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Kim M, Ahn SY, Kim T, Jung SH, Song GY, Yang DH, Lee JJ, Kim MY, Park JH, Shin MG, Ahn JS, Kim HJ, Kim DDH. Prognostic analysis according to European LeukemiaNet 2022 risk stratification for elderly patients with acute myeloid leukemia treated with decitabine. Hematology 2024; 29:2324417. [PMID: 38433437 DOI: 10.1080/16078454.2024.2324417] [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: 08/08/2023] [Accepted: 02/23/2024] [Indexed: 03/05/2024] Open
Abstract
OBJECTIVES This study aimed to evaluate the prognostic significance of the revised European LeukemiaNet (ELN)-2022 risk stratification model for 123 elderly acute myeloid leukemia (AML) patients treated with decitabine chemotherapy. RESULTS Based on the ELN-2022 risk stratification, 15 (12.2%), 51 (41.5%), and 57 (46.3%) patients were classified as having favorable, intermediate, and high-risk AML, respectively. In comparison with the ELN-2017 risk stratification, the ELN-2022 risk stratification re-assigned 26 (21.1%) and three (2.4%) patients to the adverse and favorable risk groups, respectively. Survival analysis revealed distinctive overall survival (OS) outcomes among the ELN-2022 risk groups (6-month OS rate: 73.3%, 52.9%, and 47.7% for favorable, intermediate, and adverse risk, respectively; P = 0.101), with a parallel trend observed in the event-free survival (EFS) (6-month EFS rate: 73.3%, 52.9%, and 45.6% for favorable, intermediate, and adverse risk, respectively; P = 0.049). Notably, both OS and EFS in the favorable risk group were significantly superior in comparison to that of the adverse risk group (OS: P = 0.040, EFS: P = 0.030). Although the ELN-2022 C-index (0.559) was greater than the ELN-2017 C-index (0.539), the result was not statistically significant (P = 0.059). Based on the event net reclassification index, we consistently observed significant improvements in the ELN-2022 risk stratification for overall survival (0.21 at 6 months). CONCLUSION In conclusion, the revised ELN-2022 risk stratification model may have improved the risk classification of elderly AML patients treated with hypomethylating agents compared to the ELN-2017 risk stratification model.
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Affiliation(s)
- Mihee Kim
- Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
| | - Seo-Yeon Ahn
- Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
| | - TaeHyung Kim
- Department of Computer Science, University of Toronto, Toronto, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Sung-Hoon Jung
- Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
| | - Ga-Young Song
- Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
| | - Deok-Hwan Yang
- Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
| | - Je-Jung Lee
- Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
| | - Mi Yeon Kim
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Jeollanam-do, Republic of Korea
| | - Ju Heon Park
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Jeollanam-do, Republic of Korea
| | - Myung-Geun Shin
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Jeollanam-do, Republic of Korea
| | - Jae-Sook Ahn
- Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Jeollanam-do, Republic of Korea
| | - Hyeoung-Joon Kim
- Hematology-Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Jeollanam-do, 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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Leung B, Aung H, Nandini A, Abdulrasool G, Lau C, Seymour L. Analytical Validation of a 37-Gene Next-Generation Sequencing Panel for Myeloid Malignancies and Review of Initial Findings Incorporating Updated 2022 Diagnostic and Prognostic Guidelines. J Mol Diagn 2024; 26:399-412. [PMID: 38367765 DOI: 10.1016/j.jmoldx.2024.01.010] [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: 02/14/2023] [Revised: 10/23/2023] [Accepted: 01/16/2024] [Indexed: 02/19/2024] Open
Abstract
Myeloid neoplasms are clonal disorders that arise via acquisition of genetic mutations leading to excessive proliferation and defective differentiation. Mutational profiling is vital as it has implications for diagnosis, prognosis, and therapeutic decision-making. Next-generation sequencing (NGS) has become a mainstay in the evaluation of myeloid malignancies, as it enables efficient characterization of multiple genetic changes. Herein, the analytical validation of the 37-gene Archer VariantPlex Core Myeloid panel is reported, using 58 DNA specimens with 87 single-nucleotide variants and 23 insertions/deletions. The panel achieved good depth of coverage, 100% analytical sensitivity and specificity for single-nucleotide variants and insertions/deletions ≤21 bp, and 100% reproducibility, with a reportable limit of detection determined as 5%. The Archer NGS panel can accurately and reproducibly detect variants of clinical significance in myeloid neoplasms. A retrospective analysis of 535 clinical specimens tested with the Archer NGS panel showed a frequency and pattern of mutations across myeloid malignancies that were similar to other published studies. A review of the diagnostic classification of patients with acute myeloid leukemia and myelodysplastic syndrome using the World Health Organization 2017/2022 and International Consensus Classification 2022 guidelines, in addition to European LeukemiaNet 2017/2022 risk stratification of patients with acute myeloid leukemia, was also performed to assess the utility of the molecular information provided by the Archer NGS panel.
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Affiliation(s)
- Becky Leung
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; School of Medicine, Griffith University, Gold Coast, Queensland, Australia.
| | - Hnin Aung
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Adayapalam Nandini
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Ghusoon Abdulrasool
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Chiyan Lau
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Louise Seymour
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; School of Medicine, University of Queensland, Brisbane, Queensland, Australia
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Benard BA, Leak LB, Azizi A, Thomas D, Gentles AJ, Majeti R. Clonal architecture predicts clinical outcomes and drug sensitivity in acute myeloid leukemia. Nat Commun 2021; 12:7244. [PMID: 34903734 PMCID: PMC8669028 DOI: 10.1038/s41467-021-27472-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/17/2021] [Indexed: 12/17/2022] Open
Abstract
The impact of clonal heterogeneity on disease behavior or drug response in acute myeloid leukemia remains poorly understood. Using a cohort of 2,829 patients, we identify features of clonality associated with clinical features and drug sensitivities. High variant allele frequency for 7 mutations (including NRAS and TET2) associate with dismal prognosis; elevated GATA2 variant allele frequency correlates with better outcomes. Clinical features such as white blood cell count and blast percentage correlate with the subclonal abundance of mutations such as TP53 and IDH1. Furthermore, patients with cohesin mutations occurring before NPM1, or transcription factor mutations occurring before splicing factor mutations, show shorter survival. Surprisingly, a branched pattern of clonal evolution is associated with superior clinical outcomes. Finally, several mutations (including NRAS and IDH1) predict drug sensitivity based on their subclonal abundance. Together, these results demonstrate the importance of assessing clonal heterogeneity with implications for prognosis and actionable biomarkers for therapy.
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Affiliation(s)
- Brooks A Benard
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University, Stanford, CA, USA
| | - Logan B Leak
- Cancer Biology Program, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Armon Azizi
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
| | - Daniel Thomas
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Andrew J Gentles
- Department of Medicine (Biomedical Informatics/Quantitative Sciences unit), Stanford University, Stanford, CA, USA
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA.
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4
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Hu X, Wang B, Chen Q, Huang A, Fu W, Liu L, Zhang Y, Tang G, Cheng H, Ni X, Gao L, Chen J, Chen L, Zhang W, Yang J, Cao S, Yu L, Wang J. A clinical prediction model identifies a subgroup with inferior survival within intermediate risk acute myeloid leukemia. J Cancer 2021; 12:4912-4923. [PMID: 34234861 PMCID: PMC8247394 DOI: 10.7150/jca.57231] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 05/19/2021] [Indexed: 12/19/2022] Open
Abstract
Intermediate risk acute myeloid leukemia (AML) comprises around 50% of AML patients and is featured with heterogeneous clinical outcomes. The study aimed to generate a prediction model to identify intermediate risk AML patients with an inferior survival. We performed targeted next generation sequencing analysis for 121 patients with 2017 European LeukemiaNet-defined intermediate risk AML, revealing 122 mutated genes, with 24 genes mutated in > 10% of patients. A prognostic nomogram characterized by white blood cell count ≥10×109/L at diagnosis, mutated DNMT3A and genes involved in signaling pathways was developed for 110 patients who were with clinical outcomes. Two subgroups were identified: intermediate low risk (ILR; 43.6%, 48/110) and intermediate high risk (IHR; 56.4%, 62/110). The model was prognostic of overall survival (OS) and relapse-free survival (RFS) (OS: Concordance index [C-index]: 0.703, 95%CI: 0.643-0.763; RFS: C-index: 0.681, 95%CI 0.620-0.741), and was successfully validated with two independent cohorts. Allogeneic hematopoietic stem cell transplantation (alloHSCT) reduced the relapse risk of IHR patients (3-year RFS: alloHSCT: 40.0±12.8% vs. chemotherapy: 8.6±5.8%, P= 0.010). The prediction model can help identify patients with an unfavorable prognosis and refine risk-adapted therapy for intermediate risk AML patients.
