1
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Yeung CCS, Eacker SM, Sala-Torra O, Beppu L, Woolston DW, Liachko I, Malig M, Stirewalt D, Fang M, Radich J. Evaluation of Acute Myeloid Leukemia Genomes using Genomic Proximity Mapping. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.31.24308228. [PMID: 38853970 PMCID: PMC11160846 DOI: 10.1101/2024.05.31.24308228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Background Cytogenetic analysis encompasses a suite of standard-of-care diagnostic testing methods that is routinely applied in cases of acute myeloid leukemia (AML) to assess chromosomal changes that are clinically relevant for risk classification and treatment decisions. Objective In this study, we assess the use of Genomic Proximity Mapping (GPM) for cytogenomic analysis of AML diagnostic specimens for detection of cytogenetic risk variants included in the European Leukemia Network (ELN) risk stratification guidelines. Methods Archival patient samples (N=48) from the Fred Hutchinson Cancer Center leukemia bank with historical clinical cytogenetic data were processed for GPM and analyzed with the CytoTerra® cloud-based analysis platform. Results GPM showed 100% concordance for all specific variants that have associated impacts on risk stratification as defined by ELN 2022 criteria, and a 72% concordance rate when considering all variants reported by the FH cytogenetic lab. GPM identified 39 additional variants, including variants of known clinical impact, not observed by cytogenetics. Conclusions GPM is an effective solution for the evaluation of known AML-associated risk variants and a source for biomarker discovery.
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Affiliation(s)
- Cecilia CS Yeung
- Translational Science and Transplantation Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Phase Genomics, Seattle, WA, USA
| | | | - Olga Sala-Torra
- Translational Science and Transplantation Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Lan Beppu
- Translational Science and Transplantation Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David W. Woolston
- Translational Science and Transplantation Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | | | - Derek Stirewalt
- Translational Science and Transplantation Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Min Fang
- Translational Science and Transplantation Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Jerald Radich
- Translational Science and Transplantation Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington Medical Center, Seattle, WA, USA
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2
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Sollier E, Kuipers J, Takahashi K, Beerenwinkel N, Jahn K. COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data. Nat Commun 2023; 14:4921. [PMID: 37582954 PMCID: PMC10427627 DOI: 10.1038/s41467-023-40378-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/19/2023] [Indexed: 08/17/2023] Open
Abstract
Reconstructing the history of somatic DNA alterations can help understand the evolution of a tumor and predict its resistance to treatment. Single-cell DNA sequencing (scDNAseq) can be used to investigate clonal heterogeneity and to inform phylogeny reconstruction. However, most existing phylogenetic methods for scDNAseq data are designed either for single nucleotide variants (SNVs) or for large copy number alterations (CNAs), or are not applicable to targeted sequencing. Here, we develop COMPASS, a computational method for inferring the joint phylogeny of SNVs and CNAs from targeted scDNAseq data. We evaluate COMPASS on simulated data and apply it to several datasets including a cohort of 123 patients with acute myeloid leukemia. COMPASS detected clonal CNAs that could be orthogonally validated with bulk data, in addition to subclonal ones that require single-cell resolution, some of which point toward convergent evolution.
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Affiliation(s)
- Etienne Sollier
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jack Kuipers
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Katharina Jahn
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
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3
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Ayala R, Carreño-Tarragona G, Barragán E, Boluda B, Larráyoz MJ, Chillón MC, Carrillo-Cruz E, Bilbao C, Sánchez-García J, Bernal T, Martinez-Cuadron D, Gil C, Serrano J, Rodriguez-Medina C, Bergua J, Pérez-Simón JA, Calbacho M, Alonso-Domínguez JM, Labrador J, Tormo M, Amigo ML, Herrera-Puente P, Rapado I, Sargas C, Vazquez I, Calasanz MJ, Gomez-Casares T, García-Sanz R, Sanz MA, Martínez-López J, Montesinos P. Impact of FLT3-ITD Mutation Status and Its Ratio in a Cohort of 2901 Patients Undergoing Upfront Intensive Chemotherapy: A PETHEMA Registry Study. Cancers (Basel) 2022; 14:cancers14235799. [PMID: 36497281 PMCID: PMC9737662 DOI: 10.3390/cancers14235799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/04/2022] [Accepted: 11/21/2022] [Indexed: 11/26/2022] Open
Abstract
FLT3−ITD results in a poor prognosis in terms of overall survival (OS) and relapse-free survival (RFS) in acute myeloid leukemia (AML). However, the prognostic usefulness of the allelic ratio (AR) to select post-remission therapy remains controversial. Our study focuses on the prognostic impact of FLT3−ITD and its ratio in a series of 2901 adult patients treated intensively in the pre-FLT3 inhibitor era and reported in the PETHEMA registry. A total of 579 of these patients (20%) harbored FLT3−ITD mutations. In multivariate analyses, patients with an FLT3−ITD allele ratio (AR) of >0.5 showed a lower complete remission (CR rate) and OS (HR 1.47, p = 0.009), while AR > 0.8 was associated with poorer RFS (HR 2.1; p < 0.001). Among NPM1/FLT3−ITD-mutated patients, median OS gradually decreased according to FLT3−ITD status and ratio (34.3 months FLT3−ITD-negative, 25.3 months up to 0.25, 14.5 months up to 0.5, and 10 months ≥ 0.5, p < 0.001). Post-remission allogeneic transplant (allo-HSCT) resulted in better OS and RFS as compared to auto-HSCT in NPM1/FLT3−ITD-mutated AML regardless of pre-established AR cutoff (≤0.5 vs. >0.5). Using the maximally selected log-rank statistics, we established an optimal cutoff of FLT3−ITD AR of 0.44 for OS, and 0.8 for RFS. We analyzed the OS and RFS according to FLT3−ITD status in all patients, and we found that the group of FLT3−ITD-positive patients with AR < 0.44 had similar 5-year OS after allo-HSCT or auto-HSCT (52% and 41%, respectively, p = 0.86), but worse RFS after auto-HSCT (p = 0.01). Among patients with FLT3−ITD AR > 0.44, allo-HSCT was superior to auto-HSCT in terms of OS and RFS. This study provides more evidence for a better characterization of patients with AML harboring FLT3−ITD mutations.
