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Chen X, Tian C, Hao Z, Pan L, Hong M, Wei W, Muyey DM, Wang H, Chen X. The impact of DNMT3A variant allele frequency and two different comutations on patients with de novo cytogenetically normal acute myeloid leukemia. Cancer Med 2023; 12:10340-10350. [PMID: 36912186 DOI: 10.1002/cam4.5764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 03/14/2023] Open
Abstract
To refine the biological and prognostic significance of DNMT3A mutations in acute myeloid leukemia (AML), we assessed the impact of DNMT3A variant allele frequency (VAF) and its comutations in this study. Using targeted next-generation sequencing, we analyzed 171 adult patients with de novo cytogenetically normal AML for DNMT3A mutations and associated comutations. DNMT3Amut was detected in 35 patients. DNMT3Amut patients were divided into DNMT3AHigh and DNMT3ALow using a cut-off VAF value of 42%. We observed that DNMT3AHigh patients at diagnosis had increasing white blood cell (WBC) counts (p < 0.001) and a higher lactate dehydrogenase (LDH) level (p = 0.027), and were associated with lower complete remission (CR) rate (p = 0.015) and shorter overall survival (OS) (p = 0.032) than DNMT3ALow patients. We classified two different comutated genetypes, including DNMT3Amut NPM1mut FLT3-ITDmut and DNMT3Amut IDH1/IDH2mut . Patients with DNMT3Amut NPM1mut FLT3-ITDmut showed worse OS (p = 0.026) and relapse-free survival (RFS) (p = 0.003) than those with DNMT3Amut IDH1/IDH2mut , and showed a shorter OS (p = 0.027) than those with DNMT3Awt NPM1mut FLT3-ITDmut . We also observed that patients with DNMT3Amut IDH1/IDH2mut had higher platelet counts (p = 0.009) and a lower BM blast percentage (p = 0.040) than those with DNMT3Awt IDH1/IDH2mut . In multivariate analyses, DNMT3AHigh was independently associated with a lower CR rate (OR = 5.883; p = 0.004) and shorter OS (HR = 3.768; p < 0.001). DNMT3Amut NPM1mut FLT3-ITDmut independently affected worse OS (HR = 6.030; p < 0.001) and RFS (HR = 8.939; p < 0.001). Our findings might be potentially useful for predicting clinical outcomes.
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Affiliation(s)
- Xian Chen
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China.,Department of Genetic Medicine, Shanxi Medical University, Jinzhong, China
| | - Chuchu Tian
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Zhuanghui Hao
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Lingang Pan
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Minglin Hong
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Wei Wei
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Daniel Muteb Muyey
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Hongwei Wang
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Xiuhua Chen
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
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Zhang YW, Su L, Tan YH, Lin H, Liu XL, Liu QJ, Sun JN, Zhang M, Du YZ, Song F, Han W, Gao SJ. Measurable residual disease detected by flow cytometry independently predicts prognoses of NPM1-mutated acute myeloid leukemia. Ann Hematol 2023; 102:337-347. [PMID: 36378304 DOI: 10.1007/s00277-022-05033-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022]
Abstract
Acute myeloid leukemia (AML) with NPM1 mutation is a distinct genetic entity with favorable outcomes. Nevertheless, emerging evidence suggests that NPM1-mutated AML is still a highly heterogeneous disorder. In this study, 266 patients with AML with NPM1 mutations were retrospectively analyzed to evaluate the associations between variant allele frequency (VAF) of NPM1 mutations, co-mutated genes, measurable residual disease (MRD), and patient outcomes. Multiparameter flow cytometry (MFC) and real-time quantitative polymerase chain reaction (RT-PCR) were used for monitoring MRD. Ultimately, 106 patients were included in the long-term follow-up period. Patients with high NPM1 VAF (≥ 42.43%) had poorer 2-year relapse-free survival (RFS) (55.7% vs. 70.2%, P = 0.017) and overall survival (OS) (63.7% vs. 82.0%, P = 0.027) than those with low VAF. DNMT3A mutations negatively influenced the outcomes of patients with NPM1 mutations. Patients with high DNMT3A VAF or NPM1/DNMT3A/FLT3-ITD triple mutations had shorter RFS and significantly lower OS than that in controls. After two cycles of chemotherapy, patients with positive MFC MRD results had lower RFS (MRD+ vs. MRD-:44.9% vs. 67.6%, P = 0.007) and OS (61.5% vs. 76.6%, P = 0.011) than those without positive MFC MRD results. In multivariate analysis, high NPM1 VAF (hazard ratio [HR] = 2.045; P = 0.034) and positive MRD after two cycles of chemotherapy (HR = 3.289; P = 0.003) were independent risk factors for RFS; MRD positivity after two cycles of chemotherapy (HR = 3.293; P = 0.008) independently predicted the OS of the patients. These results indicate that VAF of both NPM1 gene itself or certain co-occurring gene pre-treatment and MRD post-treatment are potential markers for restratifying the prognoses of patients AML having NPM1 mutations.
