in the IC group, but not in the HMA or HMA/VEN groups. The HMA/VEN group had better outcomes than the HMA group in many clusters (C1, 2, 3, and 5); however, the addition of VEN to HMA or IC did not improve the survival outcomes compared with those of HMA alone in C7 and C9 (predominant for -5, del(5q), -7, -17/abn(17p), complex karyotypes, and mutated TP53). The study highlights the limitations of ELN genetic risk stratification in older adults with AML. It emphasizes the need for a more comprehensive approach that considers co-occurring somatic mutations to guide treatment selection in older adults with AML.
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Affiliation(s)
- Silvia Park
- Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea; Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea; Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Tong Yoon Kim
- Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea; Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul
| | - Byung-Sik Cho
- Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea; Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul.
| | - Daehun Kwag
- Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea; Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul
| | - Jong-Mi Lee
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul
| | - MyungShin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul
| | - Jamin Koo
- Department of Chemical Engineering, Hongik University, Seoul, Korea; ImpriMedKorea Inc, Seoul
| | - Anjali Raman
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt University, Nashville, TN
| | - Tae Kon Kim
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt University, Nashville, TN
| | - Hee-Je Kim
- Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea; Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul
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9
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Yim D, Khuntia J, Parameswaran V, Meyers A. Preliminary Evidence of the Use of Generative AI in Health Care Clinical Services: Systematic Narrative Review. JMIR Med Inform 2024; 12:e52073. [PMID: 38506918 PMCID: PMC10993141 DOI: 10.2196/52073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/12/2023] [Accepted: 01/30/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Generative artificial intelligence tools and applications (GenAI) are being increasingly used in health care. Physicians, specialists, and other providers have started primarily using GenAI as an aid or tool to gather knowledge, provide information, train, or generate suggestive dialogue between physicians and patients or between physicians and patients' families or friends. However, unless the use of GenAI is oriented to be helpful in clinical service encounters that can improve the accuracy of diagnosis, treatment, and patient outcomes, the expected potential will not be achieved. As adoption continues, it is essential to validate the effectiveness of the infusion of GenAI as an intelligent technology in service encounters to understand the gap in actual clinical service use of GenAI. OBJECTIVE This study synthesizes preliminary evidence on how GenAI assists, guides, and automates clinical service rendering and encounters in health care The review scope was limited to articles published in peer-reviewed medical journals. METHODS We screened and selected 0.38% (161/42,459) of articles published between January 1, 2020, and May 31, 2023, identified from PubMed. We followed the protocols outlined in the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines to select highly relevant studies with at least 1 element on clinical use, evaluation, and validation to provide evidence of GenAI use in clinical services. The articles were classified based on their relevance to clinical service functions or activities using the descriptive and analytical information presented in the articles. RESULTS Of 161 articles, 141 (87.6%) reported using GenAI to assist services through knowledge access, collation, and filtering. GenAI was used for disease detection (19/161, 11.8%), diagnosis (14/161, 8.7%), and screening processes (12/161, 7.5%) in the areas of radiology (17/161, 10.6%), cardiology (12/161, 7.5%), gastrointestinal medicine (4/161, 2.5%), and diabetes (6/161, 3.7%). The literature synthesis in this study suggests that GenAI is mainly used for diagnostic processes, improvement of diagnosis accuracy, and screening and diagnostic purposes using knowledge access. Although this solves the problem of knowledge access and may improve diagnostic accuracy, it is oriented toward higher value creation in health care. CONCLUSIONS GenAI informs rather than assisting or automating clinical service functions in health care. There is potential in clinical service, but it has yet to be actualized for GenAI. More clinical service-level evidence that GenAI is used to streamline some functions or provides more automated help than only information retrieval is needed. To transform health care as purported, more studies related to GenAI applications must automate and guide human-performed services and keep up with the optimism that forward-thinking health care organizations will take advantage of GenAI.
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Affiliation(s)
- Dobin Yim
- Loyola University, Maryland, MD, United States
| | - Jiban Khuntia
- University of Colorado Denver, Denver, CO, United States
| | | | - Arlen Meyers
- University of Colorado Denver, Denver, CO, United States
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10
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Kubota Y, Gu X, Terkawi L, Bodo J, Przychodzen BP, Awada H, Williams N, Gurnari C, Kawashima N, Aly M, Durmaz A, Mori M, Ponvilawan B, Kewan T, Bahaj W, Meggendorfer M, Jha BK, Visconte V, Rogers HJ, Haferlach T, Maciejewski JP. Molecular and clinical analyses of PHF6 mutant myeloid neoplasia provide their pathogenesis and therapeutic targeting. Nat Commun 2024; 15:1832. [PMID: 38418452 PMCID: PMC10901781 DOI: 10.1038/s41467-024-46134-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 02/12/2024] [Indexed: 03/01/2024] Open
Abstract
PHF6 mutations (PHF6MT) are identified in various myeloid neoplasms (MN). However, little is known about the precise function and consequences of PHF6 in MN. Here we show three main findings in our comprehensive genomic and proteomic study. Firstly, we show a different pattern of genes correlating with PHF6MT in male and female cases. When analyzing male and female cases separately, in only male cases, RUNX1 and U2AF1 are co-mutated with PHF6. In contrast, female cases reveal co-occurrence of ASXL1 mutations and X-chromosome deletions with PHF6MT. Next, proteomics analysis reveals a direct interaction between PHF6 and RUNX1. Both proteins co-localize in active enhancer regions that define the context of lineage differentiation. Finally, we demonstrate a negative prognostic role of PHF6MT, especially in association with RUNX1. The negative effects on survival are additive as PHF6MT cases with RUNX1 mutations have worse outcomes when compared to cases carrying single mutation or wild-type.
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Affiliation(s)
- Yasuo Kubota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xiaorong Gu
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Laila Terkawi
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Juraj Bodo
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Bartlomiej P Przychodzen
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hussein Awada
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Nakisha Williams
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Naomi Kawashima
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mai Aly
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Arda Durmaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Minako Mori
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ben Ponvilawan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Tariq Kewan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Waled Bahaj
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Babal K Jha
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Center for Immunotherapy and Precision Immuno-Oncology, Lerner Research Institute (LRI) Cleveland Clinic, Cleveland, OH, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Heesun J Rogers
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | | | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
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11
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Didi I, Alliot JM, Dumas PY, Vergez F, Tavitian S, Largeaud L, Bidet A, Rieu JB, Luquet I, Lechevalier N, Delabesse E, Sarry A, De Grande AC, Bérard E, Pigneux A, Récher C, Simoncini D, Bertoli S. Artificial intelligence-based prediction models for acute myeloid leukemia using real-life data: A DATAML registry study. Leuk Res 2024; 136:107437. [PMID: 38215555 DOI: 10.1016/j.leukres.2024.107437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/19/2023] [Accepted: 01/05/2024] [Indexed: 01/14/2024]
Abstract
We designed artificial intelligence-based prediction models (AIPM) using 52 diagnostic variables from 3687 patients included in the DATAML registry treated with intensive chemotherapy (IC, N = 3030) or azacitidine (AZA, N = 657) for an acute myeloid leukemia (AML). A neural network called multilayer perceptron (MLP) achieved a prediction accuracy for overall survival (OS) of 68.5% and 62.1% in the IC and AZA cohorts, respectively. The Boruta algorithm could select the most important variables for prediction without decreasing accuracy. Thirteen features were retained with this algorithm in the IC cohort: age, cytogenetic risk, white blood cells count, LDH, platelet count, albumin, MPO expression, mean corpuscular volume, CD117 expression, NPM1 mutation, AML status (de novo or secondary), multilineage dysplasia and ASXL1 mutation; and 7 variables in the AZA cohort: blood blasts, serum ferritin, CD56, LDH, hemoglobin, CD13 and disseminated intravascular coagulation (DIC). We believe that AIPM could help hematologists to deal with the huge amount of data available at diagnosis, enabling them to have an OS estimation and guide their treatment choice. Our registry-based AIPM could offer a large real-life dataset with original and exhaustive features and select a low number of diagnostic features with an equivalent accuracy of prediction, more appropriate to routine practice.