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Affiliation(s)
- Rosa Ayala
- Hematology Department, Hospital Universitario 12 de Octubre, i+12, CNIO, CIBERONC, Complutense University, 28041 Madrid, Spain
| | - Gonzalo Carreño-Tarragona
- Hematology Department, Hospital Universitario 12 de Octubre, i+12, CNIO, CIBERONC, Complutense University, 28041 Madrid, Spain
| | - Eva Barragán
- Molecular Biology Unit, Hospital Universitari i Politécnic-IIS La Fe, 46026 Valencia, Spain
| | - Blanca Boluda
- Hematology Department, Hospital Universitari i Politécnic-IIS La Fe, CIBERONC, 46026 Valencia, Spain
| | | | - María Carmen Chillón
- Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC and Center for Cancer Research-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
| | - Estrella Carrillo-Cruz
- Hospital Universitario Virgen del Rocío, Instituto de Biomedicina (IBIS/CSIC/CIBERONC), Universidad de Sevilla, 41120 Sevilla, Spain
| | - Cristina Bilbao
- Hospital Universitario de Gran Canaria Dr. Negrín, 35002 Las Palmas de Gran Canaria, Spain
| | | | - Teresa Bernal
- Hospital Universitario Central de Asturias, Instituto de Investigación del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - David Martinez-Cuadron
- Hematology Department, Hospital Universitari i Politécnic-IIS La Fe, CIBERONC, 46026 Valencia, Spain
| | - Cristina Gil
- Hospital General Universitario de Alicante, 03010 Alicante, Spain
| | - Josefina Serrano
- IMIBIC, Hematology, Hospital Universitario Reina Sofía, UCO, 14004 Córdoba, Spain
| | | | - Juan Bergua
- Hospital Universitario San Pedro de Alcántara, 10001 Cáceres, Spain
| | - José A. Pérez-Simón
- Hospital Universitario Virgen del Rocío, Instituto de Biomedicina (IBIS/CSIC/CIBERONC), Universidad de Sevilla, 41120 Sevilla, Spain
| | - María Calbacho
- Hematology Department, Hospital Universitario 12 de Octubre, i+12, CNIO, CIBERONC, Complutense University, 28041 Madrid, Spain
| | | | - Jorge Labrador
- Research Unit, Hematology Department, Hospital Universitario de Burgos, Universidad Isabel I, 09006 Burgos, Spain
| | - Mar Tormo
- Hematology Department, Hospital Clínico Universitario-INCLIVA, 46026 Valencia, Spain
| | - Maria Luz Amigo
- Hospital Universitario Morales Messeguer, 30008 Murcia, Spain
| | | | - Inmaculada Rapado
- Hematology Department, Hospital Universitario 12 de Octubre, i+12, CNIO, CIBERONC, Complutense University, 28041 Madrid, Spain
| | - Claudia Sargas
- Molecular Biology Unit, Hospital Universitari i Politécnic-IIS La Fe, 46026 Valencia, Spain
| | - Iria Vazquez
- CIMA LAB Diagnostics, Universidad de Navarra, 31008 Pamplona, Spain
| | | | - Teresa Gomez-Casares
- Hospital Universitario de Gran Canaria Dr. Negrín, 35002 Las Palmas de Gran Canaria, Spain
| | - Ramón García-Sanz
- Hospital Universitario de Salamanca (HUS/IBSAL), CIBERONC and Center for Cancer Research-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
| | - Miguel A. Sanz
- Hematology Department, Hospital Universitari i Politécnic-IIS La Fe, CIBERONC, 46026 Valencia, Spain
| | - Joaquín Martínez-López
- Hematology Department, Hospital Universitario 12 de Octubre, i+12, CNIO, CIBERONC, Complutense University, 28041 Madrid, Spain
- Correspondence: (J.M.-L.); (P.M.); Tel.: +34-917-792-788 (J.M.-L.); +34-961-244-925 (P.M.); Fax: +34-961-246-201 (P.M.)
| | - Pau Montesinos
- Hematology Department, Hospital Universitari i Politécnic-IIS La Fe, CIBERONC, 46026 Valencia, Spain
- Correspondence: (J.M.-L.); (P.M.); Tel.: +34-917-792-788 (J.M.-L.); +34-961-244-925 (P.M.); Fax: +34-961-246-201 (P.M.)
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4
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Poor outcome of pediatric patients with acute myeloid leukemia harboring high FLT3/ITD allelic ratios. Nat Commun 2022; 13:3679. [PMID: 35760968 PMCID: PMC9237020 DOI: 10.1038/s41467-022-31489-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 06/17/2022] [Indexed: 11/08/2022] Open
Abstract
Activating FLT3 mutations are the most common mutations in acute myeloid leukemia (AML), but the optimal threshold of FLT3/ITD allelic ratio (AR) among pediatric AML patients remains controversial. Here, we present the outcome and prognostic significance of FLT3/ITD AR analysis among pediatric patients with AML from the TARGET dataset. Applying fitting curve models and threshold effect analysis using the restrictive cubic spline function following Cox proportional hazards models identifies the cut-off value of 0.5 on FLT3/ITD AR. Moreover, we observe that high FLT3/ITD AR patients have an inferior outcome when compared to low AR patients. Our study also demonstrates that stem cell transplantation may improve the outcome in pediatric AML patients with high FLT3/ITD AR and may be further improved when combined with additional therapies such as Gemtuzumab Ozogamicin. These findings underline the importance of individualized treatment of pediatric AML. Activating FLT3 mutations are the most common mutations in AML. Here, the authors explore the relationship between the FLT3/ITD allelic ratio and prognosis in pediatric AML patients and identify an optimal threshold to stratify patients.
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5
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Kim T, Lee H, Capo‐Chichi J, Chang MH, Yoo YS, Basi G, Ketela T, Smith AC, Tierens A, Zhang Z, Minden MD, Kim DDH. Single cell proteogenomic sequencing identifies a relapse-fated AML subclone carrying FLT3-ITD with CN-LOH at chr13q. EJHAEM 2022; 3:426-433. [PMID: 35846029 PMCID: PMC9175792 DOI: 10.1002/jha2.390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 01/09/2023]
Abstract
Internal tandem duplication of the Feline McDonough Sarcoma (FMS)-like tyrosine kinase 3 (FLT3-ITD) is one of the most clinically relevant mutations in acute myeloid leukemia (AML), with a high FLT3-ITD allelic ratio (AR) (≥0.5) being strongly associated with poor prognosis. FLT3-ITDs are heterogeneous, varying in size and location, with some patients having multiple FLT3-ITDs. Bulk cell-based approaches are limited in their ability to reveal the clonal structure in such cases. Using single-cell proteogenomic sequencing (ScPGseq), we attempted to identify a relapse-fated subclone in an AML case with mutations in WT1, NPM1, and FLT3 tyrosine kinase domain and two FLT3-ITDs (21 bp and 39 bp) (low AR) at presentation, then relapsed only with WT1 and NPM1 mutations and one FLT3-ITD (high AR). This relapse-fated subclone at presentation (∼2.1% of sequenced cells) was characterized by the presence of a homozygous 21 bp FLT3-ITD resulting from copy neutral loss of heterozygosity (CN-LOH) of chr13q and an aberrant, immature myeloid cell surface signature, contrast to the cell surface phenotype at presentation. In contrast to results from multicolor flow-cytometry, ScPGseq not only enabled the early detection of rare relapse-fated subclone showing immature myeloid signature but also highlighted the presence of homozygous 21 bp FLT3-ITDs in the clone at presentation.
