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Johnson SM, Haberberger J, Galeotti J, Ramkissoon L, Coombs CC, Richardson DR, Foster MC, Duncan D, Montgomery ND, Ferguson NL, Zeidner JF. Comprehensive genomic profiling reveals molecular subsets of ASXL1-mutated myeloid neoplasms. Leuk Lymphoma 2024; 65:209-218. [PMID: 37921062 DOI: 10.1080/10428194.2023.2277672] [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: 07/11/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023]
Abstract
A large-scale genomic analysis of patients with ASXL1-mutated myeloid disease has not been performed to date. We reviewed comprehensive genomic profiling results from 6043 adults to characterize clinicopathologic features and co-mutation patterns by ASXL1 mutation status. ASXL1 mutations occurred in 1414 patients (23%). Mutation co-occurrence testing revealed strong co-occurrence (p < 0.01) between mutations in ASXL1 and nine genes (SRSF2, U2AF1, RUNX1, SETBP1, EZH2, STAG2, CUX1, CSF3R, CBL). Further analysis of patients with these co-mutations yielded several novel findings. Co-mutation patterns supported that ASXL1/SF3B1 co-mutation may be biologically distinct from ASXL1/non-SF3B1 spliceosome co-mutation. In AML, ASXL1/SRSF2 co-mutated patients frequently harbored STAG2 mutations (42%), which were dependent on the presence of both ASXL1 and SRSF2 mutation (p < 0.05). STAG2 and SETBP1 mutations were also exclusive in ASXL1/SRSF2 co-mutated patients and associated with divergent chronic myeloid phenotypes. Our findings support that certain multi-mutant genotypes may be biologically relevant in ASXL1-mutated myeloid disease.
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Affiliation(s)
- Steven M Johnson
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | | | - Jonathan Galeotti
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Lori Ramkissoon
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Catherine C Coombs
- Division of Hematology, Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- UC Irvine, Irvine, CA, USA
| | - Daniel R Richardson
- Division of Hematology, Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Matthew C Foster
- Division of Hematology, Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Novartis Pharmaceuticals, Cambridge, MA, USA
| | - Daniel Duncan
- Foundation Medicine, Inc, Cambridge, MA, USA
- GRAIL, Inc, Durham, NC, USA
| | - Nathan D Montgomery
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- NeoGenomics Laboratories, Aliso Viejo, CA, USA
| | | | - Joshua F Zeidner
- Division of Hematology, Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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2
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Sheikhi M, Rostami M, Ferns G, Ayatollahi H, Siyadat P, Ayatollahi Y, Khoshnegah Z. Prognostic significance of ASXL1 mutations in acute myeloid leukemia: A systematic review and meta-analysis. CASPIAN JOURNAL OF INTERNAL MEDICINE 2024; 15:202-214. [PMID: 38807730 PMCID: PMC11129077 DOI: 10.22088/cjim.15.2.202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 01/18/2023] [Accepted: 02/26/2023] [Indexed: 05/30/2024]
Abstract
Background Although genetic mutations in additional sex-combs-like 1 (ASXL1) are prevalent in acute myeloid leukemia (AML), their exact impact on the AML prognosis remains uncertain. Hence, the present article was carried out to explore the prognostic importance of ASXL1 mutations in AML. Methods We thoroughly searched electronic scientific databases to find eligible papers. Twenty-seven studies with an overall number of 8,953 participants were selected for the current systematic review. The hazard ratio (HR) and 95% confidence interval (CI) for overall survival (OS), event-free survival (EFS), and relapse-free survival (RFS) were extracted from all studies with multivariate or univariate analysis. Pooled HRs and p-values were also calculated as a part of our work. Results The pooled HR for OS in multivariable analysis indicated that ASXL1 significantly diminished survival in AML patients (pooled HR: 1.67; 95% CI: 1.342-2.091). Conclusions ASXL1 mutations may confer a poor prognosis in AML. Hence, they may be regarded as potential prognostic factors. However, more detailed studies with different ASXL1 mutations are suggested to shed light on this issue.