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Affiliation(s)
| | | | - Pierre-Yves Dumas
- Centre Hospitalier Universitaire de Bordeaux, Service d'Hématologie Clinique et de Thérapie Cellulaire, Bordeaux, France; Université de Bordeaux, Bordeaux, France; Institut National de la Santé et de la Recherche Médicale, U1035 Bordeaux, France
| | - François Vergez
- Centre Hospitalo-Universitaire de Toulouse, Institut Universitaire du Cancer Toulouse-Oncopole, Laboratoire d'hématologie, Toulouse, France; Centre de Recherches en Cancérologie de Toulouse, Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - Suzanne Tavitian
- Centre Hospitalo-Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse-Oncopole, Service d'hématologie, Toulouse, France
| | - Laëtitia Largeaud
- Centre Hospitalo-Universitaire de Toulouse, Institut Universitaire du Cancer Toulouse-Oncopole, Laboratoire d'hématologie, Toulouse, France; Centre de Recherches en Cancérologie de Toulouse, Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - Audrey Bidet
- CHU Bordeaux, Laboratoire d'Hématologie Biologique, F-33000 Bordeaux, France
| | - Jean-Baptiste Rieu
- Centre Hospitalo-Universitaire de Toulouse, Institut Universitaire du Cancer Toulouse-Oncopole, Laboratoire d'hématologie, Toulouse, France
| | - Isabelle Luquet
- Centre Hospitalo-Universitaire de Toulouse, Institut Universitaire du Cancer Toulouse-Oncopole, Laboratoire d'hématologie, Toulouse, France
| | - Nicolas Lechevalier
- CHU Bordeaux, Laboratoire d'Hématologie Biologique, F-33000 Bordeaux, France
| | - Eric Delabesse
- Centre Hospitalo-Universitaire de Toulouse, Institut Universitaire du Cancer Toulouse-Oncopole, Laboratoire d'hématologie, Toulouse, France; Centre de Recherches en Cancérologie de Toulouse, Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - Audrey Sarry
- Centre Hospitalo-Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse-Oncopole, Service d'hématologie, Toulouse, France
| | - Anne-Charlotte De Grande
- Centre Hospitalier Universitaire de Bordeaux, Service d'Hématologie Clinique et de Thérapie Cellulaire, Bordeaux, France
| | - Emilie Bérard
- Department of Epidemiology, Health Economics and Public Health, UMR 1295 CERPOP, University of Toulouse, INSERM, UPS, Toulouse University Hospital (CHU), Toulouse, France
| | - Arnaud Pigneux
- Centre Hospitalier Universitaire de Bordeaux, Service d'Hématologie Clinique et de Thérapie Cellulaire, Bordeaux, France; Université de Bordeaux, Bordeaux, France
| | - Christian Récher
- Centre de Recherches en Cancérologie de Toulouse, Université Toulouse 3 Paul Sabatier, Toulouse, France; Centre Hospitalo-Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse-Oncopole, Service d'hématologie, Toulouse, France
| | - David Simoncini
- IRIT UMR 5505-CNRS, Université Toulouse I Capitole, Toulouse, France
| | - Sarah Bertoli
- Centre de Recherches en Cancérologie de Toulouse, Université Toulouse 3 Paul Sabatier, Toulouse, France; Centre Hospitalo-Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse-Oncopole, Service d'hématologie, Toulouse, France.
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12
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Weng W, Chen Y, Wang Y, Ying P, Guo X, Ruan J, Song H, Xu W, Zhang J, Xu X, Tang Y. A scoring system based on fusion genes to predict treatment outcomes of the non-acute promyelocytic leukemia pediatric acute myeloid leukemia. Front Med (Lausanne) 2023; 10:1258038. [PMID: 37942413 PMCID: PMC10628016 DOI: 10.3389/fmed.2023.1258038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023] Open
Abstract
Background Fusion genes are considered to be one of the major drivers behind cancer initiation and progression. Meanwhile, non-acute promyelocytic leukemia (APL) pediatric patients with acute myeloid leukemia (AML) in children had limited treatment efficacy. Hence, we developed and validated a simple clinical scoring system for predicting outcomes in non-APL pediatric patients with AML. Method A total of 184 non-APL pediatric patients with AML who were admitted to our hospital and an independent dataset (318 patients) from the TARGET database were included. Least absolute shrinkage and selection operation (LASSO) and Cox regression analysis were used to identify prognostic factors. Then, a nomogram score was developed to predict the 1, 3, and 5 years overall survival (OS) based on their clinical characteristics and fusion genes. The accuracy of the nomogram score was determined by calibration curves and receiver operating characteristic (ROC) curves. Additionally, an internal verification cohort was used to assess its applicability. Results Based on Cox and LASSO regression analyses, a nomogram score was constructed using clinical characteristics and OS-related fusion genes (CBFβ::MYH11, RUNX1::RUNX1T1, KMT2A::ELL, and KMT2A::MLLT10), yielded good calibration and concordance for predicting OS of non-APL pediatric patients with AML. Furthermore, patients with higher scores exhibited worse outcomes. The nomogram score also demonstrated good discrimination and calibration in the whole cohort and internal validation. Furthermore, artificial neural networks demonstrated that this nomogram score exhibits good predictive performance. Conclusion Our model based on the fusion gene is a prognostic biomarker for non-APL pediatric patients with AML. The nomogram score can provide personalized prognosis prediction, thereby benefiting clinical decision-making.
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Affiliation(s)
- Wenwen Weng
- Division/Center of Hematology-Oncology, Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health Hangzhou, Hangzhou, China
| | - Yanfei Chen
- Division/Center of Hematology-Oncology, Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health Hangzhou, Hangzhou, China
| | - Yuwen Wang
- Division/Center of Hematology-Oncology, Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health Hangzhou, Hangzhou, China
| | - Peiting Ying
- Division/Center of Hematology-Oncology, Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health Hangzhou, Hangzhou, China
| | - Xiaoping Guo
- Division/Center of Hematology-Oncology, Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health Hangzhou, Hangzhou, China
| | - Jinfei Ruan
- Division/Center of Hematology-Oncology, Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health Hangzhou, Hangzhou, China
| | - Hua Song
- Division/Center of Hematology-Oncology, Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health Hangzhou, Hangzhou, China
| | - Weiqun Xu
- Division/Center of Hematology-Oncology, Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health Hangzhou, Hangzhou, China
| | - Jingying Zhang
- Division/Center of Hematology-Oncology, Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health Hangzhou, Hangzhou, China
| | - Xiaojun Xu
- Division/Center of Hematology-Oncology, Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health Hangzhou, Hangzhou, China
| | - Yongmin Tang
- Division/Center of Hematology-Oncology, Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health Hangzhou, Hangzhou, China
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13
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Mori M, Kubota Y, Durmaz A, Gurnari C, Goodings C, Adema V, Ponvilawan B, Bahaj WS, Kewan T, LaFramboise T, Meggendorfer M, Haferlach C, Barnard J, Wlodarski M, Visconte V, Haferlach T, Maciejewski JP. Genomics of deletion 7 and 7q in myeloid neoplasm: from pathogenic culprits to potential synthetic lethal therapeutic targets. Leukemia 2023; 37:2082-2093. [PMID: 37634012 PMCID: PMC10539177 DOI: 10.1038/s41375-023-02003-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/27/2023] [Accepted: 08/08/2023] [Indexed: 08/28/2023]
Abstract
Complete or partial deletions of chromosome 7 (-7/del7q) belong to the most frequent chromosomal abnormalities in myeloid neoplasm (MN) and are associated with a poor prognosis. The disease biology of -7/del7q and the genes responsible for the leukemogenic properties have not been completely elucidated. Chromosomal deletions may create clonal vulnerabilities due to haploinsufficient (HI) genes contained in the deleted regions. Therefore, HI genes are potential targets of synthetic lethal strategies. Through the most comprehensive multimodal analysis of more than 600 -7/del7q MN samples, we elucidated the disease biology and qualified a list of most consistently deleted and HI genes. Among them, 27 potentially synthetic lethal target genes were identified with the following properties: (i) unaffected genes by hemizygous/homozygous LOF mutations; (ii) prenatal lethality in knockout mice; and (iii) vulnerability of leukemia cells by CRISPR and shRNA knockout screens. In -7/del7q cells, we also identified 26 up or down-regulated genes mapping on other chromosomes as downstream pathways or compensation mechanisms. Our findings shed light on the pathogenesis of -7/del7q MNs, while 27 potential synthetic lethal target genes and 26 differential expressed genes allow for a therapeutic window of -7/del7q.
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Affiliation(s)
- Minako Mori
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
- Department of Hematology, National Hospital Organization Kyoto Medical Center, Kyoto, Japan
| | - Yasuo Kubota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Arda Durmaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
- Department of Biomedicine and Prevention, Ph.D. in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Charnise Goodings
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Vera Adema
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ben Ponvilawan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Waled S Bahaj
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Tariq Kewan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | | | | | - John Barnard
- Department of Quantitative Health Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Marcin Wlodarski
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | | | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
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14
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Angelakis A, Soulioti I, Filippakis M. Diagnosis of acute myeloid leukaemia on microarray gene expression data using categorical gradient boosted trees. Heliyon 2023; 9:e20530. [PMID: 37860531 PMCID: PMC10582309 DOI: 10.1016/j.heliyon.2023.e20530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023] Open
Abstract
We define an iterative method for dimensionality reduction using categorical gradient boosted trees and Shapley values and created four machine learning models which potentially could be used as diagnostic tests for acute myeloid leukaemia (AML). For the final Catboost model we use a dataset of 2177 individuals using as features 16 probe sets and the age in order to classify if someone has AML or is healthy. The dataset is multicentric and consists of data from 27 organizations, 25 cities, 15 countries and 4 continents. The performance of our last model is specificity: 0.9909, sensitivity: 0.9985, F1-score: 0.9976 and its ROC-AUC: 0.9962 using ten fold cross validation. On an inference dataset the perormance is: specificity: 0.9909, sensitivity: 0.9969, F1-score: 0.9969 and its ROC-AUC: 0.9939. To the best of our knowledge the performance of our model is the best one in the literature, as regards the diagnosis of AML using similar or not data. Moreover, there has not been any bibliographic reference which associates AML or any other type of cancer with the 16 probe sets we used as features in our final model.