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Affiliation(s)
- Xiaoxia Hu
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Bianhong Wang
- Department of Hematology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China.,Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Qi Chen
- Department of Health Statistics, Second Military Medical University, Shanghai 200433, China
| | - Aijie Huang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Weijia Fu
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Lixia Liu
- Acornmed Biotechnology Co., Ltd. Beijing, 100176, China
| | - Ying Zhang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Gusheng Tang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Hui Cheng
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Xiong Ni
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Lei Gao
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Jie Chen
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Li Chen
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Weiping Zhang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Jianmin Yang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd. Beijing, 100176, China
| | - Li Yu
- Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China.,Department of Hematology and Oncology, Shenzhen University General Hospital; Shenzhen University International Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518000, China
| | - Jianmin Wang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
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5
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Wang B, Guan W, Lv N, Li T, Yu F, Huang Y, Wang Y, Li L, Yu L. Genetic features and efficacy of decitabine-based chemotherapy in elderly patients with acute myeloid leukemia. HEMATOLOGY (AMSTERDAM, NETHERLANDS) 2021; 26:371-379. [PMID: 33971800 DOI: 10.1080/16078454.2021.1921434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
OBJECTIVES The outcome of elderly acute myeloid leukemia (AML) patients is poor, which was traditionally attributed to patient- and leukemia-related factors. However, studies about the genetic features of these elderly patients have not been integrated and the genetic mechanism of their poor outcome is less known. METHODS Here, we used next generation sequencing (NGS) to identify the genetic features of elderly AML patients and confirmed the efficacy of chemotherapy based on molecular aberrations. Mutations in 111 genes relevant to hematological malignancy was analysed by virtue of NGS and the genetic differences were compared between elderly (n=52) and young (n=161) AML patients. Furthermore, the outcome of decitabine-based chemotherapy was identified in elderly patients. RESULTS Frequencies of adverse genetic alterations, such as RUNX1 and secondary-type mutations (ASXL1, STAG2 and spliceosome), were much higher in elderly patients, while the frequency of WT1 mutations was much lower. Moreover, epigenetic mutations such as DNMT3A, TET2, ASXL1 and IDH2, were also more common in elderly patients. Furthermore, there were 39 elderly patients receiving the decitabine-based chemotherapy, and the results showed that the overall response rate (ORR) and complete remission rate (CR) were 76.9% and 71.8%, respectively. The median overall survival (OS) for those older patients was 12 months, and the 2-year OS probability was 20.5%. DISCUSSION Our study provides deep understanding into the molecular mechanisms of the poor outcome of elderly AML patients. CONCLUSION Epigenetic mutations play an important role, and decitabine-based regimen can be used as alternative first-line chemotherapy for elderly patients.
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Affiliation(s)
- Bianhong Wang
- Department of Hematology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, People's Republic of China.,Department of Hematology, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Wei Guan
- Department of Hematology, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Na Lv
- Department of Hematology, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Ting Li
- Annoroad Gene Technology, Beijing, People's Republic of China
| | - Fan Yu
- Department of Hematology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, People's Republic of China
| | - Yuehua Huang
- Department of Hematology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, People's Republic of China
| | - Yanying Wang
- Department of Hematology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, People's Republic of China
| | - Lihong Li
- Department of Hematology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, People's Republic of China
| | - Li Yu
- Department of Hematology, Chinese PLA General Hospital, Beijing, People's Republic of China.,Department of Hematology and Oncology, Shenzhen University General Hospital; Shenzhen University International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People's Republic of China
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6
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Papuc SM, Erbescu A, Cisleanu D, Ozunu D, Enache C, Dumitru I, Lupoaia Andrus E, Gaman M, Popov VM, Dobre M, Stanca O, Angelescu S, Berbec N, Colita A, Vladareanu AM, Bumbea H, Arghir A. Delineation of Molecular Lesions in Acute Myeloid Leukemia Patients at Diagnosis: Integrated Next Generation Sequencing and Cytogenomic Studies. Genes (Basel) 2021; 12:genes12060846. [PMID: 34070898 PMCID: PMC8229708 DOI: 10.3390/genes12060846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/19/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disorder characterized by a wide range of genetic defects. Cytogenetics, molecular and genomic technologies have proved to be helpful for deciphering the mutational landscape of AML and impacted clinical practice. Forty-eight new AML patients were investigated with an integrated approach, including classical and molecular cytogenetics, array-based comparative genomic hybridization and targeted next generation sequencing (NGS). Various genetic defects were identified in all the patients using our strategy. Targeted NGS revealed known pathogenic mutations as well as rare or unreported variants with deleterious predictions. The mutational screening of the normal karyotype (NK) group identified clinically relevant variants in 86.2% of the patients; in the abnormal cytogenetics group, the mutation detection rate was 87.5%. Overall, the highest mutation prevalence was observed for the NPM1 gene, followed by DNMT3A, FLT3 and NRAS. An unexpected co-occurrence of KMT2A translocation and DNMT3A-R882 was identified; alterations of these genes, which are involved in epigenetic regulation, are considered to be mutually exclusive. A microarray analysis detected CNVs in 25% of the NK AML patients. In patients with complex karyotypes, the microarray analysis made a significant contribution toward the accurate characterization of chromosomal defects. In summary, our results show that the integration of multiple investigative strategies increases the detection yield of genetic defects with potential clinical relevance.
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Affiliation(s)
- Sorina Mihaela Papuc
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Alina Erbescu
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Diana Cisleanu
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Diana Ozunu
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Cristina Enache
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Ion Dumitru
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Elena Lupoaia Andrus
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Mihaela Gaman
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | | | - Maria Dobre
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Oana Stanca
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Silvana Angelescu
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Nicoleta Berbec
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Andrei Colita
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Ana-Maria Vladareanu
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Horia Bumbea
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Aurora Arghir
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
- Correspondence: ; Tel.: +40-2-1319-2732-207; Fax: +40-2-1319-4528
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Chen X, Zhu H, Qiao C, Zhao S, Liu L, Wang Y, Jin H, Qian S, Wu Y. Next-generation sequencing reveals gene mutations landscape and clonal evolution in patients with acute myeloid leukemia. ACTA ACUST UNITED AC 2021; 26:111-122. [PMID: 33491606 DOI: 10.1080/16078454.2020.1858610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVES The study aims to understand geneome diversification and complexity that developed in Acute myeloid leukemia (AML). METHODS Next-generation sequencing (NGS) was used to identify the genetic profiles of 22 genes relevant to hematological malignancy in 204 patients with de novo non-M3 AML. RESULTS At time of initial diagnosis, at least one mutation was identified in 80.9% of patients (165/204). The most commonly mutated gene was NPM1 (22.1%), followed by ASXL1 (18.1%), TET2 (18.1%), IDH2 (15.7%), CEBPA (14.7%), FLT3-ITD (13.2%) and DNMT3A (11.8%). Mutations landscape analysis indicated several patterns of co-occurring and mutual exclusive gene mutations. Some correlation was observed between gene mutations and clinicohematological features. Multivariate analysis showed that age >60 years, karyotypes, IDH2 and KIT mutations were the independent unfavorable prognostic factors for OS; NPM1-mut/ FLT3-ITD-wt was independently correlated with prolonged OS; whereas the independent poor risk factors for RFS were karyotypes, high WBC and RUNX1 mutation. According to different genotype demonstrated by multivariate analysis, 163 patients with intermediate-risk cytogenetics were classified into three subgroups: patients with NPM1-mut/ FLT3-ITD-wt or biallelic CEBPA mutation as favorable risk, patients with KIT, IDH2, TP53 or NRAS mutations as unfavorable risk, and the remaining was the intermediate risk. We also obtain information of clonal evolution during leukemia progression by observing five patients who underwent repeat NGS at relapse in our cohort. CONCLUSION NGS techniques is a useful tool for discovering related gene mutations and clonal evolution in AML genomes, leading to novel targeted therapeutic approaches that could improve patients outcomes.