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Affiliation(s)
- Maryam Sheikhi
- Cancer Molecular Pathology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehrdad Rostami
- Departments of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Gordon Ferns
- Division of Medical Education, Brighton and Sussex Medical School, Brighton, United Kingdom
| | - Hossein Ayatollahi
- Cancer Molecular Pathology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Payam Siyadat
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Yasamin Ayatollahi
- Cancer Molecular Pathology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Khoshnegah
- Department of Laboratory Hematology and Blood Banking, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
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3
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Yang L, Wei X, Gong Y. Prognosis and risk factors for ASXL1 mutations in patients with newly diagnosed acute myeloid leukemia and myelodysplastic syndrome. Cancer Med 2024; 13:e6871. [PMID: 38146893 PMCID: PMC10807681 DOI: 10.1002/cam4.6871] [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: 07/05/2023] [Revised: 11/29/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023] Open
Abstract
OBJECTIVE The objective of the study was to determine the prognosis and risk factors for additional sex combs like 1 (ASXL1) mutations in patients with acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). POPULATION AND METHODS This retrospective study enrolled 219 adult patients with newly diagnosed AML and MDS, who were treated in West China Hospital from October 2018 to January 2022. The primary clinical outcome was evaluated by overall survival (OS) followed up to January 2023. Kaplan-Meier analysis and Cox multivariate regression analysis were performed to identify potential prognostic parameters in patients with ASXL1 mutations (mt). RESULTS A total of 34 (15.53%) ASXL1mt were detected, which occurred more frequently in the elderly and MDS cohorts (p < 0.001). Significantly lower blasts% (p < 0.001) and higher frequencies of mutant RUNX1, SRSF2, STAG2, EZH2, and SETBP1 (p < 0.02) were observed in the ASXL1mt cohort. Patients with ASXL1mt manifested with a worse complete remission rate (p = 0.011), and an inferior OS was shown in subgroups with MDS, co-mutations of RUNX1, SRSF2, or NRAS, as well as mutations in G646W (p < 0.05). Multivariate analysis considering age, diagnosis, co-mutations, and mutation site confirmed an independently adverse prognosis of mutations in G646W (HR = 4.302, 95% CI: 1.150-16.097) or RUNX1 co-mutations (HR = 4.620, 95% CI: 1.385-15.414) in the ASXL1mt cohort. CONCLUSION Our study indicated that mutations in G646W or RUNX1 co-mutations are closely associated with a dismal clinical outcome in patients with AML and MDS harboring ASXL1mt. Considering the poor prognosis and risk factors in patients with ASXL1mt, more available treatments should be pursued.
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Affiliation(s)
- Liqing Yang
- Department of Hematology, West China HospitalSichuan UniversityChengduSichuanChina
- Department of HematologyFujian Medical University Union Hospital, Fujian Medical UniversityFuzhouFujianChina
| | - Xiaoyu Wei
- Department of Hematology, West China HospitalSichuan UniversityChengduSichuanChina
| | - Yuping Gong
- Department of Hematology, West China HospitalSichuan UniversityChengduSichuanChina
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Jia WB, Liu JT, Yang XY, Wu HY, Wei YH, Can C, Wang RQ, He N, Gu CY, Ma DX, Ji CY. [Clinical features and survival analysis in non-M(3) acute myeloid leukemia patients with ASXL1 gene mutation]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2022; 43:833-840. [PMID: 36709197 PMCID: PMC9669635 DOI: 10.3760/cma.j.issn.0253-2727.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Indexed: 11/29/2022]
Abstract
Objective: To examine the survival rates and clinical characteristics of people with newly discovered non-M(3) acute myeloid leukemia (AML) who carry the ASXL1 gene mutation. Methods: From January 2016 to April 2021, the clinical information of patients with newly diagnosed non-M(3) AML at Shandong University's Qilu Hospital was retrospectively examined, and their clinical characteristics and survival were compared and analyzed. Gene mutation was detected by next-generation sequencing. Results: ① The study included 256 AML patients who were initially diagnosed and had complete data, including 47 cases of ASXL1 gene mutation-positive (ASXL1(+)) patients and 209 cases of ASXL1 gene mutation-negative (ASXL1(-)) patients. All patients were divided into three groups: elderly (≥60 years old, n=92) , middle-aged (45-59 years old, n=92) , and young (≤44 years old, n=72) . ②WBC, and