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Affiliation(s)
- Athanasios Angelakis
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Amsterdam Public Health Research Institute, University of Amsterdam Data Science Center, Netherlands
| | - Ioanna Soulioti
- Department of Biology, National and Kapodistrian University of Athens, Greece
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15
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Lee H, Han JH, Kim JK, Yoo J, Yoon JH, Cho BS, Kim HJ, Lim J, Jekarl DW, Kim Y. Machine Learning Predicts 30-Day Outcome among Acute Myeloid Leukemia Patients: A Single-Center, Retrospective, Cohort Study. J Clin Med 2023; 12:5940. [PMID: 37762881 PMCID: PMC10531920 DOI: 10.3390/jcm12185940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Acute myeloid leukemia (AML) is a clinical emergency requiring treatment and results in high 30-day (D30) mortality. In this study, the prediction of D30 survival was studied using a machine learning (ML) method. The total cohort consisted of 1700 survivors and 130 non-survivors at D30. Eight clinical and 42 laboratory variables were collected at the time of diagnosis by pathology. Among them, six variables were selected by a feature selection method: induction chemotherapy (CTx), hemorrhage, infection, C-reactive protein, blood urea nitrogen, and lactate dehydrogenase. Clinical and laboratory data were entered into the training model for D30 survival prediction, followed by testing. Among the tested ML algorithms, the decision tree (DT) algorithm showed higher accuracy, the highest sensitivity, and specificity values (95% CI) of 90.6% (0.918-0.951), 70.4% (0.885-0.924), and 92.1% (0.885-0.924), respectively. DT classified patients into eight specific groups with distinct features. Group 1 with CTx showed a favorable outcome with a survival rate of 97.8% (1469/1502). Group 6, with hemorrhage and the lowest fibrinogen level at diagnosis, showed the worst survival rate of 45.5% (25/55) and 20.5 days. Prediction of D30 survival among AML patients by classification of patients with DT showed distinct features that might support clinical decision-making.
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Affiliation(s)
- Howon Lee
- Department of Laboratory Medicine, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 07345, Republic of Korea
| | - Jay Ho Han
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Jae Kwon Kim
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Jaeeun Yoo
- Department of Laboratory Medicine, Incheon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Incheon 21431, Republic of Korea;
| | - Jae-Ho Yoon
- Division of Hematology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Byung Sik Cho
- Division of Hematology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Hee-Je Kim
- Division of Hematology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Jihyang Lim
- Department of Laboratory Medicine, Eunpyeong St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 03312, Republic of Korea
| | - Dong Wook Jekarl
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Research and Development Institute for In Vitro Diagnostic Medical Devices, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
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16
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Attardi E, Savi A, Borsellino B, Piciocchi A, Cipriani M, Ottone T, Fabiani E, Divona M, Travaglini S, Pascale MR, Awada H, Durmaz A, Visconte V, Della Porta MG, Venditti A, Maciejewski JP, Gurnari C, Voso MT. Applicability of 2022 classifications of acute myeloid leukemia in the real-world setting. Blood Adv 2023; 7:5122-5131. [PMID: 37327116 PMCID: PMC10477447 DOI: 10.1182/bloodadvances.2023010173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023] Open
Abstract
The increasing knowledge of molecular genetics of acute myeloid leukemia (AML) necessitated the update of previous diagnostic and prognostic schemes, which resulted in the development of the World Health Organization (WHO), the International Consensus Classification (ICC), and the new European LeukemiaNet (ELN) recommendations in 2022. We aimed to provide a real-world application of the new models, unravel differences and similarities, and test their implementation in clinical AML diagnosis. A total of 1001 patients diagnosed with AML were reclassified based on the new schemes. The overall diagnostic changes between the WHO 2016 and the WHO 2022 and ICC classifications were 22.8% and 23.7%, respectively, with a 13.1% difference in patients' distribution between ICC and WHO 2022. The 2022 ICC "not otherwise specified" and WHO "defined by differentiation" AML category sizes shrank when compared with that in WHO 2016 (24.1% and 26.8% respectively, vs 38.7%), particularly because of an expansion of the myelodysplasia (MDS)-related group. Of 397 patients with a MDS-related AML according to the ICC, 55.9% were defined by the presence of a MDS-related karyotype. The overall restratification between ELN 2017 and ELN 2022 was 12.9%. The 2022 AML classifications led to a significant improvement of diagnostic schemes. In the real-world setting, conventional cytogenetics, usually rapidly available and less expensive than molecular characterization, stratified 56% of secondary AML, still maintaining a powerful diagnostic role. Considering the similarities between WHO and ICC diagnostic schemes, a tentative scheme to generate a unified model is desirable.
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Affiliation(s)
- Enrico Attardi
- Department of Biomedicine and Prevention, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Arianna Savi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Beatrice Borsellino
- Department of Biomedicine and Prevention, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Alfonso Piciocchi
- Italian Group for Adult Hematologic Diseases (GIMEMA) Foundation, Rome, Italy
| | - Marta Cipriani
- Italian Group for Adult Hematologic Diseases (GIMEMA) Foundation, Rome, Italy
- Department of Statistical Sciences, University of Rome La Sapienza, Rome, Italy
| | - Tiziana Ottone
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Neuro-Oncohematology Unit, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia, Rome, Italy
| | - Emiliano Fabiani
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- UniCamillus-Saint Camillus International University of Health Sciences, Rome, Italy
| | - Mariadomenica Divona
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- UniCamillus-Saint Camillus International University of Health Sciences, Rome, Italy
| | - Serena Travaglini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Maria Rosaria Pascale
- Department of Biomedicine and Prevention, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Hussein Awada
- Translational Hematology and Oncology Research Department, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH
| | - Arda Durmaz
- Translational Hematology and Oncology Research Department, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH
| | - Valeria Visconte
- Translational Hematology and Oncology Research Department, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH
| | - Matteo Giovanni Della Porta
- IRCCS Humanitas Clinical & Research Center and Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Adriano Venditti
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Jaroslaw P. Maciejewski
- Translational Hematology and Oncology Research Department, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH
| | - Carmelo Gurnari
- Department of Biomedicine and Prevention, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Translational Hematology and Oncology Research Department, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH
| | - Maria Teresa Voso
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Neuro-Oncohematology Unit, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia, Rome, Italy
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17
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McCarter JGW, Nemirovsky D, Famulare CA, Farnoud N, Mohanty AS, Stone-Molloy ZS, Chervin J, Ball BJ, Epstein-Peterson ZD, Arcila ME, Stonestrom AJ, Dunbar A, Cai SF, Glass JL, Geyer MB, Rampal RK, Berman E, Abdel-Wahab OI, Stein EM, Tallman MS, Levine RL, Goldberg AD, Papaemmanuil E, Zhang Y, Roshal M, Derkach A, Xiao W. Interaction between myelodysplasia-related gene mutations and ontogeny in acute myeloid leukemia. Blood Adv 2023; 7:5000-5013. [PMID: 37142255 PMCID: PMC10471939 DOI: 10.1182/bloodadvances.2023009675] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/01/2023] [Accepted: 04/17/2023] [Indexed: 05/06/2023] Open
Abstract
Accurate classification and risk stratification are critical for clinical decision making in patients with acute myeloid leukemia (AML). In the newly proposed World Health Organization and International Consensus classifications of hematolymphoid neoplasms, the presence of myelodysplasia-related (MR) gene mutations is included as 1 of the diagnostic criteria for AML, AML-MR, based largely on the assumption that these mutations are specific for AML with an antecedent myelodysplastic syndrome. ICC also prioritizes MR gene mutations over ontogeny (as defined in the clinical history). Furthermore, European LeukemiaNet (ELN) 2022 stratifies these MR gene mutations into the adverse-risk group. By thoroughly annotating a cohort of 344 newly diagnosed patients with AML treated at the Memorial Sloan Kettering Cancer Center, we show that ontogeny assignments based on the database registry lack accuracy. MR gene mutations are frequently observed in de novo AML. Among the MR gene mutations, only EZH2 and SF3B1 were associated with an inferior outcome in the univariate analysis. In a multivariate analysis, AML ontogeny had independent prognostic values even after adjusting for age, treatment, allo-transplant and genomic classes or ELN risks. Ontogeny also helped stratify the outcome of AML with MR gene mutations. Finally, de novo AML with MR gene mutations did not show an adverse outcome. In summary, our study emphasizes the importance of accurate ontogeny designation in clinical studies, demonstrates the independent prognostic value of AML ontogeny, and questions the current classification and risk stratification of AML with MR gene mutations.