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Affiliation(s)
- Xiao Chen
- Department of Hematology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, People's Republic of China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing, People's Republic of China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, People's Republic of China
| | - Han Zhu
- Department of Hematology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, People's Republic of China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing, People's Republic of China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, People's Republic of China
| | - Chun Qiao
- Department of Hematology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, People's Republic of China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing, People's Republic of China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, People's Republic of China
| | - Sishu Zhao
- Department of Hematology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, People's Republic of China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing, People's Republic of China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, People's Republic of China
| | - Lu Liu
- Department of Hematology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, People's Republic of China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing, People's Republic of China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, People's Republic of China
| | - Yan Wang
- Department of Hematology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, People's Republic of China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing, People's Republic of China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, People's Republic of China
| | - Huimin Jin
- Department of Hematology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, People's Republic of China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing, People's Republic of China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, People's Republic of China
| | - Sixuan Qian
- Department of Hematology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, People's Republic of China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing, People's Republic of China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, People's Republic of China
| | - Yujie Wu
- Department of Hematology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, People's Republic of China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing, People's Republic of China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, People's Republic of China
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8
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Zhang R, Wang L, Chen P, Gao X, Wang S, Li F, Dou L, Gao C, Li Y, Liu D. Haematologic malignancies with unfavourable gene mutations benefit from donor lymphocyte infusion with/without decitabine for prophylaxis of relapse after allogeneic HSCT: A pilot study. Cancer Med 2021; 10:3165-3176. [PMID: 33932107 PMCID: PMC8124122 DOI: 10.1002/cam4.3763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/30/2020] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
Relapse is the main cause of treatment failure for leukaemia patients with unfavourable gene mutations who receive allogeneic haematopoietic stem cell transplantation (allo‐HSCT). There is no consensus on the indication of donor lymphocyte infusion (DLI) for prophylaxis of relapse after allo‐HSCT. To evaluate the tolerance and efficacy of prophylactic DLI in patients with unfavourable gene mutations such as FLT3‐ITD, TP53, ASXL1, DNMT3A or TET2, we performed a prospective, single‐arm study. Prophylactic use of decitabine followed by DLI was planned in patients with TP53 or epigenetic modifier gene mutations. The prophylaxis was planned in 46 recipients: it was administered in 28 patients and it was not administered in 18 patients due to contraindications. No DLI‐associated pancytopenia was observed. The cumulative incidences of grade II–IV and III–IV acute graft‐versus‐host disease (GVHD) at 100 days post‐DLI were 25.8% and 11.0%, respectively. The rates of chronic GVHD, non‐relapse mortality and relapse at 3 years post‐DLI were 21.6%, 25.0% and 26.1%, respectively. The 3‐year relapse‐free survival and overall survival (OS) rates were 48.9% and 48.2%, respectively. Acute GVHD (HR: 2.30, p = 0.016) and relapse (HR: 2.46, p = 0.003) after DLI were independently associated with inferior OS. Data in the current study showed the feasibility of prophylactic DLI with/without decitabine in the early stage after allo‐HSCT in patients with unfavourable gene mutations.
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Affiliation(s)
- Rui Zhang
- Department of Hematology, Chinese PLA General Hospital, Beijing, China.,Department of Hematology, People's Hospital of Cangzhou, Hebei, China
| | - Lili Wang
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Peng Chen
- Department of Hematology, the 7th Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xiaoning Gao
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Shuhong Wang
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Fei Li
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Liping Dou
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Chunji Gao
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Yan Li
- Department of Hematology, Chinese PLA General Hospital, Beijing, China.,Department of Hematology, Peking University Third Hospital, Beijing, China
| | - Daihong Liu
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
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9
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Guan W, Zhou L, Li Y, Yang E, Liu Y, Lv N, Fu L, Ding Y, Wang N, Fang N, Liu Q, Wang B, Li F, Zhang J, Wang M, Wang L, Jing Y, Li Y, Yu L. Profiling of somatic mutations and fusion genes in acute myeloid leukemia patients with FLT3-ITD or FLT3-TKD mutation at diagnosis reveals distinct evolutionary patterns. Exp Hematol Oncol 2021; 10:27. [PMID: 33836835 PMCID: PMC8033687 DOI: 10.1186/s40164-021-00207-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/04/2021] [Indexed: 12/26/2022] Open
Abstract
Background The receptor tyrosine kinase FLT3 with internal tandem duplications within the juxtamembrane domain (FLT3-ITD) is a poor prognostic factor; however, the prognostic significance of missense mutation in the tyrosine kinase domain (FLT3-TKD) is controversial. Furthermore, the accompanying mutations and fusion genes with FLT3 mutations are unclear in acute myeloid leukemia (AML). Methods We investigated FLT3 mutations and their correlation with other gene mutations and gene fusions through two RNA-seq based next-generation sequencing (NGS) method and prognostic impact in 207 de novo AML patients. Results FLT3-ITD mutations were positive in 58 patients (28%), and FLT3-TKD mutations were positive in 20 patients (9.7%). FLT3-ITD was associated with a higher white blood cell count (WBC, mean 72.9 × 109/L vs. 24.2 × 109/L, P = 0.000), higher bone marrow blasts (mean 65.9% vs. 56.0%, P = 0.024), and NK-AML (normal karyotype) (64.8% vs. 48.4%, P = 0.043). NPM1 and DNMT3A mutations were enriched in FLT3-ITD (53.5% vs. 15.3%, P = 0.000; 34.6% vs. 13%, P = 0.003). However, the mutations of CEBPA were excluded in FLT3-AML (3.8% vs. 0% vs. 19.8%, P = 0.005). Mutations of Ras and TP53 were unlikely associated with FLT3-ITD (1.9% vs. 20.6%, P = 0.006; 0% vs. 6.1%, P = 0.04). The common fusion genes (> 10%) in FLT3-ITD had MLL-rearrangement and NUP98-rearrangement, while the common fusion genes in FLT3-TKD had AML1-ETO and MLL-rearrangement. Two novel fusion genes PRDM16-SKI and EFAN2-ZNF238 were identified in FLT3-ITD patients. Gene fusions and NPM1 mutation were mutually excluded in FLT3-ITD and FLT3-TKD patients. Their patterns of mutual exclusivity and cooperation among mutated genes suggest that additional driver genetic alterations are required and reveal two evolutionary patterns of FLT3 pathogenesis. Patients with FLT3-ITD had a lower CR (complete remission) rate, lower 3-year OS (overall survival), DFS (disease-free survival), and EFS (event-free survival) compared to FLT3wtAML. NK-AML with FLT3-ITD had a lower 3-year OS, DFS, and EFS than those without, while FLT3-TKD did not influence the survival in whole cohort and NK-AML. Besides, we found that FLT3-ITD/TET2 bimutation defined a poor prognostic subgroup. Conclusions Our study offers deep insights into the molecular pathogenesis and biology of AML with FLT3-ITD and FLT3-TKD by providing the profiles of concurrent molecular alterations and the clinical impact of FLT3-ITD and FLT3-TKD on AML patients.