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Affiliation(s)
- TaeHyung Kim
- Division of Medical Oncology and HematologyPrincess Margaret Cancer CentreTorontoOntarioCanada,Department of Computer ScienceUniversity of TorontoTorontoOntarioCanada,The Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoOntarioCanada
| | - Hyewon Lee
- Division of Medical Oncology and HematologyPrincess Margaret Cancer CentreTorontoOntarioCanada,Center for Hematologic MalignanciesNational Cancer CenterGoyangRepublic of Korea
| | - Jose‐Mario Capo‐Chichi
- Department of Clinical Laboratory GeneticsGenome Diagnostics Laboratory Medicine ProgramUniversity of TorontoTorontoOntarioCanada
| | - Myung Hee Chang
- Division of Medical Oncology and HematologyPrincess Margaret Cancer CentreTorontoOntarioCanada,Division of Oncology‐HematologyDepartment of Internal MedicineNational Health Insurance Service Ilsan HospitalGoyangRepublic of Korea
| | - Young Seok Yoo
- Division of Medical Oncology and HematologyPrincess Margaret Cancer CentreTorontoOntarioCanada
| | - Gurbaksh Basi
- Princess Margaret Genomics CentrePrincess Margaret Cancer CentreTorontoOntarioCanada
| | - Troy Ketela
- Princess Margaret Genomics CentrePrincess Margaret Cancer CentreTorontoOntarioCanada
| | - Adam C. Smith
- Laboratory Medicine ProgramUniversity Health NetworkTorontoOntarioCanada,Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Anne Tierens
- Laboratory Medicine ProgramUniversity Health NetworkTorontoOntarioCanada,Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Zhaolei Zhang
- Department of Computer ScienceUniversity of TorontoTorontoOntarioCanada,The Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoOntarioCanada,Department of Molecular GeneticsUniversity of TorontoTorontoOntarioCanada
| | - Mark D. Minden
- Division of Medical Oncology and HematologyPrincess Margaret Cancer CentreTorontoOntarioCanada
| | - Dennis Dong Hwan Kim
- Division of Medical Oncology and HematologyPrincess Margaret Cancer CentreTorontoOntarioCanada,Hans Messner Allogeneic Blood and Marrow Transplant UnitPrincess Margaret Cancer CentreTorontoOntarioCanada
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6
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Kim JJ, Lee KS, Lee TG, Lee S, Shin S, Lee ST. A comparative study of next-generation sequencing and fragment analysis for the detection and allelic ratio determination of FLT3 internal tandem duplication. Diagn Pathol 2022; 17:14. [PMID: 35081962 PMCID: PMC8790841 DOI: 10.1186/s13000-022-01202-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Currently, FLT3 internal tandem duplication (ITD) is tested by fragment analysis. With next-generation sequencing (NGS), however, not only FLT3 ITD but also other mutations can be detected, which can provide more genetic information on disease. METHODS We retrospectively reviewed the results of two tests-fragment analysis and a custom-designed, hybridization capture-based, targeted NGS panel-performed simultaneously. We used the Pindel algorithm to detect FLT3 ITD mutations. RESULTS Among 277 bone marrow aspirate samples tested by NGS and fragment analysis, the results revealed 99.6% concordance in FLT3 ITD detection. Overall, the allele frequency (AF) attained by NGS positively correlated with the standard allelic ratio (AR) attained by fragment analysis, with a Spearman correlation coefficient (r) of 0.757 (95% confidence interval: 0.627-0.846; p < 0.001). It was concluded that an AF of 0.11 attained by NGS is the most appropriate cutoff value (with 85.3% sensitivity and 86.7% specificity) for high mutation burden criterion presented by guidelines. CONCLUSION Sensitive FLT3 ITD detection with comprehensive information of other mutation offered by NGS could be a useful tool in clinical laboratories. Future studies will be needed to evaluate and standardize NGS AF cutoff to predict actual clinical outcomes.
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Affiliation(s)
- Jin Ju Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Kwang Seob Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Taek Gyu Lee
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Republic of Korea
| | - Seungjae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
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7
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Sivakumar S, San Lucas FA, Jakubek YA, Ozcan Z, Fowler J, Scheet P. Pan cancer patterns of allelic imbalance from chromosomal alterations in 33 tumor types. Genetics 2021; 217:1-12. [PMID: 33683368 PMCID: PMC8045738 DOI: 10.1093/genetics/iyaa021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/22/2020] [Indexed: 12/14/2022] Open
Abstract
Somatic copy number alterations (SCNAs) serve as hallmarks of tumorigenesis and often result in deviations from one-to-one allelic ratios at heterozygous loci, leading to allelic imbalance (AI). The Cancer Genome Atlas (TCGA) reports SCNAs identified using a circular binary segmentation algorithm, providing segment mean copy number estimates from single-nucleotide polymorphism DNA microarray total intensities (log R ratio), but not allele-specific intensities ("B allele" frequencies) that inform of AI. Our approach provides more sensitive identification of SCNAs by modeling the "B allele" frequencies jointly, thereby bolstering the catalog of chromosomal alterations in this widely utilized resource. Here we present AI summaries for all 33 tumor sites in TCGA, including those induced by SCNAs and copy-neutral loss-of-heterozygosity (cnLOH). We identified AI in 94% of the tumors, higher than in previous reports. Recurrent events included deletions of 17p, 9q, 3p, amplifications of 8q, 1q, 7p, as well as mixed event types on 8p and 13q. We also observed both site-specific and pan-cancer (spanning 17p) cnLOH, patterns which have not been comprehensively characterized. The identification of such cnLOH events elucidates tumor suppressors and multi-hit pathways to carcinogenesis. We also contrast the landscapes inferred from AI- and total intensity-derived SCNAs and propose an automated procedure to improve and adjust SCNAs in TCGA for cases where high levels of aneuploidy obscured baseline intensity identification. Our findings support the exploration of additional methods for robust automated inference procedures and to aid empirical discoveries across TCGA.
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Affiliation(s)
- Smruthy Sivakumar
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - F Anthony San Lucas
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yasminka A Jakubek
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zuhal Ozcan
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Jerry Fowler
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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8
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Lai SH, Li YC, Zhang S, Deng R, Deng Y, Fan FY. Whole genome, exon mutation and transcriptomic profiling of acute myeloid leukemia: A case report. Oncol Lett 2021; 22:559. [PMID: 34084226 PMCID: PMC8161460 DOI: 10.3892/ol.2021.12820] [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: 03/19/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022] Open
Abstract
The present study aimed to observe previously unidentified gene mutation and expression profiles associated with acute myeloid leukemia (AML) at the individual level, based on the blood samples of a father-son pair. Genomic DNA and RNA samples from blood serum were collected. Whole-genome sequencing (WGS) and whole-exome sequencing (WES), as well as mRNA sequencing of the son, were performed. For the father's sample, a total of 3,897,164 single nucleotide polymorphisms (SNPs) and 780,834 insertion and deletions (indels) were identified. Regarding amino acid translation, there were 11,316 non-synonymous, 12 stop-loss, 12,033 synonymous, 92 stop-gain SNPs, 63 frameshift insertions, 73 frameshift deletions, 242 non-frameshift insertions, 248 non-frameshift deletions, four stop-gains and two stop-loss for indel variants. Among the AML-related genes that had been previously identified, 14 genes were found in the father's exon region. For WES of the son's DNA, 96,639 SNPs were identified, including 10,504 non-synonymous SNPs. Seven mutant genes were found in sons' exon region compared with 121 AML-related genes. Based on the transcriptomic sequencing, there were 54 differentially expressed mRNAs, including 31 upregulated and 23 downregulated mRNAs. In the exon region, 10,072 SNPs were detected, and different types of alternative splicing in the son's sample were observed. Overall, whole genome, exon mutation and transcriptomic profiling of the present two patients with AML may provide a new insight into the molecular events governing the development of AML.
