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Banaszak LG, Giudice V, Zhao X, Wu Z, Gao S, Hosokawa K, Keyvanfar K, Townsley DM, Gutierrez-Rodrigues F, Fernandez Ibanez MDP, Kajigaya S, Young NS. Abnormal RNA splicing and genomic instability after induction of DNMT3A mutations by CRISPR/Cas9 gene editing. Blood Cells Mol Dis 2018; 69:10-22. [PMID: 29324392 DOI: 10.1016/j.bcmd.2017.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/31/2017] [Accepted: 12/31/2017] [Indexed: 12/20/2022]
Abstract
DNA methyltransferase 3A (DNMT3A) mediates de novo DNA methylation. Mutations in DNMT3A are associated with hematological malignancies, most frequently acute myeloid leukemia. DNMT3A mutations are hypothesized to establish a pre-leukemic state, rendering cells vulnerable to secondary oncogenic mutations and malignant transformation. However, the mechanisms by which DNMT3A mutations contribute to leukemogenesis are not well-defined. Here, we successfully created four DNMT3A-mutated K562 cell lines with frameshift mutations resulting in truncated DNMT3A proteins. DNMT3A-mutated cell lines exhibited significantly impaired growth and increased apoptotic activity compared to wild-type (WT) cells. Consistent with previous studies, DNMT3A-mutated cells displayed impaired differentiation capacity. RNA-seq was used to compare transcriptomes of DNMT3A-mutated and WT cells; DNMT3A ablation resulted in downregulation of genes involved in spliceosome function, causing dysfunction of RNA splicing. Unexpectedly, we observed DNMT3A-mutated cells to exhibit marked genomic instability and an impaired DNA damage response compared to WT. CRISPR/Cas9-mediated DNMT3A-mutated K562 cells may be used to model effects of DNMT3A mutations in human cells. Our findings implicate aberrant splicing and induction of genomic instability as potential mechanisms by which DNMT3A mutations might predispose to malignancy.
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Affiliation(s)
- Lauren G Banaszak
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA.
| | - Valentina Giudice
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Xin Zhao
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Zhijie Wu
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Shouguo Gao
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Kohei Hosokawa
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Keyvan Keyvanfar
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Danielle M Townsley
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Fernanda Gutierrez-Rodrigues
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Maria Del Pilar Fernandez Ibanez
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1202, USA
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Tsai CH, Hou HA, Tang JL, Kuo YY, Chiu YC, Lin CC, Liu CY, Tseng MH, Lin TY, Liu MC, Liu CW, Lin LI, Yao M, Li CC, Huang SY, Ko BS, Hsu SC, Lin CT, Wu SJ, Chen CY, Tsay W, Chuang EY, Chou WC, Tien HF. Prognostic impacts and dynamic changes of cohesin complex gene mutations in de novo acute myeloid leukemia. Blood Cancer J 2017; 7:663. [PMID: 29288251 PMCID: PMC5802563 DOI: 10.1038/s41408-017-0022-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/08/2017] [Accepted: 10/12/2017] [Indexed: 12/17/2022] Open
Affiliation(s)
- Cheng-Hong Tsai
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Tai-Cheng Stem Cell Therapy Center, National Taiwan University, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
| | - Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Jih-Luh Tang
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Tai-Cheng Stem Cell Therapy Center, National Taiwan University, Taipei, Taiwan
| | - Yuan-Yeh Kuo
- Graduate Institute of Oncology, National Taiwan University, Taipei, Taiwan
| | - Yu-Chiao Chiu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Chien-Chin Lin
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan
| | - Chieh-Yu Liu
- Biostatistics Consulting Laboratory, School of Nursing and Center of General Education, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan
| | - Mei-Hsuan Tseng
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Tzung-Yi Lin
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming-Chih Liu
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chia-Wen Liu
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Liang-In Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming Yao
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chi-Cheng Li
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Tai-Cheng Stem Cell Therapy Center, National Taiwan University, Taipei, Taiwan
| | - Shang-Yi Huang
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Bor-Sheng Ko
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Szu-Chun Hsu
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Ting Lin
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Tai-Cheng Stem Cell Therapy Center, National Taiwan University, Taipei, Taiwan
| | - Shang-Ju Wu
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Yuan Chen
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Woei Tsay
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Eric Y Chuang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Chien Chou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
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53