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Affiliation(s)
- Wei Guan
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Lei Zhou
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Yan Li
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.,Department of Hematology, Peking University Third Hospital, 49 North Garden Road, Beijing, 100191, China
| | - Erna Yang
- Department of Hematology and Oncology, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Carlson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, 1098 Xueyuan AVE, Shenzhen, 518060, China
| | - Yangyang Liu
- Beijing USCI Medical Laboratory Co., Ltd, Beijing, China
| | - Na Lv
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.,Department of Hematology and Oncology, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Carlson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, 1098 Xueyuan AVE, Shenzhen, 518060, China
| | - Lin Fu
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Yi Ding
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Nan Wang
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Nan Fang
- Beijing USCI Medical Laboratory Co., Ltd, Beijing, China
| | - Qian Liu
- Beijing USCI Medical Laboratory Co., Ltd, Beijing, China
| | - Binan Wang
- Beijing USCI Medical Laboratory Co., Ltd, Beijing, China
| | - Fuwei Li
- Beijing USCI Medical Laboratory Co., Ltd, Beijing, China
| | - Juan Zhang
- Beijing USCI Medical Laboratory Co., Ltd, Beijing, China
| | - Maoquan Wang
- School of Medicine, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Lili Wang
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Yu Jing
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Yonghui Li
- Department of Hematology and Oncology, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Carlson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, 1098 Xueyuan AVE, Shenzhen, 518060, China
| | - Li Yu
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China. .,Department of Hematology and Oncology, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Carlson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, 1098 Xueyuan AVE, Shenzhen, 518060, China.
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10
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Yang F, Anekpuritanang T, Press RD. Clinical Utility of Next-Generation Sequencing in Acute Myeloid Leukemia. Mol Diagn Ther 2021; 24:1-13. [PMID: 31848884 DOI: 10.1007/s40291-019-00443-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acute myeloid leukemia (AML) is a genetically heterogeneous disease that, even with current advancements in therapy, continues to have a poor prognosis. Recurrent somatic mutations have been identified in a core set of pathogenic genes including FLT3 (25-30% prevalence), NPM1 (25-30%), DNMT3A (25-30%), IDH1/2 (5-15%), and TET2 (5-15%), with direct diagnostic, prognostic, and targeted therapeutic implications. Advances in the understanding of the complex mechanisms of AML leukemogenesis have led to the development and recent US Food and Drug Administration (FDA) approval of several targeted therapies: midostaurin and gilteritinib targeting activated FLT3, and ivosidenib and enasidenib targeting mutated IDH1/2. Several additional drug candidates targeting other recurrently mutated gene pathways in AML are also being actively developed. Furthermore, outside of the realm of predicting responses to targeted therapies, many other mutated genes, which comprise the so-called long tail of oncogenic drivers in AML, have been shown to provide clinically useful diagnostic and prognostic information for AML patients. Many of these recurrently mutated genes have also been shown to be excellent biomarkers for post-treatment minimal residual disease (MRD) monitoring for assessing treatment response and predicting future relapse. In addition, the identification of germline mutations in a set of genes predisposing to myeloid malignancies may directly inform treatment decisions (particularly stem cell transplantation) and impact other family members. Recent advances in sequencing technology have made it practically and economically feasible to evaluate many genes simultaneously using next-generation sequencing (NGS). Mutation screening with NGS panels has been recommended by national and international professional guidelines as the standard of care for AML patients. NGS-based detection of the heterogeneous genes commonly mutated in AML has practical clinical utility for disease diagnosis, prognosis, prediction of targeted therapy response, and MRD monitoring.
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Affiliation(s)
- Fei Yang
- Department of Pathology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, L113, Portland, OR, 97239, USA.,Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Tauangtham Anekpuritanang
- Department of Pathology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, L113, Portland, OR, 97239, USA.,Department of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Richard D Press
- Department of Pathology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, L113, Portland, OR, 97239, USA. .,Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.
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11
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Wilhelmson AS, Porse BT. CCAAT enhancer binding protein alpha (CEBPA) biallelic acute myeloid leukaemia: cooperating lesions, molecular mechanisms and clinical relevance. Br J Haematol 2020; 190:495-507. [PMID: 32086816 PMCID: PMC7496298 DOI: 10.1111/bjh.16534] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recent advances in sequencing technologies have allowed for the identification of recurrent mutations in acute myeloid leukaemia (AML). The transcription factor CCAAT enhancer binding protein alpha (CEBPA) is frequently mutated in AML, and biallelic CEBPA-mutant AML was recognised as a separate disease entity in the recent World Health Organization classification. However, CEBPA mutations are co-occurring with other aberrations in AML, and together these lesions form the clonal hierarchy that comprises the leukaemia in the patient. Here, we aim to review the current understanding of co-occurring mutations in CEBPA-mutated AML and their implications for disease biology and clinical outcome. We will put emphasis on patterns of cooperation, how these lesions cooperate with CEBPA mutations and the underlying potential molecular mechanisms. Finally, we will relate this to patient outcome and future options for personalised medicine.
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Affiliation(s)
- Anna S Wilhelmson
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.,Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bo T Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.,Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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12
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Xiong Q, Huang S, Li YH, Lv N, Lv C, Ding Y, Liu WW, Wang LL, Chen Y, Sun L, Zhao Y, Liao SY, Zhang MQ, Zhu BL, Yu L. Single‑cell RNA sequencing of t(8;21) acute myeloid leukemia for risk prediction. Oncol Rep 2020; 43:1278-1288. [PMID: 32323795 PMCID: PMC7057921 DOI: 10.3892/or.2020.7507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/22/2020] [Indexed: 12/12/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) of bone marrow or peripheral blood samples from patients with acute myeloid leukemia (AML) enables the characterization of heterogeneous malignant cells. A total of 87 cells from two patients with t(8;21) AML were analyzed using scRNA-seq. Clustering methods were used to separate leukemia cells into different sub-populations, and the expression patterns of specific marker genes were used to annotate these populations. Among the 31 differentially expressed genes in the cells of a patient who relapsed after hematopoietic stem cell transplantation, 13 genes were identified to be associated with leukemia. Furthermore, three genes, namely AT-rich interaction domain 2, lysine methyltransferase 2A and synaptotagmin binding cytoplasmic RNA interacting protein were validated as possible prognostic biomarkers using two bulk expression datasets. Taking advantage of scRNA-seq, the results of the present study may provide clinicians with several possible biomarkers to predict the prognostic outcomes of t(8;21) AML.
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Affiliation(s)
- Qian Xiong
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Sai Huang
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Yong-Hui Li
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Na Lv
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Chao Lv
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Yi Ding
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Wen-Wen Liu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Li-Li Wang
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Yang Chen
- School of Medicine, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, P.R. China
| | - Liang Sun
- School of Medicine, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, P.R. China
| | - Yi Zhao
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Sheng-You Liao
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Michael Q Zhang
- School of Medicine, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, P.R. China
| | - Bao-Li Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Li Yu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, P.R. China
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13
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Xu L, Durruthy-Durruthy R, Eastburn DJ, Pellegrino M, Shah O, Meyer E, Zehnder J. Clonal Evolution and Changes in Two AML Patients Detected with A Novel Single-Cell DNA Sequencing Platform. Sci Rep 2019; 9:11119. [PMID: 31366893 PMCID: PMC6668401 DOI: 10.1038/s41598-019-47297-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 07/08/2019] [Indexed: 12/25/2022] Open
Abstract
Next-generation sequencing (NGS) is used to detect gene variants in genetically complex cell populations of cancer patient samples. Traditional bulk analysis can only provide average variant allele frequencies of the targeted genes across all sampled cells. It fails to resolve mutational co-occurrences and may miss rare cancer cells. Genome analysis at the single cell level offers the opportunity to more fully resolve clonal architecture. Peripheral blood mononuclear cells were sampled from acute myeloid leukemia patients longitudinally and single-cell DNA sequencing libraries were generated with a novel droplet-based microfluidics approach. Molecular profiling of single nucleotide variants across thousands of cells revealed genetic chimerism in patients after bone marrow transplantation (BMT). Importantly, hierarchical clustering analysis of single nucleotide variants (SNVs) uncovered a distinct oncogenic clone of cells carrying mutated tumor-suppressor and/or oncogene(s). This novel single-cell DNA sequencing approach enabled precise monitoring of engraftment and revealed clonal evolution of oncogenic cells during the progression and treatment of the disease.