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Affiliation(s)
- Si-Han Lai
- Hematology Department and Hematopoietic Stem Cell Transplantation Center, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Ye-Cheng Li
- Hematology Department and Hematopoietic Stem Cell Transplantation Center, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Shan Zhang
- Hematology Department and Hematopoietic Stem Cell Transplantation Center, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Rui Deng
- Hematology Department and Hematopoietic Stem Cell Transplantation Center, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Yan Deng
- Hematology Department and Hematopoietic Stem Cell Transplantation Center, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Fang-Yi Fan
- Hematology Department and Hematopoietic Stem Cell Transplantation Center, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
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9
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Luo Y, Lu Y, Long B, Lin Y, Yang Y, Xu Y, Zhang X, Zhang J. Blocking DNA Damage Repair May Be Involved in Stattic (STAT3 Inhibitor)-Induced FLT3-ITD AML Cell Apoptosis. Front Cell Dev Biol 2021; 9:637064. [PMID: 33796529 PMCID: PMC8007876 DOI: 10.3389/fcell.2021.637064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
The FMS-like tyrosine kinase 3 (FLT3)- internal tandem duplication (ITD) mutation can be found in approximately 25% of all acute myeloid leukemia (AML) cases and is associated with a poor prognosis. The main treatment for FLT3-ITD-positive AML patients includes genotoxic therapy and FLT3 inhibitors, which are rarely curative. Inhibiting STAT3 activity can improve the sensitivity of solid tumor cells to radiotherapy and chemotherapy. This study aimed to explore whether Stattic (a STAT3 inhibitor) affects FLT3-ITD AML cells and the underlying mechanism. Stattic can inhibit the proliferation, promote apoptosis, arrest cell cycle at G0/G1, and suppress DNA damage repair in MV4-11cells. During the process, through mRNA sequencing, we found that DNA damage repair-related mRNA are also altered during the process. In summary, the mechanism by which Stattic induces apoptosis in MV4-11cells may involve blocking DNA damage repair machineries.
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Affiliation(s)
- Yuxuan Luo
- Department of Pediatric, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Department of Hematology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ying Lu
- Department of Hematology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Department of Blood Transfusion, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Bing Long
- Department of Hematology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Sen Yat-sen Institute of Hematology, Guangzhou, China
| | - Yansi Lin
- Department of General Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanling Yang
- Department of Hematology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yichuang Xu
- Department of Hematology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiangzhong Zhang
- Department of Hematology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Sen Yat-sen Institute of Hematology, Guangzhou, China
| | - Jingwen Zhang
- Department of Hematology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Sen Yat-sen Institute of Hematology, Guangzhou, China
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10
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Descriptive and Functional Genomics in Acute Myeloid Leukemia (AML): Paving the Road for a Cure. Cancers (Basel) 2021; 13:cancers13040748. [PMID: 33670178 PMCID: PMC7916915 DOI: 10.3390/cancers13040748] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/24/2021] [Accepted: 02/01/2021] [Indexed: 12/18/2022] Open
Abstract
Over the past decades, genetic advances have allowed a more precise molecular characterization of AML with the identification of novel oncogenes and tumor suppressors as part of a comprehensive AML molecular landscape. Recent advances in genetic sequencing tools also enabled a better understanding of AML leukemogenesis from the preleukemic state to posttherapy relapse. These advances resulted in direct clinical implications with the definition of molecular prognosis classifications, the development of treatment recommendations based on minimal residual disease (MRD) measurement and the discovery of novel targeted therapies, ultimately improving AML patients' overall survival. The more recent development of functional genomic studies, pushed by novel molecular biology technologies (short hairpin RNA (shRNA) and CRISPR-Cas9) and bioinformatics tools design on one hand, along with the engineering of humanized physiologically relevant animal models on the other hand, have opened a new genomics era resulting in a greater knowledge of AML physiopathology. Combining descriptive and functional genomics will undoubtedly open the road for an AML cure within the next decades.
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11
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Marensi V, Keeshan KR, MacEwan DJ. Pharmacological impact of FLT3 mutations on receptor activity and responsiveness to tyrosine kinase inhibitors. Biochem Pharmacol 2020; 183:114348. [PMID: 33242449 DOI: 10.1016/j.bcp.2020.114348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/19/2020] [Accepted: 11/19/2020] [Indexed: 01/09/2023]
Abstract
Acute myelogenous leukaemia (AML) is an aggressive blood cancer characterized by the rapid proliferation of immature myeloid blast cells, resulting in a high mortality rate. The 5-year overall survival rate for AML patients is approximately 25%. Circa 35% of all patients carry a mutation in the FLT3 gene which have a poor prognosis. Targeting FLT3 receptor tyrosine kinase has become a treatment strategy in AML patients possessing FLT3 mutations. The most common mutations are internal tandem duplications (ITD) within exon 14 and a single nucleotide polymorphism (SNP) that leads to a point mutation in the D835 of the tyrosine kinase domain (TKD). Variations in the ITD sequence and the occurrence of other point mutations that lead to ligand-independent FLT3 receptor activation create difficulties in developing personalized therapeutic strategies to overcome observed mutation-driven drug resistance. Midostaurin and quizartinib are tyrosine kinase inhibitors (TKIs) with inhibitory efficacy against FLT3-ITD, but exhibit limited clinical impact. In this review, we focus on the structural aspects of the FLT3 receptor and correlate those mutations with receptor activation and the consequences for molecular and clinical responsiveness towards therapies targeting FLT3-ITD positive AML.
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Affiliation(s)
- Vanessa Marensi
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Karen R Keeshan
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - David J MacEwan
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
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12
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Davis L, Khoo KJ, Zhang Y, Maizels N. POLQ suppresses interhomolog recombination and loss of heterozygosity at targeted DNA breaks. Proc Natl Acad Sci U S A 2020; 117:22900-22909. [PMID: 32873648 PMCID: PMC7502765 DOI: 10.1073/pnas.2008073117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interhomolog recombination (IHR) occurs spontaneously in somatic human cells at frequencies that are low but sufficient to ameliorate some genetic diseases caused by heterozygous mutations or autosomal dominant mutations. Here we demonstrate that DNA nicks or double-strand breaks (DSBs) targeted by CRISPR-Cas9 to both homologs can stimulate IHR and associated copy-neutral loss of heterozygosity (cnLOH) in human cells. The frequency of IHR is 10-fold lower at nicks than at DSBs, but cnLOH is evident in a greater fraction of recombinants. IHR at DSBs occurs predominantly via reciprocal end joining. At DSBs, depletion of POLQ caused a dramatic increase in IHR and in the fraction of recombinants exhibiting cnLOH, suggesting that POLQ promotes end joining in cis, which limits breaks available for recombination in trans These results define conditions that may produce cnLOH as a mutagenic signature in cancer and may, conversely, promote therapeutic correction of both compound heterozygous and dominant negative mutations associated with genetic disease.