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Affiliation(s)
- Joseph G. W. McCarter
- Department of Epidemiology & Biostatistics, Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Memorial Sloan Kettering Kids, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David Nemirovsky
- Department of Epidemiology & Biostatistics, Biostatistics Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Noushin Farnoud
- Department of Epidemiology & Biostatistics, Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Abhinita S. Mohanty
- Department of Pathology and Laboratory Medicine, Diagnostic Molecular Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zoe S. Stone-Molloy
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jordan Chervin
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Brian J. Ball
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Maria E. Arcila
- Department of Pathology and Laboratory Medicine, Diagnostic Molecular Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Aaron J. Stonestrom
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrew Dunbar
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sheng F. Cai
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacob L. Glass
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark B. Geyer
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Raajit K. Rampal
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ellin Berman
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Omar I. Abdel-Wahab
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Molecular Cancer Medicine Service, Human Oncogenesis & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eytan M. Stein
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Martin S. Tallman
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross L. Levine
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Molecular Cancer Medicine Service, Human Oncogenesis & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Aaron D. Goldberg
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elli Papaemmanuil
- Department of Epidemiology & Biostatistics, Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yanming Zhang
- Department of Pathology and Laboratory Medicine, Cytogenetics Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mikhail Roshal
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andriy Derkach
- Department of Epidemiology & Biostatistics, Biostatistics Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wenbin Xiao
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY
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18
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Tanaka A, Nishimura K, Saika W, Kon A, Koike Y, Tatsumi H, Takeda J, Nomura M, Zang W, Nakayama M, Matsuda M, Yamazaki H, Fukumoto M, Ito H, Hayashi Y, Kitamura T, Kawamoto H, Takaori-Kondo A, Koseki H, Ogawa S, Inoue D. SETBP1 is dispensable for normal and malignant hematopoiesis. Leukemia 2023; 37:1802-1811. [PMID: 37464069 DOI: 10.1038/s41375-023-01970-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
SETBP1 is a potential epigenetic regulator whose hotspot mutations preventing proteasomal degradation are recurrently detected in myeloid malignancies with poor prognosis. It is believed that the mutant SETBP1 exerts amplified effects of wild-type SETBP1 rather than neomorphic functions. This indicates that dysregulated quantitative control of SETBP1 would result in the transformation of hematopoietic cells. However, little is known about the roles of endogenous SETBP1 in malignant and normal hematopoiesis. Thus, we integrated the analyses of primary AML and healthy samples, cancer cell lines, and a newly generated murine model, Vav1-iCre;Setbp1fl/fl. Despite the expression in long-term hematopoietic stem cells, SETBP1 depletion in normal hematopoiesis minimally alters self-renewal, differentiation, or reconstitution in vivo. Indeed, its loss does not profoundly alter transcription or chromatin accessibilities. Furthermore, although AML with high SETBP1 mRNA is associated with genetic and clinical characteristics for dismal outcomes, SETBP1 is dispensable for the development or maintenance of AML. Contrary to the evidence that SETBP1 mutations are restricted to myeloid malignancies, dependency on SETBP1 mRNA expression is not observed in AML. These unexpected results shed light on the unrecognized idea that a physiologically nonessential gene can act as an oncogene when the machinery of protein degradation is damaged.
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Affiliation(s)
- Atsushi Tanaka
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koutarou Nishimura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Wataru Saika
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Department of Hematology, Shiga University of Medical Science, Shiga, Japan
| | - Ayana Kon
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yui Koike
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Hiromi Tatsumi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - June Takeda
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masaki Nomura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Facility for iPS Cell Therapy, CiRA Foundation, Kyoto, Japan
| | - Weijia Zang
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manabu Nakayama
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, Chiba, Japan
| | - Masashi Matsuda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Hiromi Yamazaki
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Miki Fukumoto
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Hiromi Ito
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Yasutaka Hayashi
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Toshio Kitamura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Daichi Inoue
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan.
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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19
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Scott EC, Baines AC, Gong Y, Moore R, Pamuk GE, Saber H, Subedee A, Thompson MD, Xiao W, Pazdur R, Rao VA, Schneider J, Beaver JA. Trends in the approval of cancer therapies by the FDA in the twenty-first century. Nat Rev Drug Discov 2023; 22:625-640. [PMID: 37344568 DOI: 10.1038/s41573-023-00723-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2023] [Indexed: 06/23/2023]
Abstract
The cancer treatment landscape has changed dramatically since the turn of the century, resulting in substantial improvements in outcomes for patients. This Review summarizes trends in the approval of oncology therapeutic products by the United States Food and Drug Administration (FDA) from January 2000 to October 2022, based on a categorization of these products by their mechanism of action and primary target. Notably, the rate of oncology indication approvals has increased in this time, driven by approvals for targeted therapies, as has the rate of introduction of new therapeutic approaches. Kinase inhibitors are the dominant product class by number of approved products and indications, yet immune checkpoint inhibitors have the second most approvals despite not entering the market until 2011. Other trends include a slight increase in the share of approvals for biomarker-defined populations and the emergence of tumour-site-agnostic approvals. Finally, we consider the implications of the trends for the future of oncology therapeutic product development, including the impact of novel therapeutic approaches and technologies.
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Affiliation(s)
- Emma C Scott
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
| | - Andrea C Baines
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Yutao Gong
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Rodney Moore
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Gulsum E Pamuk
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Haleh Saber
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Ashim Subedee
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
- National Cancer Institute, Rockville, MD, USA
| | - Matthew D Thompson
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Wenming Xiao
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Richard Pazdur
- Oncology Center of Excellence, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - V Ashutosh Rao
- Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Julie Schneider
- Oncology Center of Excellence, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Julia A Beaver
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
- Oncology Center of Excellence, U.S. Food and Drug Administration, Silver Spring, MD, USA
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20
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Gedefaw L, Liu CF, Ip RKL, Tse HF, Yeung MHY, Yip SP, Huang CL. Artificial Intelligence-Assisted Diagnostic Cytology and Genomic Testing for Hematologic Disorders. Cells 2023; 12:1755. [PMID: 37443789 PMCID: PMC10340428 DOI: 10.3390/cells12131755] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/21/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Artificial intelligence (AI) is a rapidly evolving field of computer science that involves the development of computational programs that can mimic human intelligence. In particular, machine learning and deep learning models have enabled the identification and grouping of patterns within data, leading to the development of AI systems that have been applied in various areas of hematology, including digital pathology, alpha thalassemia patient screening, cytogenetics, immunophenotyping, and sequencing. These AI-assisted methods have shown promise in improving diagnostic accuracy and efficiency, identifying novel biomarkers, and predicting treatment outcomes. However, limitations such as limited databases, lack of validation and standardization, systematic errors, and bias prevent AI from completely replacing manual diagnosis in hematology. In addition, the processing of large amounts of patient data and personal information by AI poses potential data privacy issues, necessitating the development of regulations to evaluate AI systems and address ethical concerns in clinical AI systems. Nonetheless, with continued research and development, AI has the potential to revolutionize the field of hematology and improve patient outcomes. To fully realize this potential, however, the challenges facing AI in hematology must be addressed and overcome.
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Affiliation(s)
- Lealem Gedefaw
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (L.G.); (C.-F.L.); (M.H.Y.Y.)
| | - Chia-Fei Liu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (L.G.); (C.-F.L.); (M.H.Y.Y.)
| | - Rosalina Ka Ling Ip
- Department of Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong, China; (R.K.L.I.); (H.-F.T.)
| | - Hing-Fung Tse
- Department of Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong, China; (R.K.L.I.); (H.-F.T.)
| | - Martin Ho Yin Yeung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (L.G.); (C.-F.L.); (M.H.Y.Y.)
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (L.G.); (C.-F.L.); (M.H.Y.Y.)
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (L.G.); (C.-F.L.); (M.H.Y.Y.)