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Affiliation(s)
- Liwen Xu
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | | | | | | | - Omid Shah
- Division of Blood and Marrow Transplantation. Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Everett Meyer
- Division of Blood and Marrow Transplantation. Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - James Zehnder
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA.
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14
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Levy MA, Santos S, Kerkhof J, Stuart A, Aref‐Eshghi E, Guo F, Hedley B, Wong H, Rauh M, Feilotter H, Berardi P, Semenuk L, Yang P, Knoll J, Ainsworth P, McLachlin CM, Chin‐Yee I, Kovacs M, Deotare U, Lazo‐Langner A, Hsia C, Keeney M, Xenocostas A, Howlett C, Lin H, Sadikovic B. Implementation of an NGS‐based sequencing and gene fusion panel for clinical screening of patients with suspected hematologic malignancies. Eur J Haematol 2019; 103:178-189. [DOI: 10.1111/ejh.13272] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/27/2019] [Accepted: 06/03/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Michael A. Levy
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Stephanie Santos
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Erfan Aref‐Eshghi
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Fen Guo
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Ben Hedley
- Pathology and Laboratory Medicine London Health Sciences Centre London Ontario Canada
| | - Henry Wong
- Clinical Laboratories Kingston Health Sciences Centre Kingston Ontario Canada
| | - Michael Rauh
- Department of Pathology and Molecular Medicine Queen's University Kingston Ontario Canada
| | - Harriet Feilotter
- Department of Pathology and Molecular Medicine Queen's University Kingston Ontario Canada
- Molecular Diagnostics Kingston Health Sciences Centre Kingston Ontario Canada
| | - Philip Berardi
- University of Ottawa Ottawa Ontario Canada
- Eastern Ontario Regional Laboratory Association (EORLA) The Ottawa Hospital Ottawa Ontario Canada
| | - Laura Semenuk
- DNA Diagnostics & Cytogenetics Laboratory Kingston Health Sciences Centre Kingston Ontario Canada
| | - Ping Yang
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Cytogenetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Joan Knoll
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Peter Ainsworth
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
- Department of Biochemistry Western University London Ontario Canada
| | | | - Ian Chin‐Yee
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Michael Kovacs
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Uday Deotare
- Hematology Division London Health Sciences Centre London Ontario Canada
- Schulich School of Medicine and Dentistry Western University London Ontario Canada
- Departments of Medicine and Oncology London Health Sciences Centre London Ontario Canada
| | - Alejandro Lazo‐Langner
- Hematology Division London Health Sciences Centre London Ontario Canada
- Department of Epidemiology and Biostatistics Western University London Ontario Canada
| | - Cyrus Hsia
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Mike Keeney
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Anargyros Xenocostas
- Hematology Division London Health Sciences Centre London Ontario Canada
- Schulich School of Medicine and Dentistry Western University London Ontario Canada
| | - Christopher Howlett
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Hanxin Lin
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
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15
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Next Generation Sequencing in AML-On the Way to Becoming a New Standard for Treatment Initiation and/or Modulation? Cancers (Basel) 2019; 11:cancers11020252. [PMID: 30795628 PMCID: PMC6406956 DOI: 10.3390/cancers11020252] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/08/2019] [Accepted: 02/12/2019] [Indexed: 12/19/2022] Open
Abstract
Acute myeloid leukemia (AML) is a clonal disease caused by genetic abberations occurring predominantly in the elderly. Next generation sequencing (NGS) analysis has led to a deeper genetic understanding of the pathogenesis and the role of recently discovered genetic precursor lesions (clonal hematopoiesis of indeterminate/oncogenic potential (CHIP/CHOP)) in the evolution of AML. These advances are reflected by the inclusion of certain mutations in the updated World Health Organization (WHO) 2016 classification and current treatment guidelines by the European Leukemia Net (ELN) and National Comprehensive Cancer Network (NCCN) and results of mutational testing are already influencing the choice and timing of (targeted) treatment. Genetic profiling and stratification of patients into molecularly defined subgroups are expected to gain ever more weight in daily clinical practice. Our aim is to provide a concise summary of current evidence regarding the relevance of NGS for the diagnosis, risk stratification, treatment planning and response assessment in AML, including minimal residual disease (MRD) guided approaches. We also summarize recently approved drugs targeting genetically defined patient populations with risk adapted- and individualized treatment strategies.
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16
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Staudt D, Murray HC, McLachlan T, Alvaro F, Enjeti AK, Verrills NM, Dun MD. Targeting Oncogenic Signaling in Mutant FLT3 Acute Myeloid Leukemia: The Path to Least Resistance. Int J Mol Sci 2018; 19:ijms19103198. [PMID: 30332834 PMCID: PMC6214138 DOI: 10.3390/ijms19103198] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 02/07/2023] Open
Abstract
The identification of recurrent driver mutations in genes encoding tyrosine kinases has resulted in the development of molecularly-targeted treatment strategies designed to improve outcomes for patients diagnosed with acute myeloid leukemia (AML). The receptor tyrosine kinase FLT3 is the most commonly mutated gene in AML, with internal tandem duplications within the juxtamembrane domain (FLT3-ITD) or missense mutations in the tyrosine kinase domain (FLT3-TKD) present in 30–35% of AML patients at diagnosis. An established driver mutation and marker of poor prognosis, the FLT3 tyrosine kinase has emerged as an attractive therapeutic target, and thus, encouraged the development of FLT3 tyrosine kinase inhibitors (TKIs). However, the therapeutic benefit of FLT3 inhibition, particularly as a monotherapy, frequently results in the development of treatment resistance and disease relapse. Commonly, FLT3 inhibitor resistance occurs by the emergence of secondary lesions in the FLT3 gene, particularly in the second tyrosine kinase domain (TKD) at residue Asp835 (D835) to form a ‘dual mutation’ (ITD-D835). Individual FLT3-ITD and FLT3-TKD mutations influence independent signaling cascades; however, little is known about which divergent signaling pathways are controlled by each of the FLT3 specific mutations, particularly in the context of patients harboring dual ITD-D835 mutations. This review provides a comprehensive analysis of the known discrete and cooperative signaling pathways deregulated by each of the FLT3 specific mutations, as well as the therapeutic approaches that hold the most promise of more durable and personalized therapeutic approaches to improve treatments of FLT3 mutant AML.
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Affiliation(s)
- Dilana Staudt
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia.
- Priority Research Centre for Cancer Research, Innovation & Translation, Faculty of Health & Medicine, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia.
| | - Heather C Murray
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia.
- Priority Research Centre for Cancer Research, Innovation & Translation, Faculty of Health & Medicine, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia.
| | - Tabitha McLachlan
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia.
- Priority Research Centre for Cancer Research, Innovation & Translation, Faculty of Health & Medicine, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia.
| | - Frank Alvaro
- Priority Research Centre for Cancer Research, Innovation & Translation, Faculty of Health & Medicine, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia.
- John Hunter Children's Hospital, Faculty of Health and Medicine, University of Newcastle, New Lambton Heights, NSW 2305, Australia.
| | - Anoop K Enjeti
- Priority Research Centre for Cancer Research, Innovation & Translation, Faculty of Health & Medicine, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia.
- Calvary Mater Hospital, Hematology Department, Waratah, NSW 2298, Australia.