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McCurdy SR, Levis MJ. Emerging molecular predictive and prognostic factors in acute myeloid leukemia. Leuk Lymphoma 2017; 59:2021-2039. [DOI: 10.1080/10428194.2017.1393669] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shannon R. McCurdy
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mark J. Levis
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Liu J, Zhou L, Fu X, Xu C, Huang S, Li Y, Gao H, Guan W, Yang L, Lv N. MicroRNAs and regulated interaction networks reveal differences between adult and pediatric acute myeloid leukemia. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:10576-10583. [PMID: 31966399 PMCID: PMC6965806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 07/09/2016] [Indexed: 06/10/2023]
Abstract
OBJECTIVES The purpose of this study was to identify featured microRNAs and their regulated network between adult and pediatric acute myeloid leukemia (AML) and find potential utility as biomarkers for diagnosis and treatment of pediatric AML. METHODS We downloaded the microRNA expression dataset GSE35320 from Gene Expression Omnibus database and selected expression chips from bone marrow of 71 pediatric AML samples and 6 adulthood AML samples. Differentially expressed microRNAs were identified by Wilcox test. The target genes of these microRNAs were predicted using an integrative method and their functional enrichment analysis was performed using DAVID. Finally, STRING database and Cytoscape software was used to construct and analyze the interaction network. RESULTS A total of 7 differentially expressed microRNAs were identified and the remarkably up-regulated and down-regulated microRNAs were miR-16 and miR-142-5p which included 323 and 22 predicted target genes, respectively. The target genes of 7 microRNAs were most associated with regulation of cell cycle, p53 signaling pathway, Wnt signaling pathway and neurotrophin signaling pathway. The interaction network of miR-16 target genes was constructed among 354 high confidence interaction pairs. The core genes of the network, such as TP53, BCL2, VEGFA, had a role in prognosis of children with AML. CONCLUSIONS The featured microRNAs and their target genes are significant in the occurrence and development of pediatric AML, which is likely to be important for the identification of therapeutic targets and biomarkers for these patients.
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Affiliation(s)
- Jing Liu
- Department of Hematology, Chinese PLA General HospitalBeijing 100853, China
| | - Lei Zhou
- Department of Hematology, Chinese PLA General HospitalBeijing 100853, China
| | - Xiaomin Fu
- Department of Geriatric Endocrinology, Chinese PLA General HospitalBeijing 100853, China
| | - Chen Xu
- Department of Hematopoietic Stem Cell Transplantation, The Affiliated Hospital to Military Medical SciencesBeijing 100071, China
| | - Sai Huang
- Department of Hematology, Chinese PLA General HospitalBeijing 100853, China
| | - Yan Li
- Department of Hematology, Chinese PLA General HospitalBeijing 100853, China
| | - Honghao Gao
- Department of Hematology, Chinese PLA General HospitalBeijing 100853, China
| | - Wei Guan
- Department of Hematology, Chinese PLA General HospitalBeijing 100853, China
| | - Lan Yang
- Department of Hematology, Chinese PLA General HospitalBeijing 100853, China
| | - Na Lv
- Department of Hematology, Chinese PLA General HospitalBeijing 100853, China
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Armstrong RN, Steeples V, Singh S, Sanchi A, Boultwood J, Pellagatti A. Splicing factor mutations in the myelodysplastic syndromes: target genes and therapeutic approaches. Adv Biol Regul 2017; 67:13-29. [PMID: 28986033 DOI: 10.1016/j.jbior.2017.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 09/19/2017] [Accepted: 09/21/2017] [Indexed: 10/25/2022]
Abstract
Mutations in splicing factor genes (SF3B1, SRSF2, U2AF1 and ZRSR2) are frequently found in patients with myelodysplastic syndromes (MDS), suggesting that aberrant spliceosome function plays a key role in the pathogenesis of MDS. Splicing factor mutations have been shown to result in aberrant splicing of many downstream target genes. Recent functional studies have begun to characterize the splicing dysfunction in MDS, identifying some key aberrantly spliced genes that are implicated in disease pathophysiology. These findings have led to the development of therapeutic strategies using splicing-modulating agents and rapid progress is being made in this field. Splicing inhibitors are promising agents that exploit the preferential sensitivity of splicing factor-mutant cells to these compounds. Here, we review the known target genes associated with splicing factor mutations in MDS, and discuss the potential of splicing-modulating therapies for these disorders.
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Affiliation(s)
- Richard N Armstrong
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Violetta Steeples
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Shalini Singh
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Andrea Sanchi
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Jacqueline Boultwood
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK.
| | - Andrea Pellagatti
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK.