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21
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Gagelmann N, Badbaran A, Salit RB, Schroeder T, Gurnari C, Pagliuca S, Panagiota V, Rautenberg C, Cassinat B, Thol F, Wolschke C, Robin M, Heuser M, Rubio MT, Maciejewski JP, Reinhardt HC, Scott BL, Kröger N. Impact of TP53 on outcome of patients with myelofibrosis undergoing hematopoietic stem cell transplantation. Blood 2023; 141:2901-2911. [PMID: 36940410 PMCID: PMC10933704 DOI: 10.1182/blood.2023019630] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/22/2023] Open
Abstract
TP53 mutations (TP53MTs) have been associated with poor outcomes in various hematologic malignancies, but no data exist regarding its role in patients with myelofibrosis undergoing hematopoietic stem cell transplantation (HSCT). Here, we took advantage of a large international multicenter cohort to evaluate the role of TP53MT in this setting. Among 349 included patients, 49 (13%) had detectable TP53MT, of whom 30 showed a multihit configuration. Median variant allele frequency was 20.3%. Cytogenetic risk was favorable (71%), unfavorable (23%), and very high (6%), with complex karyotype present in 36 patients (10%). Median survival of patients with TP53MT was 1.5 vs 13.5 years for those with wild-type TP53 (TP53WT; P < .001). Outcome was driven by multihit TP53MT constellation (P < .001), showing 6-year survival of 56% for individuals with single-hit vs 25% for those with multihit TP53MT vs 64% for those with TP53WT. Outcome was independent of current transplantation-specific risk factors and conditioning intensity. Similarly, cumulative incidence of relapse was 17% for single-hit vs 52% for multihit vs 21% for TP53WT. Ten patients with TP53MT (20%) presented as leukemic transformation vs only 7 (2%) in the TP53WT group (P < .001). Out of the 10 patients with TP53MT, 8 showed multihit constellation. Median time to leukemic transformation was shorter for multihit and single-hit TP53MT (0.7 and 0.5 years, respectively) vs 2.5 years for TP53WT. In summary, multihit TP53MT represents a very high-risk group in patients with myelofibrosis who are undergoing HSCT, whereas single-hit TP53MT alone showed similar outcome to patients with nonmutated TP53, informing prognostication for survival and relapse together with current transplantation-specific tools.
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Affiliation(s)
- Nico Gagelmann
- Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anita Badbaran
- Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Rachel B. Salit
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Thomas Schroeder
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, University Hospital of Essen, Essen, Germany
| | - Carmelo Gurnari
- Translational Hematology and Oncology Research Department, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy
| | - Simona Pagliuca
- Department of Hematology, Brabois Hospital, Centre Hospitalier Régional Universitaire, Nancy, France
| | - Victoria Panagiota
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Christina Rautenberg
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, University Hospital of Essen, Essen, Germany
| | - Bruno Cassinat
- Laboratoire de Biologie Cellulaire, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Christine Wolschke
- Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marie Robin
- Service d'Hématologie-Greffe, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Marie-Thérèse Rubio
- Department of Hematology, Brabois Hospital, Centre Hospitalier Régional Universitaire, Nancy, France
| | - Jaroslaw P. Maciejewski
- Translational Hematology and Oncology Research Department, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH
- Leukemia Program, Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, University Hospital of Essen, Essen, Germany
| | - Bart L. Scott
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Nicolaus Kröger
- Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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22
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Eckardt JN, Röllig C, Metzeler K, Heisig P, Stasik S, Georgi JA, Kroschinsky F, Stölzel F, Platzbecker U, Spiekermann K, Krug U, Braess J, Görlich D, Sauerland C, Woermann B, Herold T, Hiddemann W, Müller-Tidow C, Serve H, Baldus CD, Schäfer-Eckart K, Kaufmann M, Krause SW, Hänel M, Berdel WE, Schliemann C, Mayer J, Hanoun M, Schetelig J, Wendt K, Bornhäuser M, Thiede C, Middeke JM. Unsupervised meta-clustering identifies risk clusters in acute myeloid leukemia based on clinical and genetic profiles. COMMUNICATIONS MEDICINE 2023; 3:68. [PMID: 37198246 DOI: 10.1038/s43856-023-00298-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 05/03/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND Increasingly large and complex biomedical data sets challenge conventional hypothesis-driven analytical approaches, however, data-driven unsupervised learning can detect inherent patterns in such data sets. METHODS While unsupervised analysis in the medical literature commonly only utilizes a single clustering algorithm for a given data set, we developed a large-scale model with 605 different combinations of target dimensionalities as well as transformation and clustering algorithms and subsequent meta-clustering of individual results. With this model, we investigated a large cohort of 1383 patients from 59 centers in Germany with newly diagnosed acute myeloid leukemia for whom 212 clinical, laboratory, cytogenetic and molecular genetic parameters were available. RESULTS Unsupervised learning identifies four distinct patient clusters, and statistical analysis shows significant differences in rate of complete remissions, event-free, relapse-free and overall survival between the four clusters. In comparison to the standard-of-care hypothesis-driven European Leukemia Net (ELN2017) risk stratification model, we find all three ELN2017 risk categories being represented in all four clusters in varying proportions indicating unappreciated complexity of AML biology in current established risk stratification models. Further, by using assigned clusters as labels we subsequently train a supervised model to validate cluster assignments on a large external multicenter cohort of 664 intensively treated AML patients. CONCLUSIONS Dynamic data-driven models are likely more suitable for risk stratification in the context of increasingly complex medical data than rigid hypothesis-driven models to allow for a more personalized treatment allocation and gain novel insights into disease biology.
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Affiliation(s)
- Jan-Niklas Eckardt
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany.
- Else Kröner Fresenius Center for Digital Health, Technical University Dresden, Dresden, Germany.
| | - Christoph Röllig
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Klaus Metzeler
- Medical Clinic and Policlinic I Hematology and Cell Therapy, University Hospital, Leipzig, Germany
| | - Peter Heisig
- Department of Software and Multimedia Technology, Technical University Dresden, Dresden, Germany
| | - Sebastian Stasik
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Julia-Annabell Georgi
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Frank Kroschinsky
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Friedrich Stölzel
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Uwe Platzbecker
- Medical Clinic and Policlinic I Hematology and Cell Therapy, University Hospital, Leipzig, Germany
| | - Karsten Spiekermann
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Utz Krug
- Department of Medicine III, Hospital Leverkusen, Leverkusen, Germany
| | - Jan Braess
- Hospital Barmherzige Brueder Regensburg, Regensburg, Germany
| | - Dennis Görlich
- Institute for Biostatistics and Clinical Research, University Muenster, Muenster, Germany
| | - Cristina Sauerland
- Institute for Biostatistics and Clinical Research, University Muenster, Muenster, Germany
| | - Bernhard Woermann
- Department of Hematology, Oncology and Tumor Immunology, Charité, Berlin, Germany
| | - Tobias Herold
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Wolfgang Hiddemann
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Carsten Müller-Tidow
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- German Consortium for Translational Cancer Research DKFZ, Heidelberg, Germany
| | - Hubert Serve
- Department of Medicine 2, Hematology and Oncology, Goethe University Frankfurt, Frankfurt, Germany
| | - Claudia D Baldus
- Department of Hematology and Oncology, University Hospital Schleswig Holstein, Kiel, Germany
| | | | - Martin Kaufmann
- Department of Hematology, Oncology and Palliative Care, Robert-Bosch Hospital, Stuttgart, Germany
| | - Stefan W Krause
- Department of Internal Medicine 5, University Hospital Erlangen, Erlangen, Germany
| | - Mathias Hänel
- Department of Internal Medicine 3, Klinikum Chemnitz GmbH, Chemnitz, Germany
| | - Wolfgang E Berdel
- Department of Internal Medicine A, University Hospital Muenster, Muenster, Germany
| | - Christoph Schliemann
- Department of Internal Medicine A, University Hospital Muenster, Muenster, Germany
| | - Jiri Mayer
- Department of Internal Medicine, Hematology and Oncology, Masaryk University Hospital, Brno, Czech Republic
| | - Maher Hanoun
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
| | - Johannes Schetelig
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Karsten Wendt
- Else Kröner Fresenius Center for Digital Health, Technical University Dresden, Dresden, Germany
- Department of Software and Multimedia Technology, Technical University Dresden, Dresden, Germany
| | - Martin Bornhäuser
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
- German Consortium for Translational Cancer Research DKFZ, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Christian Thiede
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Jan Moritz Middeke
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
- Else Kröner Fresenius Center for Digital Health, Technical University Dresden, Dresden, Germany
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23
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Lai C, Bhansali RS, Kuo EJ, Mannis G, Lin RJ. Older Adults With Newly Diagnosed AML: Hot Topics for the Practicing Clinician. Am Soc Clin Oncol Educ Book 2023; 43:e390018. [PMID: 37155946 DOI: 10.1200/edbk_390018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Over the past decade, our understanding of AML pathogenesis and pathophysiology has improved significantly with mutational profiling. This has led to translational advances in therapeutic options, as there have been 10 new US Food and Drug Administration (FDA) approvals for AML therapies since 2017, half of which target specific driver mutations in FLT3, IDH1, or IDH2. These new agents have expanded the therapeutic armamentarium for AML, particularly for patients who are considered ineligible for intensive chemotherapy with anthracycline- and cytarabine-containing regimens. These new treatment options are relevant because the median age at diagnosis is 68 years, and outcomes for patients older than 60 years have historically been dismal. However, the optimal approach to incorporating novel agents into frontline regimens remains a clinical challenge, particularly with regard to sequencing of therapies, considering the role of allogeneic hematopoietic stem cell transplantation and managing toxicities.