age were higher in patients with ASXL1 mutations compared to ASXL1(-) patients, while complete response after the first round of treatment (CR(1)) was lower (P<0.05) . In the elderly group, WBC and the proportion of aberrant cells in nuclear cells in ASXL1(+) patients were higher than those in ASXL1(-) patients (P<0.05) . In the young group, the WBC of ASXL1(+) patients was higher than that of ASXL1(-) patients (z=-2.314, P=0.021) . ③IDH2 mutation and ASXL1 mutation was related (P=0.018, r=0.34) . In ASXL1(+) patients, the proportion of peripheral blasts in the high VAF group (VAF>40% ) was higher than that in the low VAF group (VAF<20% ) , and the proportion of aberrant nuclear cells was higher in the duplication and replacement mutation patients than in the deletion mutation patients (P<0.05) . ④The overall survival (OS) and progression-free survival (PFS) of ASXL1(+) patients were shorter than those of ASXL1(-) patients (median, 10 months vs 20 months, 10 months vs 17 months; P<0.05) . The proportion number of aberrant cells in nuclear cells (≥20% ) , complex karyotypes, and TET2 mutation were all independent risk variables that had an impact on the prognosis of ASXL1(+) patients, according to multivariate analysis (P<0.05) . Conclusion: ASXL1-mutated non-M(3) AML patients have higher WBC in peripheral blood, a higher proportion of aberrant cells in nuclear cells, lower CR(1) rate, and shorter OS and PFS. Additionally, a poor prognosis is linked to higher VAF, duplication, and substitution mutations in the ASXL1 gene, as well as the high proportion of aberrant cells in nuclear cells, complex karyotype, and TET2 mutation.
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Affiliation(s)
- W B Jia
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - J T Liu
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - X Y Yang
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - H Y Wu
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - Y H Wei
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - C Can
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - R Q Wang
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - N He
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - C Y Gu
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - D X Ma
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - C Y Ji
- Department of Hematology, Qilu Hospital, Shandong University, Jinan 250012, China
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Lipilkin PV, Kulaeva ED, Mashkina EV. Prognostic value of ASXL1 mutations in acute myeloid leukemia: A meta-analysis. Leuk Res 2022; 120:106910. [PMID: 35785697 DOI: 10.1016/j.leukres.2022.106910] [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: 05/12/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Mutations in ASXL1 are being investigated for prognostic value in AML, but the relationship between these mutations and prognosis for patients with AML remains unclear. Therefore, we are conducting a meta-analysis to estimate the effect of mutations in ASXL1 to determine their prognostic significance. METHODS Eight studies were selected by searching PubMed, Embase, Web of Science, ClinicalTrials, and the Cochrane Library databases. Hazard ratios (HRs) and their 95% confidence intervals (CIs) for overall survival (OS) and event-free survival (EFS) were pooled to assess the effect of ASXL1 mutations on the prognosis in AML patients. RESULTS A total of 8 studies with 4143 patients were included in this meta-analysis. The pooled HRs for OS and EFS revealed that AML patients with ASXL1 mutations had a significantly poor prognosis as compared with those without mutations (OS: HR = 1.59, 95% CI = 1.34-1.88, p < 0.00001; EFS: HR = 1.63, 95% CI = 1.27-2.08, p < 0.0001). Mutations in ASXL1 showed no strong relationship with other AML-specific mutations and FAB subtypes. DISCUSSION This meta-analysis showed that AML patients with ASXL1 mutations had a poor prognosis, which may be a reason to include the diagnostics of this mutation in the prognostic scales for assessing risk in patients with AML.
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Affiliation(s)
- P V Lipilkin
- Rostov State Medical University, Department of Hematology and Transfusiology (with courses in Clinical Laboratory Diagnosis, Genetics and Laboratory Genetics), 29, Nakhichevansky lane, Rostov-on-Don 344022, Russia.
| | - E D Kulaeva
- Southern Federal University, Academy of Biology and Biotechnology, Department of Genetics, Human and Animal Genetics Laboratory, 194/1 Stachki Ave, Rostov-on-Don 344090, Russia.
| | - E V Mashkina
- Southern Federal University, Academy of Biology and Biotechnology, Department of Genetics, Human and Animal Genetics Laboratory, 194/1 Stachki Ave, Rostov-on-Don 344090, Russia.