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Affiliation(s)
- Luther Davis
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195
| | - Kevin J Khoo
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195
| | - Yinbo Zhang
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195
| | - Nancy Maizels
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195;
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195
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13
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Schmidt-Arras D, Böhmer FD. Mislocalisation of Activated Receptor Tyrosine Kinases - Challenges for Cancer Therapy. Trends Mol Med 2020; 26:833-847. [PMID: 32593582 DOI: 10.1016/j.molmed.2020.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 12/20/2022]
Abstract
Activating mutations in genes encoding receptor tyrosine kinases (RTKs) mediate proliferation, cell migration, and cell survival, and are therefore important drivers of oncogenesis. Numerous targeted cancer therapies are directed against activated RTKs, including small compound inhibitors, and immunotherapies. It has recently been discovered that not only certain RTK fusion proteins, but also many full-length RTKs harbouring activating mutations, notably RTKs of the class III family, are to a large extent mislocalised in intracellular membranes. Active kinases in these locations cause aberrant activation of signalling pathways. Moreover, low levels of activated RTKs at the cell surface present an obstacle for immunotherapy. We outline here why understanding of the mechanisms underlying mislocalisation will help in improving existing and developing novel therapeutic strategies.
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Affiliation(s)
- Dirk Schmidt-Arras
- Christian-Albrechts-University Kiel, Institute of Biochemistry, 24118 Kiel, Germany.
| | - Frank-D Böhmer
- Institute of Molecular Cell Biology, CMB, Jena University Hospital, Jena, Germany
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14
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Kawase T, Nakazawa T, Eguchi T, Tsuzuki H, Ueno Y, Amano Y, Suzuki T, Mori M, Yoshida T. Effect of Fms-like tyrosine kinase 3 (FLT3) ligand (FL) on antitumor activity of gilteritinib, a FLT3 inhibitor, in mice xenografted with FL-overexpressing cells. Oncotarget 2019; 10:6111-6123. [PMID: 31692922 PMCID: PMC6817455 DOI: 10.18632/oncotarget.27222] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/10/2019] [Indexed: 12/31/2022] Open
Abstract
Therapeutic effects of FLT3 inhibitors have been reported in acute myeloid leukemia (AML) with constitutively activating FLT3 mutations, including internal tandem duplication (ITD) and point mutation, which are found in approximately one-third of AML patients. One of the critical issues of treatment with FLT3 inhibitors in FLT3-mutated AML is drug resistance. FLT3 ligand (FL) represents a mechanism of resistance to FLT3 inhibitors, including quizartinib, midostaurin, and sorafenib, in AML cells harboring both wild-type and mutant FLT3 (FLT3wt/FLT3mut). Here, we investigated the effect of FL on the efficacy of gilteritinib, a FLT3 inhibitor, in AML-derived cells in vitro and in mice. In contrast to other FLT3 inhibitors, FL stimulation had little effect on growth inhibition or apoptosis induction by gilteritinib. The antitumor activity of gilteritinib was also comparable between xenograft mouse models injected with FL-expressing and mock MOLM-13 cells. In the FLT3 signaling analyses, gilteritinib inhibited FLT3wt and FLT3-ITD to a similar degree in HEK293 and Ba/F3 cells, and similarly suppressed FLT3 downstream signaling molecules (including ERK1/2 and STAT5) in both the presence and absence of FL in MOLM-13 cells. Co-crystal structure analysis showed that gilteritinib bound to the ATP-binding pocket of FLT3. These results suggest that gilteritinib has therapeutic potential in FLT3-mutated AML patients with FL overexpression.
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Affiliation(s)
- Tatsuya Kawase
- Drug Discovery Research, Astellas Pharma, Tsukuba-shi, Ibaraki, Japan
| | - Taisuke Nakazawa
- Drug Discovery Research, Astellas Pharma, Tsukuba-shi, Ibaraki, Japan
| | - Tomohiro Eguchi
- Drug Discovery Research, Astellas Pharma, Tsukuba-shi, Ibaraki, Japan
| | - Hirofumi Tsuzuki
- Drug Discovery Research, Astellas Pharma, Tsukuba-shi, Ibaraki, Japan
| | - Yoko Ueno
- Drug Discovery Research, Astellas Pharma, Tsukuba-shi, Ibaraki, Japan
| | - Yasushi Amano
- Drug Discovery Research, Astellas Pharma, Tsukuba-shi, Ibaraki, Japan
| | - Tomoyuki Suzuki
- Drug Discovery Research, Astellas Pharma, Tsukuba-shi, Ibaraki, Japan
| | - Masamichi Mori
- Drug Discovery Research, Astellas Pharma, Tsukuba-shi, Ibaraki, Japan
| | - Taku Yoshida
- Drug Discovery Research, Astellas Pharma, Tsukuba-shi, Ibaraki, Japan
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15
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Walker CJ, Kohlschmidt J, Eisfeld AK, Mrózek K, Liyanarachchi S, Song C, Nicolet D, Blachly JS, Bill M, Papaioannou D, Oakes CC, Giacopelli B, Genutis LK, Maharry SE, Orwick S, Archer KJ, Powell BL, Kolitz JE, Uy GL, Wang ES, Carroll AJ, Stone RM, Byrd JC, de la Chapelle A, Bloomfield CD. Genetic Characterization and Prognostic Relevance of Acquired Uniparental Disomies in Cytogenetically Normal Acute Myeloid Leukemia. Clin Cancer Res 2019; 25:6524-6531. [PMID: 31375516 DOI: 10.1158/1078-0432.ccr-19-0725] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/06/2019] [Accepted: 07/30/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Uniparental disomy (UPD) is a way cancer cells duplicate a mutated gene, causing loss of heterozygosity (LOH). Patients with cytogenetically normal acute myeloid leukemia (CN-AML) do not have microscopically detectable chromosome abnormalities, but can harbor UPDs. We examined the prognostic significance of UPDs and frequency of LOH in patients with CN-AML.Experimental Design: We examined the frequency and prognostic significance of UPDs in a set of 425 adult patients with de novo CN-AML who were previously sequenced for 81 genes typically mutated in cancer. Associations of UPDs with outcome were analyzed in the 315 patients with CN-AML younger than 60 years. RESULTS We detected 127 UPDs in 109 patients. Most UPDs were large and typically encompassed all or most of the affected chromosome arm. The most common UPDs occurred on chromosome arms 13q (7.5% of patients), 6p (2.8%), and 11p (2.8%). Many UPDs significantly cooccurred with mutations in genes they encompassed, including 13q UPD with FLT3-internal tandem duplication (FLT3-ITD; P < 0.001), and 11p UPD with WT1 mutations (P = 0.02). Among patients younger than 60 years, UPD of 11p was associated with longer overall survival (OS) and 13q UPD with shorter disease-free survival (DFS) and OS. In multivariable models that accounted for known prognostic markers, including FLT3-ITD and WT1 mutations, UPD of 13q maintained association with shorter DFS, and UPD of 11p maintained association with longer OS. CONCLUSIONS LOH mediated by UPD is a recurrent feature of CN-AML. Detection of UPDs of 13q and 11p might be useful for genetic risk stratification of patients with CN-AML.
