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Yoo JW, Ahn A, Lee JM, Jo S, Kim S, Lee JW, Cho B, Kim Y, Kim M, Chung NG. Spectrum of Genetic Mutations in Korean Pediatric Acute Lymphoblastic Leukemia. J Clin Med 2022; 11:jcm11216298. [PMID: 36362526 PMCID: PMC9658397 DOI: 10.3390/jcm11216298] [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: 10/07/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
The wide application of next-generation sequencing (NGS) technologies has led to the discovery of multiple genetic alterations in pediatric acute lymphoblastic leukemia (ALL). In this work, we aimed to investigate the mutational spectrum in pediatric ALL. We employed a St. Mary’s customized NGS panel comprising 67 leukemia-related genes. Samples were collected from 139 pediatric ALL patients. Eighty-five patients (61.2%) harbored at least one mutation. In B-cell ALL, the RAS pathway is the most involved pathway, and the three most frequently mutated genes were NRAS (22.4%), KRAS (19.6%), and PTPN11 (8.4%). NRAS and PTPN11 were significantly associated with a high hyperdiploidy karyotype (p = 0.018 and p < 0.001, respectively). In T-cell ALL, the three most frequently mutated genes were NOTCH1 (37.5%), FBXW7 (16.6%), and PTEN (6.2%). Several pairs of co-occurring mutations were found: NRAS with SETD, NRAS with PTPN11 in B-cell ALL (p = 0.024 and p = 0.020, respectively), and NOTCH1 with FBXW7 in T-cell ALL (p < 0.001). The most frequent newly emerged mutation in relapsed ALL was NT5C2. We procured comprehensive genetic information regarding Korean pediatric ALL using NGS technology. Our findings strengthen the current knowledge of recurrent somatic mutations in pediatric ALL.
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Affiliation(s)
- Jae Won Yoo
- Department of Pediatrics, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Ari Ahn
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Jong-Mi Lee
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Suejung Jo
- Department of Pediatrics, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Seongkoo Kim
- Department of Pediatrics, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Jae Wook Lee
- Department of Pediatrics, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Bin Cho
- Department of Pediatrics, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Yonggoo Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Myungshin Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Correspondence: (M.K.); (N.-G.C.); Tel.: +82-2-2258-1645 (M.K.); +82-2-2258-6188 (N.-G.C.)
| | - Nack-Gyun Chung
- Department of Pediatrics, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Correspondence: (M.K.); (N.-G.C.); Tel.: +82-2-2258-1645 (M.K.); +82-2-2258-6188 (N.-G.C.)
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Ma J, Wen X, Xu Z, Xia P, Jin Y, Lin J, Qian J. Predicting the influence of Circ_0059706 expression on prognosis in patients with acute myeloid leukemia using classical statistics and machine learning. Front Genet 2022; 13:961142. [PMID: 36338954 PMCID: PMC9633654 DOI: 10.3389/fgene.2022.961142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Various circular RNA (circRNA) molecules are abnormally expressed in acute myeloid leukemia (AML), and associated with disease occurrence and development, as well as patient prognosis. The roles of circ_0059706, a circRNA derived from ID1, in AML remain largely unclear. Results: Here, we reported circ_0059706 expression in de novo AML and its association with prognosis. We found that circ_0059706 expression was significantly lower in AML patients than in controls (p < 0.001). Survival analysis of patients with AML divided into two groups according to high and low circ_0059706 expression showed that overall survival (OS) of patients with high circ_0059706 expression was significantly longer than that of those with low expression (p < 0.05). Further, female patients with AML and those aged >60 years old in the high circ_0059706 expression group had longer OS than male patients and those younger than 60 years. Multiple regression analysis showed that circ_0059706 was an independent factor-affecting prognosis of all patients with AML. To evaluate the prospects for application of circ_0059706 in machine learning predictions, we developed seven types of algorithm. The gradient boosting (GB) model exhibited higher performance in prediction of 1-year prognosis and 3-year prognosis, with AUROC 0.796 and 0.847. We analyzed the importance of variables and found that circ_0059706 expression level was the first important variables among all 26 factors included in the GB algorithm, suggesting the importance of circ_0059706 in prediction model. Further, overexpression of circ_0059706 inhibited cell growth and increased apoptosis of leukemia cells in vitro. Conclusion: These results provide evidence that high expression of circ_0059706 is propitious for patient prognosis and suggest circ_0059706 as a potential new biomarker for diagnosis and prognosis evaluation in AML, with high predictive value and good prospects for application in machine learning algorithms.