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Genetic Characteristics According to Subgroup of Acute Myeloid Leukemia with Myelodysplasia-Related Changes. J Clin Med 2022; 11:jcm11092378. [PMID: 35566503 PMCID: PMC9105081 DOI: 10.3390/jcm11092378] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 12/19/2022] Open
Abstract
Acute myeloid leukemia with myelodysplasia-related changes (AML-MRC) includes heterogeneous conditions such as previous history and specific cytogenetic and morphological properties. In this study, we analyze genetic aberrations using an RNA-based next-generation sequencing (NGS) panel assay in 45 patients with AML-MRC and detect 4 gene fusions of KMT2A-SEPT9, KMT2A-ELL, NUP98-NSD1, and RUNX1-USP42 and 81 somatic mutations. Overall, all patients had genetic aberrations comprising of not only cytogenetic changes, but also gene fusions and mutations. We also demonstrated several characteristic genetic mutations according to the AML-MRC subgroup. TP53 was the most commonly mutated gene (n = 11, 24%) and all were found in the AML-MRC subgroup with myelodysplastic syndrome-defining cytogenetic abnormalities (AML-MRC-C) (p = 0.002). These patients showed extremely poor overall survival not only in AML-MRC, but also within the AML-MRC-C subgroup. The ASXL1 (n = 9, 20%) and SRSF2 (n = 7, 16%) mutations were associated with the AML-MRC subgroup with >50% dysplasia in at least two lineages (AML-MRC-M) and were frequently co-mutated (55%, 6/11, p < 0.001). Both mutations could be used as surrogate markers to diagnose AML-MRC, especially when the assessment of multilineage dysplasia was difficult. IDH1/IDH2 (n = 13, 29%) were most commonly mutated in AML-MRC, followed by CEBPA (n = 5, 11%), PTPN11 (n = 5, 11%), FLT3 (n = 4, 9%), IDH1 (n = 4, 9%), and RUNX1 (n = 4, 9%). These mutations were not limited in any AML-MRC subgroup and could have more significance as a risk factor or susceptibility marker for target therapy in not only AML-MRC, but also other AML categories.
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Wang D, Yuan X, Guo H, Yan S, Wang G, Wang Y, Wang T, He J, Peng X. Bohring-Opitz syndrome caused by a novel ASXL1 mutation (c.3762delT) in an IVF baby: A case report. Medicine (Baltimore) 2022; 101:e28759. [PMID: 35119035 PMCID: PMC8812699 DOI: 10.1097/md.0000000000028759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/17/2022] [Indexed: 01/04/2023] Open
Abstract
RATIONALE Bohring-Opitz syndrome is a severe congenital disorder associated with a de novo mutation in the additional sex combs-like 1 (ASXL1) gene, and it is characterized by symptoms that include developmental delay and musculoskeletal and neurological features. PATIENT CONCERNS The patient was a girl, an in vitro fertilization (IVF) baby, with delayed motor development, drooling, short stature, slow growth, low muscle tone, image diagnosis of hypoplasia of the corpus callosum, delayed tooth eruption, high palatal arch, adduction of the thumb, drooling, not chewing, excessive joint activity, and ligament relaxation. DIAGNOSIS Whole-exome sequencing analysis detected 1 novel disruptive frameshift mutation in ASXL1 in the proband but wild-type ASXL1 in both parents. INTERVENTIONS Approximately 1 year of rehabilitation training, which included exercise therapy, toy imitation operation, cognition of daily objects, daily living skills training, gesture language training, oral muscle training, and hand movement training. OUTCOMES After approximately 1 year of training, the patient was 3 years old and able to eat normally without drooling. She was able to grasp objects and pick them up after they fell. She was able to grasp small objects and actively played with toys. In addition, she was able to crawl on the floor (at slow speed, with poor initiative), stand with assistance, and walk with assistance; she was unstable when standing unassisted (standing unassisted for 8 seconds at most during training). LESSON ASXL1 c.3762delT is a novel mutation that may be caused by IVF. This finding suggests that appropriate gene mutation detection approaches may be necessary for IVF technology.