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Affiliation(s)
| | - Jessica Kohlschmidt
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.,Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | | | - Krzysztof Mrózek
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | | | - Chi Song
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, Ohio
| | - Deedra Nicolet
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.,Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - James S Blachly
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Marius Bill
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | | | | | - Brian Giacopelli
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Luke K Genutis
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Sophia E Maharry
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Shelley Orwick
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Kellie J Archer
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.,Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, Ohio
| | - Bayard L Powell
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina
| | - Jonathan E Kolitz
- Monter Cancer Center, Zucker School of Medicine at Hofstra/Northwell, Lake Success, New York
| | - Geoffrey L Uy
- Washington University School of Medicine in St. Louis, Siteman Cancer Center, St. Louis, Missouri
| | - Eunice S Wang
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | | | | | - John C Byrd
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
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16
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Tumor heterogeneity of acute myeloid leukemia: insights from single-cell sequencing. BLOOD SCIENCE 2019; 1:73-76. [PMID: 35402804 PMCID: PMC8975104 DOI: 10.1097/bs9.0000000000000015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/11/2019] [Indexed: 11/25/2022] Open
Abstract
Individual tumors comprise genetically and epigenetically heterogeneous subclones, each of which is presumably associated with a distinct function, such as self-renewal or drug sensitivity. The dissection of such intratumoral heterogeneity is crucial to understand how tumors evolve during disease progression and under the selection of therapeutic intervention. As a paradigm of cancer intratumoral heterogeneity and clonal evolution, acute myeloid leukemia (AML) has been shown to possess complex clonal architecture based on karyotype studies, as well as deep sequencing of mixed cellular populations using next-generation sequencing (NGS) technologies. The recent development of single-cell sequencing (SCS) methods provides a powerful tool to allow analysis of genomes, transcriptomes, proteomes, and epigenomes at an individual cell level. The technologies applied in AML have broadened our understanding of AML heterogeneity and provided new insights for the development of novel therapeutic strategies. In this review, we summarize the progress in the research of AML heterogeneity using SCS technology and discuss the limitations and future direction regarding how SCS can contribute to AML prognosis and treatment.
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17
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Lobashevsky AL, Krueger-Sersen M, Britton RM, Littrell CA, Singh S, Cui CP, Kashi Z, Martin RK, Breman AM, Vance GH, Farag SS. Pretransplant HLA typing revealed loss of heterozygosity in the major histocompatibility complex in a patient with acute myeloid leukemia. Hum Immunol 2019; 80:257-262. [DOI: 10.1016/j.humimm.2019.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 02/12/2019] [Accepted: 02/17/2019] [Indexed: 12/26/2022]
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18
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Assessing copy number abnormalities and copy-neutral loss-of-heterozygosity across the genome as best practice in diagnostic evaluation of acute myeloid leukemia: An evidence-based review from the cancer genomics consortium (CGC) myeloid neoplasms working group. Cancer Genet 2018; 228-229:218-235. [DOI: 10.1016/j.cancergen.2018.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 12/19/2022]
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19
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Annesley CE, Rabik C, Duffield AS, Rau RE, Magoon D, Li L, Huff V, Small D, Loeb DM, Brown P. Knock-in of the Wt1 R394W mutation causes MDS and cooperates with Flt3/ITD to drive aggressive myeloid neoplasms in mice. Oncotarget 2018; 9:35313-35326. [PMID: 30450160 PMCID: PMC6219680 DOI: 10.18632/oncotarget.26238] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 09/05/2018] [Indexed: 12/18/2022] Open
Abstract
Wilms tumor 1 (WT1) is a zinc finger transcriptional regulator, and has been implicated as both a tumor suppressor and oncogene in various malignancies. Mutations in the DNA-binding domain of the WT1 gene are described in 10-15% of normal-karyotype AML (NK-AML) in pediatric and adult patients. Similar WT1 mutations have been reported in adult patients with myelodysplastic syndrome (MDS). WT1 mutations have been independently associated with treatment failure and poor prognosis in NK-AML. Internal tandem duplication (ITD) mutations of FMS-like tyrosine kinase 3 (FLT3) commonly co-occur with WT1-mutant AML, suggesting a cooperative role in leukemogenesis. The functional role of WT1 mutations in hematologic malignancies appears to be complex and is not yet fully elucidated. Here, we describe the hematologic phenotype of a knock-in mouse model of a Wt1 mutation (R394W), described in cases of human leukemia. We show that Wt1 +/R394W mice develop MDS which becomes 100% penetrant in a transplant model, exhibit an aberrant expansion of myeloid progenitor cells, and demonstrate enhanced self-renewal of hematopoietic progenitor cells in vitro. We crossbred Wt1 +/R394W mice with knock-in Flt3 +/ITD mice, and show that mice with both mutations (Flt3 +/ITD/Wt1 +/R394W) develop a transplantable MDS/MPN, with more aggressive features compared to either single mutant mouse model.
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Affiliation(s)
| | - Cara Rabik
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amy S Duffield
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rachel E Rau
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Daniel Magoon
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Li Li
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vicki Huff
- Department of Molecular Genetics/Cancer Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Donald Small
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David M Loeb
- Current affiliation: Departments of Pediatrics and Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Patrick Brown
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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20
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Tarlock K, Zhong S, He Y, Ries R, Severson E, Bailey M, Morley S, Balasubramanian S, Erlich R, Lipson D, Otto GA, Vergillo JA, Kolb EA, Ross JS, Mughal T, Stephens PJ, Miller V, Meshinchi S, He J. Distinct age-associated molecular profiles in acute myeloid leukemia defined by comprehensive clinical genomic profiling. Oncotarget 2018; 9:26417-26430. [PMID: 29899868 PMCID: PMC5995178 DOI: 10.18632/oncotarget.25443] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/27/2018] [Indexed: 02/07/2023] Open
Abstract
Large scale comprehensive genomic profiling (CGP) has led to an improved understanding of oncogenic mutations in acute myeloid leukemia (AML), as well as identification of alterations that can serve as targets for potential therapeutic intervention. We sought to gain insight into age-associated variants in AML through comparison of extensive DNA and RNA-based GP results from pediatric and adult AML. Sequencing of 932 AML specimens (179 pediatric (age 0-18), 753 adult (age ≥ 19)) from diagnostic, relapsed, and refractory times points was performed. Comprehensive DNA (405 genes) and RNA (265) sequencing to identify a variety of structural and short variants was performed. We found that structural variants were highly prevalent in the pediatric cohort compared to the adult cohort (57% vs. 30%; p < 0.001), with certain structural variants detected only in the pediatric cohort. Fusions were the most common structural variant and were highly prevalent in AML in very young children occurring in 68% of children < 2 years of age. We observed an inverse trend in the prevalence of fusions compared to the average number of mutations per patient. In contrast to pediatric AML, adult AML was marked by short variants and multiple mutations per patient. Mutations that were common in adult AML were much less common in the adolescent and young adult cohort and were rare or absent in the pediatric cohort. Clinical CGP demonstrates the biologic differences in pediatric vs. adult AML that have significant therapeutic impacts on prognosis, therapeutic allocation, disease monitoring, and the use of more targeted therapies.