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Affiliation(s)
- Yun-Wei Zhang
- Hematology Department, First Hospital of Jilin University, Changchun, 130021, China
| | - Long Su
- Hematology Department, First Hospital of Jilin University, Changchun, 130021, China
| | - Ye-Hui Tan
- Hematology Department, First Hospital of Jilin University, Changchun, 130021, China
| | - Hai Lin
- Hematology Department, First Hospital of Jilin University, Changchun, 130021, China
| | - Xiao-Liang Liu
- Hematology Department, First Hospital of Jilin University, Changchun, 130021, China
| | - Qiu-Ju Liu
- Hematology Department, First Hospital of Jilin University, Changchun, 130021, China
| | - Jing-Nan Sun
- Hematology Department, First Hospital of Jilin University, Changchun, 130021, China
| | - Ming Zhang
- Hematology Department, First Hospital of Jilin University, Changchun, 130021, China
| | - Ya-Zhe Du
- Hematology Department, First Hospital of Jilin University, Changchun, 130021, China
| | - Fei Song
- Hematology Department, First Hospital of Jilin University, Changchun, 130021, China
| | - Wei Han
- Hematology Department, First Hospital of Jilin University, Changchun, 130021, China
| | - Su-Jun Gao
- Hematology Department, First Hospital of Jilin University, Changchun, 130021, China.
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Nauheim D, Moskal D, Renslo B, Chadwick M, Jiang W, Yeo CJ, Nevler A, Bowne W, Lavu H. KRAS mutation allele frequency threshold alters prognosis in right-sided resected pancreatic cancer. J Surg Oncol 2022; 126:314-321. [PMID: 35333412 DOI: 10.1002/jso.26860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/18/2022] [Accepted: 03/05/2022] [Indexed: 12/17/2022]
Abstract
BACKGROUND Next-generation sequencing (NGS) provides information on genetic mutations and mutant allele frequency in tumor specimens. We investigated the prognostic significance of KRAS mutant allele frequency in patients with right-sided pancreatic ductal adenocarcinoma (PDAC) treated with surgical resection. METHODS A retrospective study reviewed patients who underwent surgical resection for PDAC and analyzed tumors with an in-house mutational panel. Microdissected samples were studied using an NGS-based assay to detect over 200 hotspot mutations in 42 genes (Pan42) commonly involved in PDAC. RESULTS A total of 144 PDAC right-sided surgical patients with a Pan42 panel were evaluated between 2015 and 2020; 121 patients (84%) harbored a KRAS mutation. Detected mutant allele frequencies were categorized as less than 20% (low mKRAS, n = 92) or greater than or equal to 20% (high mKRAS, n = 29). High mKRAS (KRAS ≥ 20%) patients were noted to have shorter disease-free survival after surgery (11.5 ± 2.1 vs. 19.5 ± 3.5 months, p = 0.03), more advanced tumor stage (p = 0.02), larger tumors (3.6 vs. 2.7 cm, p = 0.001), greater tumor cellularity (26% vs. 18%, p = 0.001), and higher rate of distant recurrence (p = 0.03) than low mKRAS patients. CONCLUSION This study demonstrates the importance of KRAS mutant allele frequency on pathological characteristics and prognosis in right-sided PDAC treated with surgery.