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Affiliation(s)
- Dongbo Wang
- Changsha Hospital for Maternal and Child Health Care of Hunan Normal University, China
| | - Xin Yuan
- The First Hospital of Hunan University of Chinese Medicine, China
| | - Haichun Guo
- Changsha Hospital for Maternal and Child Health Care of Hunan Normal University, China
| | - Shuyuan Yan
- Changsha Hospital for Maternal and Child Health Care of Hunan Normal University, China
| | - Guohong Wang
- Changsha Hospital for Maternal and Child Health Care of Hunan Normal University, China
| | - Yanling Wang
- Changsha Hospital for Maternal and Child Health Care of Hunan Normal University, China
| | - Tuanmei Wang
- Changsha Hospital for Maternal and Child Health Care of Hunan Normal University, China
| | - Jun He
- Changsha Hospital for Maternal and Child Health Care of Hunan Normal University, China
| | - Xiangwen Peng
- Changsha Hospital for Maternal and Child Health Care of Hunan Normal University, China
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8
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Ebian HF, Elshorbagy S, Mohamed H, Embaby A, Khamis T, Sameh R, Sabbah NA, Hussein S. Clinical implication and prognostic significance of FLT3-ITD and ASXL1 mutations in Egyptian AML patients: A single-center study. Cancer Biomark 2021; 32:379-389. [PMID: 34487021 DOI: 10.3233/cbm-210024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Both Fms-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD) and Additional Sex Comb-like 1 (ASXL1) mutations are frequent and early genetic alteration events in acute myeloid leukemia (AML) patients. These genetic alterations may be associated with an unfavorable prognosis. OBJECTIVE Up to our knowledge, this is the first study performed to evaluate the clinical implication and prognostic significance of FLT3-ITD and ASXL1 mutations and their coexistence on the outcome of Egyptian AML patients. METHODS Our study included 83 patients with AML who were subjected to immunophenotyping and detection of FLT3-ITD and ASXL1 gene mutation by polymerase chain reaction (PCR) and real-time PCR, respectively. RESULTS FLT3-ITD and ASXL1 mutations were detected in 20.5% and 18.1% of AML patients respectively. Seven patients (8.4%) had co-expression of both genes' mutations. FLT3-ITD mutation was significantly higher in younger age, higher WBCs count and poor cytogenetic risk patients (P= 0.01, < 0.001 and 0.008 respectively). ASXL1 mutation was significantly higher in intermediate cytogenetic risk patients (P= 0.2). The mean period of survival and relapse-free survival (RFS) were significantly reduced in FLT3-ITD and ASXL1 mutations compared with their non-mutant types (P= 0.01 and 0.03 respectively). Both mutations were independent risk factors for overall survival (OS) and (RFS) in univariate and multivariate analysis in AML patients. CONCLUSION FLT3-ITD and ASXL1 gene mutations or their coexistence can predict a poor prognosis in AML patients.
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Affiliation(s)
- Huda F Ebian
- Clinical Pathology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Sherin Elshorbagy
- Oncology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Haitham Mohamed
- Hematology Oncology Unit/Internal Medicine Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Ahmad Embaby
- Hematology Oncology Unit/Internal Medicine Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Tarek Khamis
- Pharmacology Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Reham Sameh
- Pathology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Norhan A Sabbah
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Samia Hussein
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
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O'Sullivan B, Seoighe C. vcfView: An Extensible Data Visualization and Quality Assurance Platform for Integrated Somatic Variant Analysis. Cancer Inform 2020; 19:1176935120972377. [PMID: 33239857 PMCID: PMC7672756 DOI: 10.1177/1176935120972377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/19/2020] [Indexed: 11/21/2022] Open
Abstract
Motivation: Somatic mutations can have critical prognostic and therapeutic implications for cancer patients. Although targeted methods are often used to assay specific cancer driver mutations, high throughput sequencing is frequently applied to discover novel driver mutations and to determine the status of less-frequent driver mutations. The task of recovering somatic mutations from these data is nontrivial as somatic mutations must be distinguished from germline variants, sequencing errors, and other artefacts. Consequently, bioinformatics pipelines for recovery of somatic mutations from high throughput sequencing typically involve a large number of analytical choices in the form of quality filters. Results: We present vcfView, an interactive tool designed to support the evaluation of somatic mutation calls from cancer sequencing data. The tool takes as input a single variant call format (VCF) file and enables researchers to explore the impacts of analytical choices on the mutant allele frequency spectrum, on mutational signatures and on annotated somatic variants in genes of interest. It allows variants that have failed variant caller filters to be re-examined to improve sensitivity or guide the design of future experiments. It is extensible, allowing other algorithms to be incorporated easily. Availability: The shiny application can be downloaded from GitHub (https://github.com/BrianOSullivanGit/vcfView). All data processing is performed within R to ensure platform independence. The app has been tested on RStudio, version 1.1.456, with base R 3.6.2 and Shiny 1.4.0. A vignette based on a publicly available data set is also available on GitHub.