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Affiliation(s)
- Katherine Tarlock
- Department of Hematology/Oncology, Seattle Children's Hospital, Seattle WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle WA, USA
| | | | - Yuting He
- Foundation Medicine, Cambridge MA, USA
| | - Rhonda Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle WA, USA
| | | | | | | | | | | | | | | | | | - E Anders Kolb
- Nemours Center for Cancer and Blood Disorders, Nemours-Alfred I. DuPont Hospital for Children, Wilmington DE, USA
| | | | - Tariq Mughal
- Foundation Medicine, Cambridge MA, USA.,Tufts University Medical Center, Boston MA, USA
| | | | | | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle WA, USA
| | - Jie He
- Foundation Medicine, Cambridge MA, USA
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21
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Dovey OM, Cooper JL, Mupo A, Grove CS, Lynn C, Conte N, Andrews RM, Pacharne S, Tzelepis K, Vijayabaskar MS, Green P, Rad R, Arends M, Wright P, Yusa K, Bradley A, Varela I, Vassiliou GS. Molecular synergy underlies the co-occurrence patterns and phenotype of NPM1-mutant acute myeloid leukemia. Blood 2017; 130:1911-1922. [PMID: 28835438 PMCID: PMC5672315 DOI: 10.1182/blood-2017-01-760595] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 07/23/2017] [Indexed: 02/06/2023] Open
Abstract
NPM1 mutations define the commonest subgroup of acute myeloid leukemia (AML) and frequently co-occur with FLT3 internal tandem duplications (ITD) or, less commonly, NRAS or KRAS mutations. Co-occurrence of mutant NPM1 with FLT3-ITD carries a significantly worse prognosis than NPM1-RAS combinations. To understand the molecular basis of these observations, we compare the effects of the 2 combinations on hematopoiesis and leukemogenesis in knock-in mice. Early effects of these mutations on hematopoiesis show that compound Npm1cA/+;NrasG12D/+ or Npm1cA;Flt3ITD share a number of features: Hox gene overexpression, enhanced self-renewal, expansion of hematopoietic progenitors, and myeloid differentiation bias. However, Npm1cA;Flt3ITD mutants displayed significantly higher peripheral leukocyte counts, early depletion of common lymphoid progenitors, and a monocytic bias in comparison with the granulocytic bias in Npm1cA/+;NrasG12D/+ mutants. Underlying this was a striking molecular synergy manifested as a dramatically altered gene expression profile in Npm1cA;Flt3ITD , but not Npm1cA/+;NrasG12D/+ , progenitors compared with wild-type. Both double-mutant models developed high-penetrance AML, although latency was significantly longer with Npm1cA/+;NrasG12D/+ During AML evolution, both models acquired additional copies of the mutant Flt3 or Nras alleles, but only Npm1cA/+;NrasG12D/+ mice showed acquisition of other human AML mutations, including IDH1 R132Q. We also find, using primary Cas9-expressing AMLs, that Hoxa genes and selected interactors or downstream targets are required for survival of both types of double-mutant AML. Our results show that molecular complementarity underlies the higher frequency and significantly worse prognosis associated with NPM1c/FLT3-ITD vs NPM1/NRAS-G12D-mutant AML and functionally confirm the role of HOXA genes in NPM1c-driven AML.
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Affiliation(s)
- Oliver M Dovey
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Jonathan L Cooper
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Annalisa Mupo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Carolyn S Grove
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Australia
- PathWest Division of Clinical Pathology, Queen Elizabeth II Medical Centre, Nedlands, Australia
| | - Claire Lynn
- Leukemia and Stem Cell Biology Group, Division of Cancer Studies, Department of Haematological Medicine, King's College London, London, United Kingdom
| | - Nathalie Conte
- Sample Phenotype Ontology Team, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Robert M Andrews
- Institute of Translation, Innovation, Methodology, and Engagement, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Suruchi Pacharne
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Konstantinos Tzelepis
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - M S Vijayabaskar
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Paul Green
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Roland Rad
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Mark Arends
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Penny Wright
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom; and
| | - Kosuke Yusa
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Allan Bradley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria, Santander, Spain
| | - George S Vassiliou
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom; and
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Pawlina-Tyszko K, Gurgul A, Szmatoła T, Ropka-Molik K, Semik-Gurgul E, Klukowska-Rötzler J, Koch C, Mählmann K, Bugno-Poniewierska M. Genomic landscape of copy number variation and copy neutral loss of heterozygosity events in equine sarcoids reveals increased instability of the sarcoid genome. Biochimie 2017; 140:122-132. [PMID: 28743673 DOI: 10.1016/j.biochi.2017.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/20/2017] [Indexed: 12/20/2022]
Abstract
Although they are the most common neoplasms in equids, sarcoids are not fully characterized at the molecular level. Therefore, the objective of this study was to characterize the landscape of structural rearrangements, such as copy number variation (CNV) and copy neutral loss of heterozygosity (cnLOH), in the genomes of sarcoid tumor cells. This information will not only broaden our understanding of the characteristics of this genome but will also improve the general knowledge of this tumor and the mechanisms involved in its generation. To this end, Equine SNP64K Illumina microarrays were applied along with bioinformatics tools dedicated for signal intensity analysis. The analysis revealed increased instability of the genome of sarcoid cells compared with unaltered skin tissue samples, which was manifested by the prevalence of CNV and cnLOH events. Many of the identified CNVs overlapped with the other research results, but the simultaneously observed variability in the number and sizes of detected aberrations indicated a need for further studies and the development of more reliable bioinformatics algorithms. The functional analysis of genes co-localized with the identified aberrations revealed that these genes are engaged in vital cellular processes. In addition, a number of these genes directly contribute to neoplastic transformation. Furthermore, large numbers of cnLOH events identified in the sarcoids suggested that they may play no less significant roles than CNVs in the carcinogenesis of this tumor. Thus, our results indicate the importance of cnLOH and CNV in equine sarcoid oncogenesis and present a direction of future research.
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Affiliation(s)
- Klaudia Pawlina-Tyszko
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Artur Gurgul
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Tomasz Szmatoła
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Katarzyna Ropka-Molik
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Ewelina Semik-Gurgul
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Jolanta Klukowska-Rötzler
- Division of Pedriatric Hematology/Oncology, Department of Clinical Research, University of Bern, Murtenstrasse 35, 3008, Bern, Switzerland; Department of Emergency Medicine, University Hospital Bern, Inselspital, 3010, Bern, Switzerland.
| | - Christoph Koch
- Swiss Institute of Equine Medicine ISME, Faculty of Veterinary Medicine, University of Bern and Agroscope, Länggassstrasse 124c, Postfach 8466, CH-3001, Bern, Switzerland.
| | - Kathrin Mählmann
- Swiss Institute of Equine Medicine ISME, Faculty of Veterinary Medicine, University of Bern and Agroscope, Länggassstrasse 124c, Postfach 8466, CH-3001, Bern, Switzerland; Equine Clinic: Surgery and Radiology, Department of Veterinary Medicine, Free University of Berlin, Oertzenweg 19b, 14163, Berlin, Germany.
| | - Monika Bugno-Poniewierska
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
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Lagunas-Rangel FA, Chávez-Valencia V. FLT3–ITD and its current role in acute myeloid leukaemia. Med Oncol 2017; 34:114. [DOI: 10.1007/s12032-017-0970-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 04/25/2017] [Indexed: 01/20/2023]
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Rebechi MT, Pratz KW. Genomic instability is a principle pathologic feature of FLT3 ITD kinase activity in acute myeloid leukemia leading to clonal evolution and disease progression. Leuk Lymphoma 2017; 58:1-11. [PMID: 28278729 DOI: 10.1080/10428194.2017.1283031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Acute Myeloid Leukemia with FLT3 ITD mutations are associated with a poor prognosis characterized by a higher relapse rate, shorter relapse free survival, and decreased likelihood of response to therapy at relapse. FLT3 ITD signaling drives cell proliferation and survival. FLT3 ITD AML disease progression is associated with cytogenetic evolution and acquired tyrosine kinase inhibitor (TKI) resistance suggesting a potential role of genomic instability. There is growing evidence demonstrating a relationship between FLT3 signaling and increased DNA damage, specifically through increased reactive oxygen species (ROS) resulting in double-strand breaks (DSB), as well as impaired DNA repair, involving deficiencies in the non-homologous end joining (NHEJ), alternative non-homologous end joining (ALT NHEJ) and homologous recombination (HR) pathways. The role of genomic instability in the pathogenesis of FLT3 ITD AML warrants further examination as it offers potential therapeutic targets.