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Affiliation(s)
- Catherine Lai
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Rahul S Bhansali
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Eric J Kuo
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA
| | - Gabriel Mannis
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA
| | - Richard J Lin
- Memorial Sloan Kettering Cancer Center, New York, NY
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24
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Bhansali RS, Pratz KW, Lai C. Recent advances in targeted therapies in acute myeloid leukemia. J Hematol Oncol 2023; 16:29. [PMID: 36966300 PMCID: PMC10039574 DOI: 10.1186/s13045-023-01424-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/14/2023] [Indexed: 03/27/2023] Open
Abstract
Acute myeloid leukemia (AML) is the most common acute leukemia in adults. While survival for younger patients over the last several decades has improved nearly sixfold with the optimization of intensive induction chemotherapy and allogeneic stem cell transplantation (alloHSCT), this effect has been largely mitigated in older and less fit patients as well as those with adverse-risk disease characteristics. However, the last 10 years has been marked by major advances in the molecular profiling of AML characterized by a deeper understanding of disease pathobiology and therapeutic vulnerabilities. In this regard, the classification of AML subtypes has recently evolved from a morphologic to a molecular and genetic basis, reflected by recent updates from the World Health Organization and the new International Consensus Classification system. After years of stagnation in new drug approvals for AML, there has been a rapid expansion of the armamentarium against this disease since 2017. Low-intensity induction therapy with hypomethylating agents and venetoclax has substantially improved outcomes, including in those previously considered to have a poor prognosis. Furthermore, targeted oral therapies against driver mutations in AML have been added to the repertoire. But with an accelerated increase in treatment options, several questions arise such as how to best sequence therapy, how to combine therapies, and if there is a role for maintenance therapy in those who achieve remission and cannot undergo alloHSCT. Moreover, certain subtypes of AML, such as those with TP53 mutations, still have dismal outcomes despite these recent advances, underscoring an ongoing unmet need and opportunity for translational advances. In this review, we will discuss recent updates in the classification and risk stratification of AML, explore the literature regarding low-intensity and novel oral combination therapies, and briefly highlight investigative agents currently in early clinical development for high-risk disease subtypes.
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Affiliation(s)
- Rahul S Bhansali
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, South Pavilion, 12th Floor, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Keith W Pratz
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, South Pavilion, 12th Floor, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Catherine Lai
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, South Pavilion, 12th Floor, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
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25
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Durmaz A, Gurnari C, Hershberger CE, Pagliuca S, Daniels N, Awada H, Awada H, Adema V, Mori M, Ponvilawan B, Kubota Y, Kewan T, Bahaj WS, Barnard J, Scott J, Padgett RA, Haferlach T, Maciejewski JP, Visconte V. A multimodal analysis of genomic and RNA splicing features in myeloid malignancies. iScience 2023; 26:106238. [PMID: 36926651 PMCID: PMC10011742 DOI: 10.1016/j.isci.2023.106238] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/12/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
RNA splicing dysfunctions are more widespread than what is believed by only estimating the effects resulting by splicing factor mutations (SFMT) in myeloid neoplasia (MN). The genetic complexity of MN is amenable to machine learning (ML) strategies. We applied an integrative ML approach to identify co-varying features by combining genomic lesions (mutations, deletions, and copy number), exon-inclusion ratio as measure of RNA splicing (percent spliced in, PSI), and gene expression (GE) of 1,258 MN and 63 normal controls. We identified 15 clusters based on mutations, GE, and PSI. Different PSI levels were present at various extents regardless of SFMT suggesting that changes in RNA splicing were not strictly related to SFMT. Combination of PSI and GE further distinguished the features and identified PSI similarities and differences, common pathways, and expression signatures across clusters. Thus, multimodal features can resolve the complex architecture of MN and help identifying convergent molecular and transcriptomic pathways amenable to therapies.
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Affiliation(s)
- Arda Durmaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Systems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | | | - Simona Pagliuca
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Clinical Hematology, CHRU de Nancy, Nancy, France
| | - Noah Daniels
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Hassan Awada
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Hussein Awada
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Vera Adema
- MD Anderson Cancer Center, Houston, TX, USA
| | - Minako Mori
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ben Ponvilawan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yasuo Kubota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Tariq Kewan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Waled S. Bahaj
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - John Barnard
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Jacob Scott
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Systems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Richard A. Padgett
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | | | - Jaroslaw P. Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Corresponding author
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26
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The Heterogeneous Complexity of Myeloid Neoplasm: Multi-Level Approaches to Study the Disease. Cancers (Basel) 2023; 15:cancers15051449. [PMID: 36900241 PMCID: PMC10000814 DOI: 10.3390/cancers15051449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
Myeloid neoplasms (MNs) include a spectrum of bone marrow malignancies that result from the clonal expansion and arrest of differentiation of myeloid progenitor cells [...].
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27
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Zhang Q, Ma R, Chen H, Guo W, Li Z, Xu K, Chen W. CD86 Is Associated with Immune Infiltration and Immunotherapy Signatures in AML and Promotes Its Progression. JOURNAL OF ONCOLOGY 2023; 2023:9988405. [PMID: 37064861 PMCID: PMC10104747 DOI: 10.1155/2023/9988405] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/21/2022] [Accepted: 07/25/2022] [Indexed: 04/18/2023]
Abstract
Background Cluster of differentiation 86 (CD86), also known as B7-2, is a molecule expressed on antigen-presenting cells that provides the costimulatory signals required for T cell activation and survival. CD86 binds to two ligands on the surface of T cells: the antigen CD28 and cytotoxic T lymphocyte-associated protein 4 (CTLA-4). By binding to CD28, CD86-together with CD80-promotes the participation of T cells in the antigen presentation process. However, the interrelationships among CD86, immunotherapy, and immune infiltration in acute myeloid leukemia (AML) are unclear. Methods The immunological effects of CD86 in various cancers (including on chemokines, immunostimulators, MHC, and receptors) were evaluated through a pan-cancer analysis using TCGA and GEO databases. The relationship between CD86 expression and mononucleotide variation, gene copy number variation, methylation, immune checkpoint blockers (ICBs), and T-cell inflammation score in AML was subsequently examined. ESTIMATE and limma packages were used to identify genes at the intersection of CD86 with StromalScore and ImmuneScore. Subsequently, GO/KEGG and PPI network analyses were performed. The immune risk score (IRS) model was constructed, and the validation set was used for verification. The predictive value was compared with the TIDE score. Results CD86 was overexpressed in many cancers, and its overexpression was associated with a poor prognosis. CD86 expression was positively correlated with the expression of CTLA4, PDCD1LG2, IDO1, HAVCR2, and other genes and negatively correlated with CD86 methylation. The expression of CD86 in AML cell lines was detected by QRT-PCR and Western blot, and the results showed that CD86 was overexpressed in AML cell lines. Immune infiltration assays showed that CD86 expression was positively correlated with CD8 T cell, Dendritic cell, macrophage, NK cell, and Th1_cell and also with immune examination site, immune regulation, immunotherapy response, and TIICs. ssGSEA showed that CD86 was enriched in immune-related pathways, and CD86 expression was correlated with mutations in the genes RB1, ERBB2, and FANCC, which are associated with responses to radiotherapy and chemotherapy. The IRS score performed better than the TIDE website score. Conclusion CD86 appears to participate in immune invasion in AML and is an important player in the tumor microenvironment in this malignancy. At the same time, the IRS score developed by us has a good effect and may provide some support for the diagnosis of AML. Thus, CD86 may serve as a potential target for AML immunotherapy.
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Affiliation(s)
- Qianqian Zhang
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ruixue Ma
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Huimin Chen
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Wentong Guo
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhenyu Li
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Key Laboratory of Bone Marrow Stem Cells, Xuzhou, Jiangsu, China
| | - Kailin Xu
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Key Laboratory of Bone Marrow Stem Cells, Xuzhou, Jiangsu, China
| | - Wei Chen
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Key Laboratory of Bone Marrow Stem Cells, Xuzhou, Jiangsu, China
- Department of Hematology, The First People's Hospital of Suqian, Suqian, Jiangsu, China
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28
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Gurnari C, Pagliuca S. Digging into the HLA pockets: A new association with acute leukaemias. Br J Haematol 2023; 200:123-125. [PMID: 36342469 PMCID: PMC10098546 DOI: 10.1111/bjh.18529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022]
Abstract
Acute leukaemias represent a highly heterogeneous group of clonal proliferations of myeloid or lymphoid blasts. In the last decade, the contribution of immunogenetics to cancer biology has elicited a renewed interest in the structures of immune adaptive responses, due to the growing body of evidence concerning their involvement into disease pathogenesis and treatment. The report by Boukouaci and colleagues suggests new associations between patterns of distribution of specific human leukocyte antigen motifs and leukaemogenesis. Commentary on Boukouaci Wahid et al. Comparative analysis of the variability of the HLA peptide-binding pockets in patients with acute leukemias" Br J Haematol 2023;200:203-215.