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Affiliation(s)
- Brian O'Sullivan
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
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10
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Jiang G, Capo-Chichi JM, Liu A, Atenafu EG, Guo R, Tierens A, Minden MD, Chang H. Acute myeloid leukemia with myelodysplasia-related changes diagnosed with multilineage dysplasia alone demonstrates a superior clinical outcome. Hum Pathol 2020; 104:117-126. [PMID: 32798550 DOI: 10.1016/j.humpath.2020.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/14/2020] [Accepted: 08/06/2020] [Indexed: 12/20/2022]
Abstract
Acute myeloid leukemia with myelodysplasia-related changes (AML-MRC) generally confers poor prognosis; however, the clinical outcome remains heterogeneous. We sought to further stratify this subentity of AML by performing a retrospective analysis of 179 adult patients with AML-MRC diagnosed at our institution. Based on 2016 World Health Organization diagnostic criteria, 44 (25%) patients had multilineage dysplasia alone (AML-MRC-M), 74 (41%) had history of myelodysplastic syndrome (MDS) or myelodysplastic/myeloproliferative disease (AML-MRC-H), and 61 (34%) had MDS-related cytogenetics (AML-MRC-C). AML-MRC-M and hematopoietic stem cell transplantation (HSCT) were associated with prolonged event-free survival (EFS) (P = 0.0051 and P < 0.0001, respectively) and overall survival (OS) (P = 0.0015 and P < 0.0001, respectively), whereas AML-MRC-C and age ≥60 years were associated with shorter EFS (P = 0.028 and P = 0.015, respectively) and OS (P = 0.021 and P = 0.013, respectively). Of note, NPM1mut did not affect the patient's outcome. Multivariable analysis confirmed HSCT and AML-MRC-C as independent predictors for EFS (P < 0.0001 and P = 0.0342, respectively) and OS (P < 0.0001 and P = 0.0295, respectively). AML-MRC-M was an independent predictor for OS (P = 0.0449). When compared with a control group of 105 patients with normal karyotype AML not otherwise specified (NK-AML-NOS), patients with AML-MRC-M had similar EFS and OS (P = 0.99 and P = 0.91, respectively). However, AML-MRC-H and AML-MRC-C were associated with shorter EFS and OS (P = 0.0002 and P < 0.0001, respectively) than the same control group. In a subset of patients, next-generation sequencing analysis showed AML-MRC-M was associated with ASXL1 mutation compared with NK-AML (56% vs 6%). In conclusion, AML-MRC-M demonstrates a superior clinical outcome compared with the rest of the AML-MRC group. They have comparable outcomes to NK-AML-NOS, and these data suggest AML-MRC-M may be considered not to be classified in the same group as patients with other AML-MRC.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Cell Lineage
- Female
- Genetic Predisposition to Disease
- Hematopoietic Stem Cell Transplantation/adverse effects
- Hematopoietic Stem Cell Transplantation/mortality
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/surgery
- Male
- Middle Aged
- Mutation
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/mortality
- Myelodysplastic Syndromes/pathology
- Myelodysplastic Syndromes/surgery
- Nuclear Proteins/genetics
- Nucleophosmin
- Progression-Free Survival
- Repressor Proteins/genetics
- Retrospective Studies
- Risk Assessment
- Risk Factors
- Time Factors
- Young Adult
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Affiliation(s)
- Gina Jiang
- Department of Laboratory Hematology, University Health Network, University of Toronto, Toronto, Canada
| | - Jose-Mario Capo-Chichi
- Department of Clinical Laboratory Genetics, Genome Diagnostics, University Health Network, Canada
| | - Aijun Liu
- Department of Hematology, Beijing Chaoyang Hospital, Capital Medical University, China
| | | | - Robert Guo
- Department of Laboratory Hematology, University Health Network, University of Toronto, Toronto, Canada
| | - Ann Tierens
- Department of Laboratory Hematology, University Health Network, University of Toronto, Toronto, Canada
| | - Mark D Minden
- Department of Hematology and Medical Oncology, University Health Network, University of Toronto, Toronto, Canada
| | - Hong Chang
- Department of Laboratory Hematology, University Health Network, University of Toronto, Toronto, Canada.