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Affiliation(s)
- Melanie T Rebechi
- a Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University , Baltimore , MD , USA
| | - Keith W Pratz
- a Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University , Baltimore , MD , USA
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25
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Revealing very small FLT3 ITD mutated clones by ultra-deep sequencing analysis has important clinical implications in AML patients. Oncotarget 2016; 6:31284-94. [PMID: 26384303 PMCID: PMC4741605 DOI: 10.18632/oncotarget.5161] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/24/2015] [Indexed: 01/21/2023] Open
Abstract
FLT3 internal tandem duplication (ITD), one of the most frequent mutations in Acute Myeloid Leukemia (AML), is reported to be an unstable marker, as it can evolve from FLT3 ITD- to ITD+ during the disease course. A single-gene sensitive mutational screening approach may be helpful for better clarifying the exact timing of mutation occurrence, especially when FLT3 ITD appears to occur late, at disease progression. We developed an amplicon-based ultra-deep-sequencing (UDS) approach for FLT3 mutational screening. We exploited this highly sensitive technology for the retrospective screening of diagnosis, relapse and follow-up samples of 5 out of 256 cytogenetically normal (CN-) AML who were FLT3 wild-type at presentation, but tested ITD+ at relapse or disease progression. Our study revealed that all patients carried a small ITD+ clone at diagnosis, which was undetectable by routine analysis (0,2–2% abundance). The dynamics of ITD+ clones from diagnosis to disease progression, assessed by UDS, reflected clonal evolution under treatment pressure. UDS appears as a valuable tool for FLT3 mutational screening and for the assessment of minimal residual disease (MRD) during follow-up, by detecting small ITD+ clones that may survive chemotherapy, evolve over time and definitely worsen the prognosis of CN-AML patients.
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Hong Q, Li Y, Chen X, Ye H, Tang L, Zhou A, Hu Y, Gao Y, Chen R, Xia Y, Duan S. CDKN2B, SLC19A3 and DLEC1 promoter methylation alterations in the bone marrow of patients with acute myeloid leukemia during chemotherapy. Exp Ther Med 2016; 11:1901-1907. [PMID: 27168825 DOI: 10.3892/etm.2016.3092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/19/2016] [Indexed: 12/30/2022] Open
Abstract
Previous studies have demonstrated that promoter hypermethylation of tumor suppressor genes contributes to the occurrence and development of acute myeloid leukemia (AML). However, the association of DNA methylation with chemotherapeutic outcomes remains unknown. In the present study, 15 patients with AML were recruited, and the promoter methylation status of cyclin-dependent kinase inhibitor 2B (CDKN2B), solute carrier family 19 member 3 (SLC19A3) and deleted in lung and esophageal cancer 1 (DLEC1) genes was examined prior to and following various chemotherapeutic regimens in order to identify any alterations. The results suggested that chemotherapy-induced hypermethylation of CDKN2B and DLEC1 may be specific to males and females, respectively, and that there were no alterations in SLC19A3 methylation following chemotherapy. These results may provide an improved understanding of gene methylation to guide the development of an individualized chemotherapy for AML. Due to the complexity of AML and the wide range of treatment types, future studies with a larger sample size are required in order to verify the results of the present investigation.
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Affiliation(s)
- Qingxiao Hong
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Yirun Li
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Xiaoying Chen
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Huadan Ye
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Linlin Tang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Annan Zhou
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Yuting Gao
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Rongrong Chen
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Yongming Xia
- Department of Hematology, Yuyao People's Hospital, Yuyao, Zhejiang 315400, P.R. China
| | - Shiwei Duan
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
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27
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Gronseth CM, McElhone SE, Storer BE, Kroeger KA, Sandhu V, Fero ML, Appelbaum FR, Estey EH, Fang M. Prognostic significance of acquired copy-neutral loss of heterozygosity in acute myeloid leukemia. Cancer 2015; 121:2900-8. [PMID: 26033747 DOI: 10.1002/cncr.29475] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/13/2015] [Accepted: 04/21/2015] [Indexed: 12/14/2022]
Abstract
BACKGROUND Chromosomal abnormalities are important in the diagnosis and prognosis of patients with acute myeloid leukemia (AML). Genomic microarray techniques detect recurrent copy-neutral loss of heterozygosity (cnLOH) in addition to copy number aberrations. However, the clinical utility has not been fully established. Therefore, in the current study, the authors examined the prognostic impact of acquired cnLOH in patients with AML, including complete remission (CR) rate, duration of CR, and overall survival (OS). METHODS A total of 112 consecutive patients with AML who were undergoing chromosome genomic array testing (CGAT) at the Seattle Cancer Care Alliance were included in the current study. DNA from the bone marrow or blood was analyzed with a microarray platform with both single-nucleotide polymorphism (SNP) probes and non-SNP probes to identify acquired cnLOH. Results were correlated with cytogenetic, molecular, immunophenotypic, and other clinicopathological findings. RESULTS Patients with cnLOH demonstrated a shorter duration of CR (hazard ratio, 1.87; P =.04) and worse OS (HR, 1.82; P = .03). Multivariate analyses confirmed the independent predictive value of cnLOH for early disease recurrence (P =.02). These results largely reflected those in patients with intermediate and unfavorable cytogenetics. Most strikingly, 13q cnLOH was found to demonstrate a 6.64-fold higher rate of disease recurrence (P =.006) and 3.45-fold worse OS (P = .02) and was enriched with the FLT3-ITD (Fms-related tyrosine kinase 3-internal tandem duplication) mutation. CONCLUSIONS CnLOH has important prognostic significance in patients with AML. CGAT can replace imbalance fluorescence in situ hybridization and the authors recommend the routine use of CGAT to detect cnLOH, particularly among patients with intermediate-risk cytogenetics.
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Affiliation(s)
| | - Scott E McElhone
- Cytogenetics Department, Seattle Cancer Care Alliance, Seattle, Washington
| | - Barry E Storer
- Clinical Statistics Department, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kathleen A Kroeger
- Cytogenetics Department, Seattle Cancer Care Alliance, Seattle, Washington
| | - Vicky Sandhu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Matthew L Fero
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Frederick R Appelbaum
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Elihu H Estey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Min Fang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Pathology, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
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