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Affiliation(s)
- Carmelo Gurnari
- Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy.,Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Simona Pagliuca
- Department of Clinical Hematology, CHRU Nancy, and CNRS UMR 7365 IMoPa, Biopole de l'Université de Loarraine, Vandoeuvre-lès-Nancy, France
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29
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Duncavage EJ, Bagg A, Hasserjian RP, DiNardo CD, Godley LA, Iacobucci I, Jaiswal S, Malcovati L, Vannucchi AM, Patel KP, Arber DA, Arcila ME, Bejar R, Berliner N, Borowitz MJ, Branford S, Brown AL, Cargo CA, Döhner H, Falini B, Garcia-Manero G, Haferlach T, Hellström-Lindberg E, Kim AS, Klco JM, Komrokji R, Lee-Cheun Loh M, Loghavi S, Mullighan CG, Ogawa S, Orazi A, Papaemmanuil E, Reiter A, Ross DM, Savona M, Shimamura A, Skoda RC, Solé F, Stone RM, Tefferi A, Walter MJ, Wu D, Ebert BL, Cazzola M. Genomic profiling for clinical decision making in myeloid neoplasms and acute leukemia. Blood 2022; 140:2228-2247. [PMID: 36130297 PMCID: PMC10488320 DOI: 10.1182/blood.2022015853] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/27/2022] [Indexed: 11/20/2022] Open
Abstract
Myeloid neoplasms and acute leukemias derive from the clonal expansion of hematopoietic cells driven by somatic gene mutations. Although assessment of morphology plays a crucial role in the diagnostic evaluation of patients with these malignancies, genomic characterization has become increasingly important for accurate diagnosis, risk assessment, and therapeutic decision making. Conventional cytogenetics, a comprehensive and unbiased method for assessing chromosomal abnormalities, has been the mainstay of genomic testing over the past several decades and remains relevant today. However, more recent advances in sequencing technology have increased our ability to detect somatic mutations through the use of targeted gene panels, whole-exome sequencing, whole-genome sequencing, and whole-transcriptome sequencing or RNA sequencing. In patients with myeloid neoplasms, whole-genome sequencing represents a potential replacement for both conventional cytogenetic and sequencing approaches, providing rapid and accurate comprehensive genomic profiling. DNA sequencing methods are used not only for detecting somatically acquired gene mutations but also for identifying germline gene mutations associated with inherited predisposition to hematologic neoplasms. The 2022 International Consensus Classification of myeloid neoplasms and acute leukemias makes extensive use of genomic data. The aim of this report is to help physicians and laboratorians implement genomic testing for diagnosis, risk stratification, and clinical decision making and illustrates the potential of genomic profiling for enabling personalized medicine in patients with hematologic neoplasms.
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Affiliation(s)
- Eric J. Duncavage
- Department of Pathology and Immunology, Washington University, St. Louis, MO
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - Courtney D. DiNardo
- Division of Cancer Medicine, Department of Leukemia, MD Anderson Cancer Center, Houston, TX
| | - Lucy A. Godley
- Section of Hematology and Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | | | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia & Fondazione IRCCS Policlinico S. Matteo, Pavia, Italy
| | - Alessandro M. Vannucchi
- Department of Hematology, Center Research and Innovation of Myeloproliferative Neoplasms, University of Florence and Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Keyur P. Patel
- Division of Pathology/Lab Medicine, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Lettering Cancer Center, New York, NY
| | - Rafael Bejar
- Division of Hematology and Oncology, University of California San Diego, La Jolla, CA
| | - Nancy Berliner
- Division of Hematology, Brigham and Women’s Hospital, Harvard University, Boston, MA
| | - Michael J. Borowitz
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Susan Branford
- Department of Genetics and Molecular Pathology, Center for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Anna L. Brown
- Department of Pathology, South Australia Heath Alliance, Adelaide, Australia
| | - Catherine A. Cargo
- Haematological Malignancy Diagnostic Service, St James’s University Hospital, Leeds, United Kingdom
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University Hospital, Ulm, Germany
| | - Brunangelo Falini
- Department of Hematology, CREO, University of Perugia, Perugia, Italy
| | | | | | - Eva Hellström-Lindberg
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Annette S. Kim
- Department of Pathology, Brigham and Women’s Hospital, Harvard University, Boston, MA
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Rami Komrokji
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL
| | - Mignon Lee-Cheun Loh
- Department of Pediatrics, Ben Towne Center for Childhood Cancer Research, Seattle Children’s Hospital, University of Washington, Seattle, WA
| | - Sanam Loghavi
- Division of Pathology/Lab Medicine, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Seishi Ogawa
- University of Kyoto School of Medicine, Kyoto, Japan
| | - Attilio Orazi
- Department of Pathology, Texas Tech University Health Sciences Center, El Paso, TX
| | | | - Andreas Reiter
- University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - David M. Ross
- Haematology Directorate, SA Pathology, Adelaide, Australia
| | - Michael Savona
- Department of Medicine, Vanderbilt University, Nashville, TN
| | - Akiko Shimamura
- Dana Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Radek C. Skoda
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Francesc Solé
- MDS Group, Institut de Recerca contra la Leucèmia Josep Carreras, Barcelona, Spain
| | - Richard M. Stone
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | - David Wu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Mario Cazzola
- Division of Hematology, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
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30
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Llop M, Sargas C, Barragán E. The role of next-generation sequencing in acute myeloid leukemia. Curr Opin Oncol 2022; 34:723-728. [PMID: 36102349 DOI: 10.1097/cco.0000000000000899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW The development of high-throughput techniques like next-generation sequencing (NGS) has unraveled the genetic profile of cancer. In this review, we discuss the role of NGS on the diagnostic, risk stratification, and follow-up of patients with acute myeloid leukemia (AML). RECENT FINDINGS NGS has become an essential tool in clinical practice for AML management. Therefore, efforts are being made to improve its applications, automation, and turnaround time. Other high-throughput techniques, such as whole genome sequencing or RNA-sequencing, can be also used to this end. However, not all institutions may be able to implement these approaches. NGS is being investigated for measurable residual disease (MRD) assessment, especially with the development of error-correction NGS. New data analysis approaches like machine learning are being investigated in order to integrate genomic and clinical data and develop comprehensive classifications and risk scores. SUMMARY NGS has proven to be a useful approach for the analysis of genomic alterations in patients with AML, which aids patient management. Current research is being directed at reducing turnaround time and simplifying processes so that these techniques can be universally integrated into clinical practice.
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Affiliation(s)
- Marta Llop
- Molecular Biology Unit, Service of Clinical Analysis. Hospital Universitari i Politècnic La Fe
- CIBERONC CB16/12/00284
| | - Claudia Sargas
- Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Eva Barragán
- Molecular Biology Unit, Service of Clinical Analysis. Hospital Universitari i Politècnic La Fe
- CIBERONC CB16/12/00284
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31
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Diagnosis and management of AML in adults: 2022 recommendations from an international expert panel on behalf of the ELN. Blood 2022; 140:1345-1377. [PMID: 35797463 DOI: 10.1182/blood.2022016867] [Citation(s) in RCA: 865] [Impact Index Per Article: 432.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/29/2022] [Indexed: 11/20/2022] Open
Abstract
The 2010 and 2017 editions of the European LeukemiaNet (ELN) recommendations for diagnosis and management of acute myeloid leukemia (AML) in adults are widely recognized among physicians and investigators. There have been major advances in our understanding of AML, including new knowledge about the molecular pathogenesis of AML, leading to an update of the disease classification, technological progress in genomic diagnostics and assessment of measurable residual disease, and the successful development of new therapeutic agents, such as FLT3, IDH1, IDH2, and BCL2 inhibitors. These advances have prompted this update that includes a revised ELN genetic risk classification, revised response criteria, and treatment recommendations.