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11
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Prats-Martín C, Burillo-Sanz S, Morales-Camacho RM, Pérez-López O, Suito M, Vargas MT, Caballero-Velázquez T, Carrillo-Cruz E, González J, Bernal R, Pérez-Simón JA. ASXL1 mutation as a surrogate marker in acute myeloid leukemia with myelodysplasia-related changes and normal karyotype. Cancer Med 2020; 9:3637-3646. [PMID: 32216059 PMCID: PMC7286456 DOI: 10.1002/cam4.2947] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/21/2020] [Accepted: 02/12/2020] [Indexed: 11/06/2022] Open
Abstract
Acute myeloid leukemia with myelodysplasia-related changes (AML-MRC) are poor outcome leukemias. Its diagnosis is based on clinical, cytogenetic, and cytomorphologic criteria, last criterion being sometimes difficult to assess. A high frequency of ASXL1 mutations have been described in this leukemia. We sequenced ASXL1 gene mutations in 61 patients with AML-MRC and 46 controls with acute myeloid leukemia without other specifications (AML-NOS) to identify clinical, cytomorphologic, and cytogenetic characteristics associated with ASXL1 mutational status. Mutated ASXL1 (ASXL1+) was observed in 31% of patients with AML-MRC compared to 4.3% in AML-NOS. Its presence in AML-MRC was associated with older age, a previous history of myelodysplastic syndrome (MDS) or myelodysplastic/myeloproliferative neoplasms (MDS/MPN), leukocytosis, presence of micromegakaryocytes in bone marrow, lower number of blasts in bone marrow, myelomonocytic/monocytic morphological features and normal karyotype. ASXL1 mutation was not observed in patients with myelodysplastic syndrome-related cytogenetic abnormalities or TP53 mutations. Differences in terms of overall survival were found only in AML-MRC patients without prior MDS or MDS/MPN and with intermediate-risk karyotype, having ASXL1+ patients a worst outcome than ASXL1-. We conclude that the ASXL1 mutation frequency is high in AML-MRC patients being its presence associated with specific characteristics including morphological signs of dysplasia. This association raises the possible role of ASXL1 as a surrogate marker in AML-MRC, which could facilitate the diagnosis of patients within this group when the karyotype is normal, and especially when the assessment of multilineage dysplasia morphologically is difficult. This mutation could be used as a worst outcome marker in de novo AML-MRC with intermediate-risk karyotype.
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Affiliation(s)
- Concepción Prats-Martín
- Department of Hematology, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS/CISC/CIBERONC), Universidad de Sevilla, Sevilla, Spain
| | - Sergio Burillo-Sanz
- Department of Immunology, Hospital Universitario Virgen del Rocío. Sevilla, Sevilla, Spain
| | - Rosario M Morales-Camacho
- Department of Hematology, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS/CISC/CIBERONC), Universidad de Sevilla, Sevilla, Spain
| | - Olga Pérez-López
- Department of Hematology, Hospital Universitario Virgen Macarena, Universidad de Sevilla, Sevilla, Spain
| | - Milagros Suito
- Department of Hematology, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS/CISC/CIBERONC), Universidad de Sevilla, Sevilla, Spain
| | - Maria T Vargas
- Department of Hematology, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS/CISC/CIBERONC), Universidad de Sevilla, Sevilla, Spain
| | - Teresa Caballero-Velázquez
- Department of Hematology, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS/CISC/CIBERONC), Universidad de Sevilla, Sevilla, Spain
| | - Estrella Carrillo-Cruz
- Department of Hematology, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS/CISC/CIBERONC), Universidad de Sevilla, Sevilla, Spain
| | - José González
- Department of Hematology, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS/CISC/CIBERONC), Universidad de Sevilla, Sevilla, Spain
| | - Ricardo Bernal
- Department of Hematology, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS/CISC/CIBERONC), Universidad de Sevilla, Sevilla, Spain
| | - José A Pérez-Simón
- Department of Hematology, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS/CISC/CIBERONC), Universidad de Sevilla, Sevilla, Spain
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