- NSW Health Pathology North, John Hunter Hospital, New Lambton Heights, NSW 2305, Australia.
| | - Nicole M Verrills
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia.
- Priority Research Centre for Cancer Research, Innovation & Translation, Faculty of Health & Medicine, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia.
| | - Matthew D Dun
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia.
- Priority Research Centre for Cancer Research, Innovation & Translation, Faculty of Health & Medicine, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia.
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17
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Mason EF, Kuo FC, Hasserjian RP, Seegmiller AC, Pozdnyakova O. A distinct immunophenotype identifies a subset of NPM1-mutated AML with TET2 or IDH1/2 mutations and improved outcome. Am J Hematol 2018; 93:504-510. [PMID: 29274134 DOI: 10.1002/ajh.25018] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 12/20/2017] [Indexed: 12/19/2022]
Abstract
Recent work has identified distinct molecular subgroups of acute myeloid leukemia (AML) with implications for disease classification and prognosis. NPM1 is one of the most common recurrently mutated genes in AML. NPM1 mutations often co-occur with FLT3-ITDs and mutations in genes regulating DNA methylation, such as DNMT3A, TET2, and IDH1/2. It remains unclear whether these genetic alterations are associated with distinct immunophenotypic findings or affect prognosis. We identified 133 cases of NPM1-mutated AML and correlated sequencing data with immunophenotypic and clinical findings. Of 84 cases (63%) that lacked monocytic differentiation ("myeloid AML"), 40 (48%) demonstrated an acute promyelocytic leukemia-like (APL-like) immunophenotype by flow cytometry, with absence of CD34 and HLA-DR and strong myeloperoxidase expression, in the absence of a PML-RARA translocation. Pathologic variants in TET2, IDH1, or IDH2 were identified in 39/40 APL-like cases. This subset of NPM1-mutated AML was associated with longer relapse-free and overall survival, when compared with cases that were positive for CD34 and/or HLA-DR. The combination of NPM1 and TET2 or IDH1/2 mutations along with an APL-like immunophenotype identifies a distinct subtype of AML. Further studies addressing its biology and clinical significance may be especially relevant in the era of IDH inhibitors and recent work showing efficacy of ATRA therapy in NPM1 and IDH1-mutated AML.
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Affiliation(s)
- Emily F. Mason
- Department of Pathology, Microbiology, and Immunology; Vanderbilt University Medical Center; Nashville Tennessee
| | - Frank C. Kuo
- Department of Pathology; Brigham and Women's Hospital, Harvard Medical School; Boston Massachusetts
| | - Robert P. Hasserjian
- Department of Pathology; Massachusetts General Hospital, Harvard Medical School; Boston Massachusetts
| | - Adam C. Seegmiller
- Department of Pathology, Microbiology, and Immunology; Vanderbilt University Medical Center; Nashville Tennessee
| | - Olga Pozdnyakova
- Department of Pathology; Brigham and Women's Hospital, Harvard Medical School; Boston Massachusetts
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18
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Wu S, Dai Y, Zhang Y, Wang X, Wang L, Ma D, Zhang L, Pang Y, Jiao Y, Niu M, Xu K, Ke X, Shi J, Cheng Z, Fu L. Mutational spectrum and prognostic stratification of intermediate-risk acute myeloid leukemia. Cancer Gene Ther 2018; 25:207-213. [PMID: 29904089 DOI: 10.1038/s41417-018-0028-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/04/2018] [Accepted: 05/10/2018] [Indexed: 02/05/2023]
Abstract
The mutational spectrum and prognostic stratification of intermediate-risk acute myeloid leukemia (IR-AML), which accounts for a substantial number of AML, are unclear. In order to explore the prognostic significance of the mutational spectrum in IR-AML, 106 IR-AML patients were collected from The Cancer Genome Atlas database. Sixty-two patients underwent chemotherapy-only, forty-four proceeded to allogeneic hematopoietic stem cell transplantation (allo-HSCT). Fifty-five patients had more than five recurrent genetic mutations. NPM1 had the highest mutation frequency, followed by DNMT3A, FLT3, RUNX1, IDH2, IDH1, and TET2. In all patients, allo-HSCT was an independent favorable factor for EFS and OS (P = 0.036, P = 0.001, respectively); age ≥60 years, FLT3-ITD and mutations in DNMT3A and RUNX1 were independent risk factors for survival (all P < 0.05). In the chemotherapy-only group, multivariate analysis showed that age ≥60 years was an independent risk factor for EFS and OS (P = 0.008, P = 0.017, respectively). In the allo-HSCT group, multivariate analysis indicated that MLL-PTD was an independent risk fact for EFS (P = 0.037), FLT3-ITD and RUNX1 mutations independently contributed to poor OS (P = 0.035, P = 0.014, respectively). In conclusion, older age was an important risk factor for IR-AML patients undergoing chemotherapy-only; FLT3-ITD, MLL-PTD and RUNX1 mutations were significant risk factors for IR-AML patients who received allo-HSCT.
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Affiliation(s)
- Sun Wu
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, 453100, China
| | - Yifeng Dai
- Laboratory of Environmental Medicine and Developmental Toxicology, Shantou University Medical College, Shantou, 515041, China
- Department of Pathology and Medical Biology, Immunoendocrinology, Division of Medical Biology, University Medical Center Groningen, Groningen, Netherlands
| | - Yuan Zhang
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, 453100, China
| | - Xiufeng Wang
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, 453100, China
| | - Lihua Wang
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, 453100, China
| | - Dong Ma
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, 453100, China
| | - Lingxiu Zhang
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, 453100, China
| | - Yifan Pang
- Department of Medicine, William Beaumont Hospital, Royal Oak, MI, 48073, USA
| | - Yang Jiao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, 310058, China
| | - Mingshan Niu
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Kailin Xu
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Xiaoyan Ke
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing, 100191, China
| | - Jinlong Shi
- Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, 475000, China
- Department of Biomedical Engineering, Chinese PLA General Hospital, Beijing, 100853, China
- Department of Medical Big Data, Chinese PLA General Hospital, Beijing, 100853, China
| | - Zhiheng Cheng
- Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, 475000, China.
| | - Lin Fu
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing, 100191, China
- Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, 475000, China
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19
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Wang S, Zhang YX, Huang T, Sui JN, Lu J, Chen XJ, Wang KK, Xi XD, Li JM, Huang JY, Chen B. Mutation profile and associated clinical features in Chinese patients with cytogenetically normal acute myeloid leukemia. Int J Lab Hematol 2018; 40:408-418. [PMID: 29573577 DOI: 10.1111/ijlh.12802] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/29/2018] [Indexed: 01/24/2023]
Affiliation(s)
- S. Wang
- State Key Laboratory of Medical Genomics; Shanghai Institute of Hematology; Rui Jin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine; Shanghai China
| | - Y.-X. Zhang
- State Key Laboratory of Medical Genomics; Shanghai Institute of Hematology; Rui Jin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine; Shanghai China
| | - T. Huang
- State Key Laboratory of Medical Genomics; Shanghai Institute of Hematology; Rui Jin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine; Shanghai China
| | - J.-N. Sui
- State Key Laboratory of Medical Genomics; Shanghai Institute of Hematology; Rui Jin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine; Shanghai China
| | - J. Lu
- State Key Laboratory of Medical Genomics; Shanghai Institute of Hematology; Rui Jin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine; Shanghai China
| | - X.-J. Chen
- State Key Laboratory of Medical Genomics; Shanghai Institute of Hematology; Rui Jin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine; Shanghai China
| | - K.-K. Wang
- State Key Laboratory of Medical Genomics; Shanghai Institute of Hematology; Rui Jin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine; Shanghai China
| | - X.-D. Xi
- State Key Laboratory of Medical Genomics; Shanghai Institute of Hematology; Rui Jin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine; Shanghai China
| | - J.-M. Li
- State Key Laboratory of Medical Genomics; Shanghai Institute of Hematology; Rui Jin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine; Shanghai China
| | - J.-Y. Huang
- State Key Laboratory of Medical Genomics; Shanghai Institute of Hematology; Rui Jin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine; Shanghai China
| | - B. Chen
- State Key Laboratory of Medical Genomics; Shanghai Institute of Hematology; Rui Jin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine; Shanghai China
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20
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Shin SY, Lee ST, Kim HJ, Cho EH, Kim JW, Park S, Jung CW, Kim SH. Mutation profiling of 19 candidate genes in acute myeloid leukemia suggests significance of DNMT3A mutations. Oncotarget 2018; 7:54825-54837. [PMID: 27359055 PMCID: PMC5342384 DOI: 10.18632/oncotarget.10240] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 05/13/2016] [Indexed: 11/25/2022] Open
Abstract
We selected 19 significantly-mutated genes in AMLs, including FLT3, DNMT3A, NPM1, TET2, RUNX1, CEBPA, WT1, IDH1, IDH2, NRAS, ASXL1, SETD2, PTPN11, TP53, KIT, JAK2, KRAS, BRAF and CBL, and performed massively parallel sequencing for 114 patients with acute myeloid leukemias, mainly including those with normal karyotypes (CN-AML). More than 80% of patients had at least one mutation in the genes tested. DNMT3A mutation was significantly associated with adverse outcome in addition to conventional risk stratification such as the European LeukemiaNet (ELN) classification. We observed clinical usefulness of mutation testing on multiple target genes and the association with disease subgroups, clinical features and prognosis in AMLs.