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56
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A 4-lncRNA scoring system for prognostication of adult myelodysplastic syndromes. Blood Adv 2017; 1:1505-1516. [PMID: 29296792 DOI: 10.1182/bloodadvances.2017008284] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/06/2017] [Indexed: 12/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) not only participate in normal hematopoiesis but also contribute to the pathogenesis of acute leukemia. However, their clinical and prognostic relevance in myelodysplastic syndromes (MDSs) remains unclear to date. In this study, we profiled lncRNA expressions in 176 adult patients with primary MDS, and identified 4 lncRNAs whose expression levels were significantly associated with overall survival (OS). We then constructed a risk-scoring system with the weighted sum of these 4 lncRNAs. Higher lncRNA scores were associated with higher marrow blast percentages, higher-risk subtypes of MDSs (based on both the Revised International Prognostic Scoring System [IPSS-R] and World Health Organization classification), complex cytogenetic changes, and mutations in RUNX1, ASXL1, TP53, SRSF2, and ZRSR2, whereas they were inversely correlated with SF3B1 mutation. Patients with higher lncRNA scores had a significantly shorter OS and a higher 5-year leukemic transformation rate compared with those with lower scores. The prognostic significance of our 4-lncRNA risk score could be validated in an independent MDS cohort. In multivariate analysis, higher lncRNA scores remained an independent unfavorable risk factor for OS (relative risk, 4.783; P < .001) irrespective of age, cytogenetics, IPSS-R, and gene mutations. To our knowledge, this is the first report to provide a lncRNA platform for risk stratification of MDS patients. In conclusion, our integrated 4-lncRNA risk-scoring system is correlated with distinctive clinical and biological features in MDS patients, and serves as an independent prognostic factor for survival and leukemic transformation. This concise yet powerful lncRNA-based scoring system holds the potential to improve the current risk stratification of MDS patients.
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57
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Clinico-biological significance of suppressor of cytokine signaling 1 expression in acute myeloid leukemia. Blood Cancer J 2017; 7:e588. [PMID: 28753595 PMCID: PMC5549259 DOI: 10.1038/bcj.2017.67] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 05/05/2017] [Indexed: 12/19/2022] Open
Abstract
Suppressor of cytokine signaling 1 (SOCS1) protein, which encodes a member of signal transducers and activators of transcription-induced inhibitors, takes part in a negative regulation of cytokine signaling. The mechanism of SOCS1 in tumor carcinogenesis is complex and there have been no studies concerning the clinic-biologic implication of SOCS1 expression in acute myeloid leukemia (AML). Here, we first identified that higher bone marrow (BM) SOCS1 expression was closely associated with older age, FLT3-ITD, NPM1 and DNMT3A mutations, but negatively correlated with CEBPA mutation in patients with de novo AML. Compared to patients with lower SOCS1 expression, those with higher expression had lower complete remission rates and shorter overall survival. Further, higher expression of SOCS1 in the BM was an independent unfavorable prognostic factor irrespective of age, white blood cell, cytogenetics and gene mutations. Next, we generated zebrafish model overexpressing SOCS1 by spi1 promoter, which showed kidney marrow from adult SOCS1 zebrafish had increased myelopoiesis, myeloid progenitors and the kidney or spleen structure were effaced and distorted, mimicking leukemia phenotype. The SOCS1/FLT3-ITD double transgenic fish could further facilitate the leukemic process. The results indicate SOCS1 plays an important role in AML and its higher expression serves as a new biomarker to risk-stratify AML patients.