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32
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A Focus on Intermediate-Risk Acute Myeloid Leukemia: Sub-Classification Updates and Therapeutic Challenges. Cancers (Basel) 2022; 14:cancers14174166. [PMID: 36077703 PMCID: PMC9454629 DOI: 10.3390/cancers14174166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/16/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Acute myeloid leukemia (AML) represents a heterogeneous group of hematopoietic neoplasms deriving from the abnormal proliferation of myeloid progenitors in the bone marrow. Patients with AML may have highly variable outcomes, which are generally dictated by individual clinical and genomic characteristics. As such, the European LeukemiaNet 2017 and 2022 guidelines categorize newly diagnosed AML into favorable-, intermediate-, and adverse-risk groups, based on their molecular and cytogenetic profiles. Nevertheless, the intermediate-risk category remains poorly defined, as many patients fall into this group as a result of their exclusion from the other two. Moreover, further genomic data with potential prognostic and therapeutic influences continue to emerge, though they are yet to be integrated into the diagnostic and prognostic models of AML. This review highlights the latest therapeutic advances and challenges that warrant refining the prognostic classification of intermediate-risk AML.
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33
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Travaglini S, Gurnari C, Antonelli S, Silvestrini G, Noguera NI, Ottone T, Voso MT. The Anti-Leukemia Effect of Ascorbic Acid: From the Pro-Oxidant Potential to the Epigenetic Role in Acute Myeloid Leukemia. Front Cell Dev Biol 2022; 10:930205. [PMID: 35938170 PMCID: PMC9352950 DOI: 10.3389/fcell.2022.930205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Data derived from high-throughput sequencing technologies have allowed a deeper understanding of the molecular landscape of Acute Myeloid Leukemia (AML), paving the way for the development of novel therapeutic options, with a higher efficacy and a lower toxicity than conventional chemotherapy. In the antileukemia drug development scenario, ascorbic acid, a natural compound also known as Vitamin C, has emerged for its potential anti-proliferative and pro-apoptotic activities on leukemic cells. However, the role of ascorbic acid (vitamin C) in the treatment of AML has been debated for decades. Mechanistic insight into its role in many biological processes and, especially, in epigenetic regulation has provided the rationale for the use of this agent as a novel anti-leukemia therapy in AML. Acting as a co-factor for 2-oxoglutarate-dependent dioxygenases (2-OGDDs), ascorbic acid is involved in the epigenetic regulations through the control of TET (ten-eleven translocation) enzymes, epigenetic master regulators with a critical role in aberrant hematopoiesis and leukemogenesis. In line with this discovery, great interest has been emerging for the clinical testing of this drug targeting leukemia epigenome. Besides its role in epigenetics, ascorbic acid is also a pivotal regulator of many physiological processes in human, particularly in the antioxidant cellular response, being able to scavenge reactive oxygen species (ROS) to prevent DNA damage and other effects involved in cancer transformation. Thus, for this wide spectrum of biological activities, ascorbic acid possesses some pharmacologic properties attractive for anti-leukemia therapy. The present review outlines the evidence and mechanism of ascorbic acid in leukemogenesis and its therapeutic potential in AML. With the growing evidence derived from the literature on situations in which the use of ascorbate may be beneficial in vitro and in vivo, we will finally discuss how these insights could be included into the rational design of future clinical trials.
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Affiliation(s)
- S. Travaglini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - C. Gurnari
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, United States
| | - S. Antonelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - G. Silvestrini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - N. I. Noguera
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Neuro-Oncohematology Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - T. Ottone
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Neuro-Oncohematology Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - M. T. Voso
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Neuro-Oncohematology Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
- *Correspondence: M. T. Voso,
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Machine learning finds new AML subtypes. Blood 2021; 138:1790-1792. [PMID: 34762131 DOI: 10.1182/blood.2021012455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/20/2021] [Indexed: 11/20/2022] Open
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Eckardt JN, Wendt K, Bornhäuser M, Middeke JM. Reinforcement Learning for Precision Oncology. Cancers (Basel) 2021; 13:4624. [PMID: 34572853 PMCID: PMC8472712 DOI: 10.3390/cancers13184624] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 01/19/2023] Open
Abstract
Precision oncology is grounded in the increasing understanding of genetic and molecular mechanisms that underly malignant disease and offer different treatment pathways for the individual patient. The growing complexity of medical data has led to the implementation of machine learning techniques that are vastly applied for risk assessment and outcome prediction using either supervised or unsupervised learning. Still largely overlooked is reinforcement learning (RL) that addresses sequential tasks by exploring the underlying dynamics of an environment and shaping it by taking actions in order to maximize cumulative rewards over time, thereby achieving optimal long-term outcomes. Recent breakthroughs in RL demonstrated remarkable results in gameplay and autonomous driving, often achieving human-like or even superhuman performance. While this type of machine learning holds the potential to become a helpful decision support tool, it comes with a set of distinctive challenges that need to be addressed to ensure applicability, validity and safety. In this review, we highlight recent advances of RL focusing on studies in oncology and point out current challenges and pitfalls that need to be accounted for in future studies in order to successfully develop RL-based decision support systems for precision oncology.
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Affiliation(s)
- Jan-Niklas Eckardt
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, 01307 Dresden, Germany; (M.B.); (J.M.M.)
| | - Karsten Wendt
- Institute of Software and Multimedia Technology, Technical University Dresden, 01069 Dresden, Germany;
| | - Martin Bornhäuser
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, 01307 Dresden, Germany; (M.B.); (J.M.M.)
- German Consortium for Translational Cancer Research, 69120 Heidelberg, Germany
- National Center for Tumor Diseases, 01307 Dresden, Germany
| | - Jan Moritz Middeke
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, 01307 Dresden, Germany; (M.B.); (J.M.M.)
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Talami A, Bettelli F, Pioli V, Giusti D, Gilioli A, Colasante C, Galassi L, Giubbolini R, Catellani H, Donatelli F, Maffei R, Martinelli S, Barozzi P, Potenza L, Marasca R, Trenti T, Tagliafico E, Comoli P, Luppi M, Forghieri F. How to Improve Prognostication in Acute Myeloid Leukemia with CBFB-MYH11 Fusion Transcript: Focus on the Role of Molecular Measurable Residual Disease (MRD) Monitoring. Biomedicines 2021; 9:biomedicines9080953. [PMID: 34440157 PMCID: PMC8391269 DOI: 10.3390/biomedicines9080953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/13/2021] [Accepted: 07/29/2021] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) carrying inv(16)/t(16;16), resulting in fusion transcript CBFB-MYH11, belongs to the favorable-risk category. However, even if most patients obtain morphological complete remission after induction, approximately 30% of cases eventually relapse. While well-established clinical features and concomitant cytogenetic/molecular lesions have been recognized to be relevant to predict prognosis at disease onset, the independent prognostic impact of measurable residual disease (MRD) monitoring by quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR), mainly in predicting relapse, actually supersedes other prognostic factors. Although the ELN Working Party recently indicated that patients affected with CBFB-MYH11 AML should have MRD assessment at informative clinical timepoints, at least after two cycles of intensive chemotherapy and after the end of treatment, several controversies could be raised, especially on the frequency of subsequent serial monitoring, the most significant MRD thresholds (most commonly 0.1%) and on the best source to be analyzed, namely, bone marrow or peripheral blood samples. Moreover, persisting low-level MRD positivity at the end of treatment is relatively common and not predictive of relapse, provided that transcript levels remain stably below specific thresholds. Rising MRD levels suggestive of molecular relapse/progression should thus be confirmed in subsequent samples. Further prospective studies would be required to optimize post-remission monitoring and to define effective MRD-based therapeutic strategies.
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Affiliation(s)
- Annalisa Talami
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
| | - Francesca Bettelli
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
| | - Valeria Pioli
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
| | - Davide Giusti
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
| | - Andrea Gilioli
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
| | - Corrado Colasante
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
| | - Laura Galassi
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
| | - Rachele Giubbolini
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
| | - Hillary Catellani
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
| | - Francesca Donatelli
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
| | - Rossana Maffei
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
| | - Silvia Martinelli
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
| | - Patrizia Barozzi
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
| | - Leonardo Potenza
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
| | - Roberto Marasca
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
| | - Tommaso Trenti
- Department of Laboratory Medicine and Pathology, Unità Sanitaria Locale, 41126 Modena, Italy;
| | - Enrico Tagliafico
- Center for Genome Research, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy;
| | - Patrizia Comoli
- Pediatric Hematology/Oncology Unit and Cell Factory, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, 27100 Pavia, Italy;
| | - Mario Luppi
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
- Correspondence: (M.L.); (F.F.); Tel.: +39-059-4222447 (F.F.); Fax: +39-059-4222386 (F.F.)
| | - Fabio Forghieri
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy; (A.T.); (F.B.); (V.P.); (D.G.); (A.G.); (C.C.); (L.G.); (R.G.); (H.C.); (F.D.); (R.M.); (S.M.); (P.B.); (L.P.); (R.M.)
- Correspondence: (M.L.); (F.F.); Tel.: +39-059-4222447 (F.F.); Fax: +39-059-4222386 (F.F.)
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