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Affiliation(s)
- Jichun Ma
- Deparrtment of Central Lab, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
| | - Xiangmei Wen
- Deparrtment of Central Lab, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
| | - Zijun Xu
- Deparrtment of Central Lab, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
| | - Peihui Xia
- Deparrtment of Central Lab, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
| | - Ye Jin
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- Deparrtment of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
| | - Jiang Lin
- Deparrtment of Central Lab, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- *Correspondence: Jiang Lin, ; Jun Qian,
| | - Jun Qian
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- Deparrtment of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- *Correspondence: Jiang Lin, ; Jun Qian,
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Hu X, Song J, Chyr J, Wan J, Wang X, Du J, Duan J, Zhang H, Zhou X, Wu X. APAview: A web-based platform for alternative polyadenylation analyses in hematological cancers. Front Genet 2022; 13:928862. [PMID: 36035147 PMCID: PMC9411867 DOI: 10.3389/fgene.2022.928862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/06/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Hematologic malignancies, such as acute promyelocytic leukemia (APL) and acute myeloid leukemia (AML), are cancers that start in blood-forming tissues and can affect the blood, bone marrow, and lymph nodes. They are often caused by genetic and molecular alterations such as mutations and gene expression changes. Alternative polyadenylation (APA) is a post-transcriptional process that regulates gene expression, and dysregulation of APA contributes to hematological malignancies. RNA-sequencing-based bioinformatic methods can identify APA sites and quantify APA usages as molecular indexes to study APA roles in disease development, diagnosis, and treatment. Unfortunately, APA data pre-processing, analysis, and visualization are time-consuming, inconsistent, and laborious. A comprehensive, user-friendly tool will greatly simplify processes for APA feature screening and mining. Results: Here, we present APAview, a web-based platform to explore APA features in hematological cancers and perform APA statistical analysis. APAview server runs on Python3 with a Flask framework and a Jinja2 templating engine. For visualization, APAview client is built on Bootstrap and Plotly. Multimodal data, such as APA quantified by QAPA/DaPars, gene expression data, and clinical information, can be uploaded to APAview and analyzed interactively. Correlation, survival, and differential analyses among user-defined groups can be performed via the web interface. Using APAview, we explored APA features in two hematological cancers, APL and AML. APAview can also be applied to other diseases by uploading different experimental data.
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Affiliation(s)
- Xi Hu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Jialin Song
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Jacqueline Chyr
- Center for Computational Systems Medicine, School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, United States
| | - Jinping Wan
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Xiaoyan Wang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Jianqiang Du
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Junbo Duan
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Huqin Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, United States
| | - Xiaoming Wu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Xiaoming Wu,
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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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Mäkinen VP, Rehn J, Breen J, Yeung D, White DL. Multi-Cohort Transcriptomic Subtyping of B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2022; 23:4574. [PMID: 35562965 PMCID: PMC9099612 DOI: 10.3390/ijms23094574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 11/17/2022] Open
Abstract
RNA sequencing provides a snapshot of the functional consequences of genomic lesions that drive acute lymphoblastic leukemia (ALL). The aims of this study were to elucidate diagnostic associations (via machine learning) between mRNA-seq profiles, independently verify ALL lesions and develop easy-to-interpret transcriptome-wide biomarkers for ALL subtyping in the clinical setting. A training dataset of 1279 ALL patients from six North American cohorts was used for developing machine learning models. Results were validated in 767 patients from Australia with a quality control dataset across 31 tissues from 1160 non-ALL donors. A novel batch correction method was introduced and applied to adjust for cohort differences. Out of 18,503 genes with usable expression, 11,830 (64%) were confounded by cohort effects and excluded. Six ALL subtypes (ETV6::RUNX1, KMT2A, DUX4, PAX5 P80R, TCF3::PBX1, ZNF384) that covered 32% of patients were robustly detected by mRNA-seq (positive predictive value ≥ 87%). Five other frequent subtypes (CRLF2, hypodiploid, hyperdiploid, PAX5 alterations and Ph-positive) were distinguishable in 40% of patients at lower accuracy (52% ≤ positive predictive value ≤ 73%). Based on these findings, we introduce the Allspice R package to predict ALL subtypes and driver genes from unadjusted mRNA-seq read counts as encountered in real-world settings. Two examples of Allspice applied to previously unseen ALL patient samples with atypical lesions are included.
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Affiliation(s)
- Ville-Petteri Mäkinen
- Computational and Systems Biology Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- Australian Centre for Precision Health, UniSA Clinical & Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
- Computational Medicine, Faculty of Medicine, University of Oulu, FI-90014 Oulu, Finland
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, FI-90014 Oulu, Finland
| | - Jacqueline Rehn
- Blood Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia; (J.R.); (D.Y.); (D.L.W.)
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia;
| | - James Breen
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia;
- South Australian Genomics Centre, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - David Yeung
- Blood Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia; (J.R.); (D.Y.); (D.L.W.)
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia;
- Australian and New Zealand Children’s Oncology Group, Clayton, VIC 3168, Australia
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, SA 5000, Australia
| | - Deborah L. White
- Blood Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia; (J.R.); (D.Y.); (D.L.W.)
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia;
- Australian and New Zealand Children’s Oncology Group, Clayton, VIC 3168, Australia
- Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Australian Genomics Health Alliance, Parkville, VIC 3052, Australia
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