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Affiliation(s)
- David Nauheim
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - David Moskal
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Bryan Renslo
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Matthew Chadwick
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Wei Jiang
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Charles J Yeo
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Avinoam Nevler
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Wilbur Bowne
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Harish Lavu
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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Effect of DNMT3A variant allele frequency and double mutation on clinicopathologic features of patients with de novo AML. Blood Adv 2021; 5:2539-2549. [PMID: 34100902 DOI: 10.1182/bloodadvances.2021004250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 04/11/2021] [Indexed: 12/18/2022] Open
Abstract
The clinicopathologic features of DNA methyltransferase 3A (DNMT3A)-mutated de novo acute myeloid leukemia (AML), and the significance of variant type, variant allele frequency (VAF), and multiple concomitant DNMT3A mutations, remain poorly defined. We examined 104 DNMT3A-mutated de novo AML patients from 2 major centers. Most (82%) had normal karyotype (NK); R882H variants were frequent(38%). The most commonly comutated genes included nucleophosmin (NPM1; 53%), Fms-related tyrosine kinase 3 (FLT3)-internal tandem duplication (25%), IDH1 (23%), IDH2 (23%), and TET2 (21%). Patients with high DNMT3A VAF at diagnosis (≥44%; DNMT3AHIGH) had more significant leukocytosis and higher blast counts in peripheral blood and bone marrow. DNMT3AHIGH cases were associated with much shorter event-free survival (EFS; 14.1 vs 56.8 months) and overall survival (OS; 18.3 months vs not reached) compared with cases of patients with low DNMT3A (DNMT3ALOW). Thirteen patients had 2 DNMT3A variants and similar VAFs at diagnosis that tracked together at multiple time points after chemotherapy and/or stem cell transplantation (SCT). In multivariable analyses performed in NK patients who received standard induction chemotherapy, presence of 2 DNMT3A mutations (hazard ratio [HR] = 3.192; P = .038) and SCT in first complete remission (HR = 0.295; P = .001) independently affected EFS; increasing marrow blast percentage (HR = 1.026; P = .025), high DNMT3A VAF (HR = 3.003; P = .010), and 2 DNMT3A mutations (HR = 4.816; P = .020) had independent effects on OS. These data support the adverse prognostic significance of DNMT3AHIGH reveal a novel association between 2 concomitant DNMT3A mutations and inferior outcome in DNMT3A-mutated de novo AML with a NK.
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Dai YJ, Hu F, He SY, Wang YY. Epigenetic landscape analysis of lncRNAs in acute myeloid leukemia with DNMT3A mutations. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:318. [PMID: 32355762 PMCID: PMC7186694 DOI: 10.21037/atm.2020.02.143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background Acute myeloid leukemia (AML) is a type of cancer that consists of a group of hematological malignancies with high heterogeneity. DNA methyltransferase 3A (DNMT3A)-mutated AML patients have a poor prognosis. Some long non-coding RNAs (lncRNAs) have been reported to enhance therapeutic sensitivity, and so could affect the overall survival rate of elderly cytogenetically normal acute myeloid leukemia (CN-AML) patients; however, studies on the lncRNA signature in DNMT3A-mutated AML are rare. Method The DNMT3A R878H conditional knock-in mouse model was constructed to explore the lncRNAs of DNMT3A mutation by using the Cuffcomparison method. Cis and trans regulation networks were used to predict candidate genes. The expression levels in leukemic cell lines and the prognostic index of these candidate genes were analyzed with the Broad Institute Cancer Cell Line Encyclopedia (CCLE) and OncoLnc databases. The data for each sample were statistically analyzed using GraphPad Prism. Results In this study, we applied the DNMT3A R878H conditional knock-in mouse model to explore the lncRNA epigenetic landscape of DNMT3A mutation by using the Cuffcomparison method. Twenty-three differentially expressed lncRNAs were identified in Dnmt3aR878H/WTMx1-Cre+ mice. We next predicted the downstream targetable genes regulated by these lncRNAs through cis and trans regulation networks and found 124 candidate genes are related to these lncRNAs. In further analysis of 124 genes, we found that increased mRNA expression levels of interleukin 1 receptor type 2 (IL1R2), Krüppel-like factor 13 (KLF13), ATPase H+ transporting V1 subunit A (ATP6V1A), proteasome 26S Subunit, non-ATPase 3 (PSMD3), and pyrroline-5-carboxylate reductase 2 (PYCR2) were associated with poor prognosis in AML. Functional analysis of these genes demonstrated that the pathways involved in autophagy, cell cycle, and hematopoietic stem cell differentiation were more enriched in Dnmt3aR878H/WTMx1-Cre+ mice. Conclusion Our study was the first to use DNMT3A R878H conditional knock-in mouse model to predict the specific lncRNAs regulated by the DNMT3A mutation in AML. Six candidate genes were found to be associated with DNMT3A mutation with poor prognosis. Our results provided a possible treatment strategy for this disease.
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Affiliation(s)
- Yu-Jun Dai
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510000, China.,Center State Key Laboratory of Oncology in South China, Guangzhou 510000, China.,Collaborative Innovation Center for Cancer Medicine, Guangzhou 510000, China
| | - Fang Hu
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510000, China.,Center State Key Laboratory of Oncology in South China, Guangzhou 510000, China.,Collaborative Innovation Center for Cancer Medicine, Guangzhou 510000, China
| | - Si-Yuan He
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Yue-Ying Wang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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