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58
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Wu SJ, Lin CT, Agathangelidis A, Lin LI, Kuo YY, Tien HF, Ghia P. Distinct molecular genetics of chronic lymphocytic leukemia in Taiwan: clinical and pathogenetic implications. Haematologica 2017; 102:1085-1090. [PMID: 28255015 PMCID: PMC5451340 DOI: 10.3324/haematol.2016.157552] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 02/16/2017] [Indexed: 11/09/2022] Open
Abstract
Differences in chronic lymphocytic leukemia between the Asian and the Western population are widely known. To further clarify these ethnic differences, we profiled the molecular genetics in a cohort of 83 newly diagnosed patients from Taiwan. In detail, we assessed: (i) the usage and the mutational status of the clonotypic immunoglobulin heavy-chain variable region (IgHV) genes, (ii) the presence of VH CDR3 stereotypes, and (iii) TP53, NOTCH1, SF3B1, BIRC3, and MYD88 mutations. The IgHV gene repertoire was biased and distinct from that observed in the West with the most common IgHV genes being IgHV3-23, IgHV3-7, and IgHV3-48 In terms of IgHV gene mutational status, 63.8% of patients carried mutated rearrangements, whereas 22.4% of patients were assigned to stereotyped subsets (6.9% to major subsets and 15.5% to minor ones). The frequencies of NOTCH1, SF3B1, BIRC3 and MYD88 mutations were 9.6%, 7.2%, 1.2%, and 2.4%, respectively; however, the frequency of TP53 mutations was significantly higher (20.5%). Patients with TP53 mutations or del(17p), SF3B1 mutations and unmutated IgHV had a worse outcome compared to the other patients. In conclusion, the differences observed in IgHV properties suggest different pathogenetic factors implicated in the development of chronic lymphocytic leukemia, while the high frequency of TP53 mutations could in part explain the dismal outcome of these patients in Taiwan.
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Affiliation(s)
- Shang-Ju Wu
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Ting Lin
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Tai-Cheng Stem Cell Therapy Center, National Taiwan University, Taipei, Taiwan
| | - Andreas Agathangelidis
- Strategic Research Program on CLL and B-cell Neoplasia Unit, Division of Experimental Oncology, Vita-Salute San Raffaele University and IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Liang-In Lin
- Department of Clinical Laboratory Science and Medical Technology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yuan-Yeh Kuo
- Graduate Institution of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Paolo Ghia
- Strategic Research Program on CLL and B-cell Neoplasia Unit, Division of Experimental Oncology, Vita-Salute San Raffaele University and IRCCS San Raffaele Scientific Institute, Milan, Italy
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Thomas M, Sukhai MA, Zhang T, Dolatshahi R, Harbi D, Garg S, Misyura M, Pugh T, Stockley TL, Kamel-Reid S. Integration of Technical, Bioinformatic, and Variant Assessment Approaches in the Validation of a Targeted Next-Generation Sequencing Panel for Myeloid Malignancies. Arch Pathol Lab Med 2017; 141:759-775. [PMID: 28557600 DOI: 10.5858/arpa.2016-0547-ra] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Detection of variants in hematologic malignancies is increasingly important because of a growing number of variants impacting diagnosis, prognosis, and treatment response, and as potential therapeutic targets. The use of next-generation sequencing technologies to detect variants in hematologic malignancies in a clinical diagnostic laboratory setting allows for efficient identification of routinely tested markers in multiple genes simultaneously, as well as the identification of novel and rare variants in other clinically relevant genes. OBJECTIVE - To apply a systematic approach to evaluate and validate a commercially available next-generation sequencing panel (TruSight Myeloid Sequencing Panel, Illumina, San Diego, California) targeting 54 genes. In this manuscript, we focused on the parameters that were used to evaluate assay performance characteristics. DATA SOURCES - Analytical validation was performed using samples containing known variants that had been identified previously. Cases were selected from different disease types, with variants in a range of genes. Panel performance characteristics were assessed and genomic regions requiring additional analysis or wet-bench approaches identified. CONCLUSIONS - We validated the performance characteristics of a myeloid next-generation sequencing panel for detection of variants. The TruSight Myeloid Sequencing Panel covers more than 95% of target regions with depth greater than 500×. However, because of unique variant types such as large insertions or deletions or genomic regions of high GC content, variants in CEBPA, FLT3, and CALR required supplementation with non-next-generation sequencing assays or with informatics approaches to address deficiencies in performance. The use of multiple bioinformatics approaches (2 variant callers and informatics scripts) allows for maximizing calling of true positives, while identifying limitations in using either method alone.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Suzanne Kamel-Reid
- From the Laboratory Medicine Program, Advanced Molecular Diagnostics Laboratory, Departments of Pathology and Genetics (Drs Thomas, Sukhai, Garg, Misyura, Stockley, and Kamel-Reid), the Princess Margaret Cancer Centre (Drs Thomas, Sukhai, Garg, Misyura, Pugh, Stockley, and Kamel-Reid and Ms Zhang), and High Performance Computing and Bioinformatics Services, Princess Margaret Genomics Centre (Dr Harbi and Mr Dolatshahi), University Health Network, Toronto, Ontario, Canada; and the Departments of Medical Biophysics (Drs Pugh and Kamel-Reid) and Laboratory Medicine and Pathobiology (Drs Stockley and Kamel-Reid), The University of Toronto, Toronto, Ontario, Canada