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Affiliation(s)
- Sang-Yong Shin
- Department of Laboratory Medicine, Center for Diagnostic Oncology, Hospital and Research Institute, National Cancer Center, Goyang, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Hee-Jin Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Jong-Won Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Silvia Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Chul Won Jung
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sun-Hee Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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21
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Saygin C, Hirsch C, Przychodzen B, Sekeres MA, Hamilton BK, Kalaycio M, Carraway HE, Gerds AT, Mukherjee S, Nazha A, Sobecks R, Goebel C, Abounader D, Maciejewski JP, Advani AS. Mutations in DNMT3A, U2AF1, and EZH2 identify intermediate-risk acute myeloid leukemia patients with poor outcome after CR1. Blood Cancer J 2018; 8:4. [PMID: 29321554 PMCID: PMC5802549 DOI: 10.1038/s41408-017-0040-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 08/01/2017] [Accepted: 08/08/2017] [Indexed: 12/11/2022] Open
Abstract
Intermediate-risk acute myeloid leukemia (IR-AML) is a clinically heterogeneous disease, for which optimal post-remission therapy is debated. The utility of next-generation sequencing information in decision making for IR-AML has yet to be elucidated. We retrospectively studied 100 IR-AML patients, defined by European Leukemia Net classification, who had mutational information at diagnosis, received intensive chemotherapy and achieved complete remission (CR) at Cleveland Clinic (CC). The Cancer Genome Atlas (TCGA) data were used for validation. In the CC cohort, median age was 58.5 years, 64% had normal cytogenetics, and 31% required >1 induction cycles to achieve CR1. In univariable analysis, patients carrying mutations in DNMT3A, U2AF1, and EZH2 had worse overall and relapse-free survival. After adjusting for other variables, the presence of these mutations maintained an independent effect on survival in both CC and TCGA cohorts. Patients who did not have the mutations and underwent hematopoietic cell transplant (HCT) had the best outcomes. HCT improved outcomes for patients who had these mutations. RUNX1 or ASXL1 mutations did not predict survival, and performance of HCT did not confer a significant survival benefit. Our results provide evidence of clinical utility in considering mutation screening to stratify IR-AML patients after CR1 to guide therapeutic decisions.
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Affiliation(s)
- Caner Saygin
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Cassandra Hirsch
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Bartlomiej Przychodzen
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mikkael A Sekeres
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Betty K Hamilton
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Matt Kalaycio
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hetty E Carraway
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Aaron T Gerds
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Sudipto Mukherjee
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Aziz Nazha
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ronald Sobecks
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Christopher Goebel
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Donna Abounader
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jaroslaw P Maciejewski
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Anjali S Advani
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
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22
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Han X, Li W, He N, Feng P, Pang Y, Ji C, Ma D. Gene mutation patterns of Chinese acute myeloid leukemia patients by targeted next-generation sequencing and bioinformatic analysis. Clin Chim Acta 2018; 479:25-37. [PMID: 29309772 DOI: 10.1016/j.cca.2018.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 12/31/2017] [Accepted: 01/04/2018] [Indexed: 12/20/2022]
Abstract
PURPOSES The conventional risk stratification of acute myeloid leukemia (AML), based on cytogenetics, cannot meet the demand for accurate prognostic evaluations. In recent years, gene mutations are found to be potential markers for more accurate risk stratification, but reports on mutation screening of Chinese AML are limited. We aim to display the mutation patterns of Chinese AML patients, reveal the genotype-phenotype correlations and make a comparison with Caucasians patients. METHODS Genome DNA from 78 patients' bone marrow were extracted for targeted gene mutation panel by next-generation sequencing (NGS) technology. Statistics and bioinformatics were used to analyze the correlations between gene mutations and clinical features, as well as the comparison of our results with the Cancer Genome Atlas Research Network (TCGA) public AML dataset. RESULTS We found patients with mutations of FLT3 and TET2 had higher bone marrow blasts, peripheral blasts and white blood cell (WBC) count, mutations of SRSF2 were related with age, and mutations of FLT3-ITD, DNMT3A, IDH1, TET2 and SRSF2 were risk factors for overall survival. What's more, we discovered 15 novel mutations and difference of mutational incidence in 6 genes between Chinese and Caucasians AML. Bioinformatic analysis revealed some relationship between gene mutations and expressions as well as drug sensitivities. CONCLUSIONS We made an investigation on the mutation patterns of Chinese AML patients by NGS technique and revealed correlations between gene mutations and clinical features. Thus we recommend routine testing of suspected genes for better prognostic prediction and individualized treatment.
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Affiliation(s)
- Xiaoyu Han
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, PR China
| | - Wei Li
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, PR China
| | - Na He
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, PR China
| | - Panpan Feng
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, PR China
| | - Yihua Pang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, PR China
| | - Chunyan Ji
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, PR China.
| | - Daoxin Ma
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, PR China.
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23
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Su L, Tan Y, Lin H, Liu X, Yu L, Yang Y, Liu S, Bai O, Yang Y, Jin F, Sun J, Liu C, Liu Q, Gao S, Li W. Mutational spectrum of acute myeloid leukemia patients with double CEBPA mutations based on next-generation sequencing and its prognostic significance. Oncotarget 2018; 9:24970-24979. [PMID: 29861846 PMCID: PMC5982761 DOI: 10.18632/oncotarget.23873] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 12/27/2017] [Indexed: 11/25/2022] Open
Abstract
The aim of this study was to profile the spectrum of genetic mutations in acute myeloid leukemia (AML) patients co-occurring with CEBPA double mutation (CEBPAdm). Between January 1, 2012, and June 30, 2017, 553 consecutive patients with de novo AML were screened for CEBPA mutations. Out of these, 81 patients classified as CEBPAdm were analyzed further by a sensitive next-generation sequencing assay for mutations in 112 candidate genes. Within the CEBPA gene itself, we found 164 mutations. The most common mutated sites were c.936_937insGAG (n = 11/164, 6.71%) and c.939_940insAAG (n = 11/164, 6.71%), followed by c.68dupC (n = 10/164, 6.10%). The most common co-occurring mutations were found in the CSF3R (n = 16/81, 19.75%), WT1 (n = 15/81, 18.52%), and GATA2 (n = 13/81, 16.05%) genes. Patients with CSF3R mutations had an inferior four-year relapse-free survival (RFS) than those with the wild-type gene (15.3% versus 46.8%, respectively; P = 0.021). Patients with WT1 mutations had an inferior five-year RFS compared with those without such mutations (0% versus 26.6%, respectively, P = 0.003). However, GATA2, CSF3R, WT1 mutations had no significant influence on the overall survival. There were some differences in the location of mutational hotspots within the CEBPA gene, as well as hotspots of other co-occurring genetic mutations, between AML patients from Chinese and Caucasian populations. Some co-occurring mutations may be potential candidates for refining the prognoses of AML patients with CEBPAdm in the Chinese population.