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60
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Bonizzato A, Gaffo E, te Kronnie G, Bortoluzzi S. CircRNAs in hematopoiesis and hematological malignancies. Blood Cancer J 2016; 6:e483. [PMID: 27740630 PMCID: PMC5098259 DOI: 10.1038/bcj.2016.81] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/11/2016] [Indexed: 12/12/2022] Open
Abstract
Cell states in hematopoiesis are controlled by master regulators and by complex circuits of a growing family of RNA species impacting cell phenotype maintenance and plasticity. Circular RNAs (circRNAs) are rapidly gaining the status of particularly stable transcriptome members with distinctive qualities. RNA-seq identified thousands of circRNAs with developmental stage- and tissue-specific expression corroborating earlier suggestions that circular isoforms are a natural feature of the cell expression program. CircRNAs are abundantly expressed also in the hematopoietic compartment. There are a number of studies on circRNAs in blood cells, a specific overview is however lacking. In this review we first present current insight in circRNA biogenesis discussing the relevance for hematopoiesis of the highly interleaved processes of splicing and circRNA biogenesis. Regarding molecular functions circRNAs modulate host gene expression, but also compete for binding of microRNAs, RNA-binding proteins or translation initiation and participate in regulatory circuits. We examine circRNA expression in the hematopoietic compartment and in hematologic malignancies and review the recent breakthrough study that identified pathogenic circRNAs derived from leukemia fusion genes. CircRNA high and regulated expression in blood cell types indicate that further studies are warranted to inform the position of these regulators in normal and malignant hematopoiesis.
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Affiliation(s)
- A Bonizzato
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - E Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - G te Kronnie
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - S Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padova, Italy
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Spinella JF, Cassart P, Richer C, Saillour V, Ouimet M, Langlois S, St-Onge P, Sontag T, Healy J, Minden MD, Sinnett D. Genomic characterization of pediatric T-cell acute lymphoblastic leukemia reveals novel recurrent driver mutations. Oncotarget 2016; 7:65485-65503. [PMID: 27602765 PMCID: PMC5323170 DOI: 10.18632/oncotarget.11796] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/24/2016] [Indexed: 11/25/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy with variable prognosis. It represents 15% of diagnosed pediatric ALL cases and has a threefold higher incidence among males. Many recurrent alterations have been identified and help define molecular subgroups of T-ALL, however the full range of events involved in driving transformation remain to be defined. Using an integrative approach combining genomic and transcriptomic data, we molecularly characterized 30 pediatric T-ALLs and identified common recurrent T-ALL targets such as FBXW7, JAK1, JAK3, PHF6, KDM6A and NOTCH1 as well as novel candidate T-ALL driver mutations including the p.R35L missense mutation in splicesome factor U2AF1 found in 3 patients and loss of function mutations in the X-linked tumor suppressor genes MED12 (frameshit mutation p.V167fs, splice site mutation g.chrX:70339329T>C, missense mutation p.R1989H) and USP9X (nonsense mutation p.Q117*). In vitro functional studies further supported the putative role of these novel T-ALL genes in driving transformation. U2AF1 p.R35L was shown to induce aberrant splicing of downstream target genes, and shRNA knockdown of MED12 and USP9X was shown to confer resistance to apoptosis following T-ALL relevant chemotherapy drug treatment in Jurkat leukemia cells. Interestingly, nearly 60% of novel candidate driver events were identified among immature T-ALL cases, highlighting the underlying genomic complexity of pediatric T-ALL, and the need for larger integrative studies to decipher the mechanisms that contribute to its various subtypes and provide opportunities to refine patient stratification and treatment.
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Affiliation(s)
| | - Pauline Cassart
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Chantal Richer
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Virginie Saillour
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Manon Ouimet
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Sylvie Langlois
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Pascal St-Onge
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Thomas Sontag
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Jasmine Healy
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Mark D. Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Daniel Sinnett
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
- Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
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62
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Genetic alterations and their clinical implications in older patients with acute myeloid leukemia. Leukemia 2016; 30:1485-92. [DOI: 10.1038/leu.2016.65] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 02/20/2016] [Accepted: 02/25/2016] [Indexed: 12/14/2022]
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63
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Hou HA, Tien HF. Mutations in epigenetic modifiers in acute myeloid leukemia and their clinical utility. Expert Rev Hematol 2016; 9:447-69. [DOI: 10.1586/17474086.2016.1144469] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan
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