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Affiliation(s)
- Long Su
- Department of Hematology, The First Hospital, Jilin University, Changchun, China
| | - YeHui Tan
- Department of Hematology, The First Hospital, Jilin University, Changchun, China
| | - Hai Lin
- Department of Hematology, The First Hospital, Jilin University, Changchun, China
| | - XiaoLiang Liu
- Department of Hematology, The First Hospital, Jilin University, Changchun, China
| | - Li Yu
- Department of Hematology, Chinese PLA General Hospital, Peking, China
| | - YanPing Yang
- Department of Hematology, The First Hospital, Jilin University, Changchun, China
| | - ShanShan Liu
- Department of Hematology, The First Hospital, Jilin University, Changchun, China
| | - Ou Bai
- Department of Hematology, The First Hospital, Jilin University, Changchun, China
| | - Yan Yang
- Department of Hematology, The First Hospital, Jilin University, Changchun, China
| | - FengYan Jin
- Department of Hematology, The First Hospital, Jilin University, Changchun, China
| | - JingNan Sun
- Department of Hematology, The First Hospital, Jilin University, Changchun, China
| | - ChunShui Liu
- Department of Hematology, The First Hospital, Jilin University, Changchun, China
| | - QiuJu Liu
- Department of Hematology, The First Hospital, Jilin University, Changchun, China
| | - SuJun Gao
- Department of Hematology, The First Hospital, Jilin University, Changchun, China
| | - Wei Li
- Department of Hematology, The First Hospital, Jilin University, Changchun, China
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24
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Lin N, Fu W, Zhao C, Li B, Yan X, Li Y. Biologico-clinical significance of DNMT3A variants expression in acute myeloid leukemia. Biochem Biophys Res Commun 2017; 494:270-277. [DOI: 10.1016/j.bbrc.2017.10.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 10/07/2017] [Indexed: 12/20/2022]
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25
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Xu Y, Li Y, Xu Q, Chen Y, Lv N, Jing Y, Dou L, Bo J, Hou G, Guo J, Wang X, Wang L, Li Y, Chen C, Yu L. Implications of mutational spectrum in myelodysplastic syndromes based on targeted next-generation sequencing. Oncotarget 2017; 8:82475-82490. [PMID: 29137279 PMCID: PMC5669905 DOI: 10.18632/oncotarget.19628] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 06/30/2017] [Indexed: 02/01/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of myeloid hematological malignancies, with a high risk of progression to acute myeloid leukemia (AML). To explore the role of acquired mutations in MDS, 111 MDS-associated genes were screened using next-generation sequencing (NGS), in 125 patients. One or more mutations were detected in 84% of the patients. Some gene mutations are specific for MDS and were associated with disease subtypes, and the patterns of mutational pathways could be associated with progressive MDS. The patterns, frequencies and functional pathways of gene mutations are different, but somehow related, between MDS and AML. Multivariate analysis suggested that patients with ≥ 2 mutations had poor progression-free survival, while GATA1/GATA2, DNMT3A and KRAS/NRAS mutations were associated with poor overall survival. Based on a novel system combining IPSS-R and molecular markers, these MDS patients were further divided into 3 more accurate prognostic subgroups. A panel of 11 target genes was proposed for genetic profiling of MDS. The study offers new insights into the molecular signatures of MDS and the genetic consistency between MDS and AML. Furthermore, results indicate that MDS could be classified by mutation combinations to guide the administration of individualized therapeutic interventions.
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Affiliation(s)
- Yuanyuan Xu
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, Hainan Branch of Chinese PLA General Hospital, Sanya 572013, Hainan Province, China
| | - Yan Li
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, Hainan Branch of Chinese PLA General Hospital, Sanya 572013, Hainan Province, China
| | - Qingyu Xu
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Medical school of Nankai University, Tianjin 300071, China
| | - Yuelong Chen
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Na Lv
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yu Jing
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Liping Dou
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Jian Bo
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Guangyuan Hou
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Jing Guo
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Xiuli Wang
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Lili Wang
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yonghui Li
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | | | - Li Yu
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, General Hospital of Shenzhen University, Shenzhen 518060, China
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26
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Xu Q, Li Y, Lv N, Jing Y, Xu Y, Li Y, Li W, Yao Z, Chen X, Huang S, Wang L, Li Y, Yu L. Correlation Between Isocitrate Dehydrogenase Gene Aberrations and Prognosis of Patients with Acute Myeloid Leukemia: A Systematic Review and Meta-Analysis. Clin Cancer Res 2017; 23:4511-4522. [PMID: 28246275 DOI: 10.1158/1078-0432.ccr-16-2628] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/23/2016] [Accepted: 02/22/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Whether isocitrate dehydrogenase (IDH) gene aberrations affected prognosis of patients with acute myeloid leukemia (AML) was controversial. Here, we conducted a meta-analysis to evaluate their prognostic value.Experimental Design: PubMed, Embase, Cochrane, and Chinese databases were searched to identify studies exploring how IDH gene aberrations affected AML outcome. Pooled HRs and relative risks (RR) were calculated, along with 95% confidence intervals (CI).Results: Thirty-three reports were included. IDH mutations seemed not to affect overall survival (OS: HR, 1.05; 95% CI, 0.89-1.23) and event-free survival (EFS: HR, 0.97; 95% CI, 0.80-1.18) when considered as a single factor, but improved accumulative incidence of relapse (CIR: HR, 1.44; 95% CI, 1.18-1.76) in patients with intermediate-risk karyotypes (IR-AML). However, IDH1 mutation conferred worse OS (HR, 1.17; 95% CI, 1.05-1.31) and EFS (HR, 1.29; 95% CI, 1.07-1.56), especially in patients with normal cytogenetics (OS: HR, 1.21; 95% CI, 1.01-1.46; EFS: HR, 1.56; 95% CI, 1.23-1.98). Prognosis of the IDH1 single-nucleotide polymorphism rs11554137 was also poor (OS: HR, 1.34; 95% CI, 1.03-1.75). IDH2 mutation improved OS (HR, 0.78; 95% CI, 0.66-0.93), particularly in IR-AML patients (OS: HR, 0.65; 95% CI, 0.49-0.86). The IDH2 (R140) mutation was associated with better OS among younger cases (HR, 0.64; 95% CI, 0.49-0.82). Treatment outcome was poor [RR for complete remission rates in IDH1 mutation: 1.21; 95% CI, 1.02-1.44; IDH2 (R172) mutation: 2.14; 95% CI, 1.61-2.85].Conclusions: Various subtypes of IDH mutations might contribute to different prognosis and be allowed to stratify IR-AML further. Clin Cancer Res; 23(15); 4511-22. ©2017 AACR.
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Affiliation(s)
- Qingyu Xu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing, China.,Medical School of Nankai University, Tianjin, China
| | - Yan Li
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing, China
| | - Na Lv
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing, China
| | - Yu Jing
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing, China
| | - Yihan Xu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing, China
| | - Yuyan Li
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing, China
| | - Wenjun Li
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing, China
| | - Zilong Yao
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing, China
| | - Xiaosu Chen
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing, China.,Medical School of Nankai University, Tianjin, China
| | - Sai Huang
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing, China
| | - Lili Wang
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing, China
| | - Yonghui Li
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing, China
| | - Li Yu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing, China.
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