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Zhang L, Deeb G, Deeb KK, Vale C, Peker Barclift D, Papadantonakis N. Measurable (Minimal) Residual Disease in Myelodysplastic Neoplasms (MDS): Current State and Perspectives. Cancers (Basel) 2024; 16:1503. [PMID: 38672585 PMCID: PMC11048433 DOI: 10.3390/cancers16081503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Myelodysplastic Neoplasms (MDS) have been traditionally studied through the assessment of blood counts, cytogenetics, and morphology. In recent years, the introduction of molecular assays has improved our ability to diagnose MDS. The role of Measurable (minimal) Residual Disease (MRD) in MDS is evolving, and molecular and flow cytometry techniques have been used in several studies. In this review, we will highlight the evolving concept of MRD in MDS, outline the various techniques utilized, and provide an overview of the studies reporting MRD and the correlation with outcomes.
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Affiliation(s)
- Linsheng Zhang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - George Deeb
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kristin K. Deeb
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Colin Vale
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Deniz Peker Barclift
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nikolaos Papadantonakis
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
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2
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Pietka G, De Lord C, Matthias G, Cheung B, Atwal S, Furtado M, Cullis J, Grey-Davies L, Narayanan S, McGregor A, Kilner M, Bosworth J, McMullin MF, Coats T, Parcharidou A, Cavenagh J, Byrne J, Iyengar S, Mohammed K, Cross N, Hubank M, Ribeiro S, Khorashad J, Wren D, O'Connor S, Taussig D. Capture-based targeted sequencing using a T-cell control in myeloid malignancies and idiopathic cytopenias. Br J Haematol 2024; 204:1325-1334. [PMID: 38462984 DOI: 10.1111/bjh.19377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/30/2024] [Accepted: 02/20/2024] [Indexed: 03/12/2024]
Abstract
We report on a study of next-generation sequencing in 257 patients undergoing investigations for cytopenias. We sequenced bone marrow aspirates using a target enrichment panel comprising 82 genes and used T cells from paired blood as a control. One hundred and sixty patients had idiopathic cytopenias, 81 had myeloid malignancies and 16 had lymphoid malignancies or other diagnoses. Forty-seven of the 160 patients with idiopathic cytopenias had evidence of somatic pathogenic variants consistent with clonal cytopenias. Only 39 genes of the 82 tested were mutated in the 241 patients with either idiopathic cytopenias or myeloid neoplasms. We confirm that T cells can be used as a control to distinguish between germline and somatic variants. The use of paired analysis with a T-cell control significantly reduced the time molecular scientists spent reporting compared to unpaired analysis. We identified somatic variants of uncertain significance (VUS) in a higher proportion (24%) of patients with myeloid malignancies or clonal cytopenias compared to less than 2% of patients with non-clonal cytopenias. This suggests that somatic VUS are indicators of a clonal process. Lastly, we show that blood depleted of lymphocytes can be used in place of bone marrow as a source of material for sequencing.
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Affiliation(s)
- Grzegorz Pietka
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Department of Translational Research, Royal Marsden Hospital NHS Trust, London, UK
| | - Corinne De Lord
- Department of Haematology, St Helier Hospital, London, UK
- Department of Haematology, Royal Marsden Hospital NHS Trust, London, UK
| | - Gwynn Matthias
- Department of Haematology, Queen Alexandra Hospital, Portsmouth, UK
| | - Betty Cheung
- Department of Haematology, Croydon University Hospital, London, UK
| | - Sangeeta Atwal
- Department of Haematology, Kingston Hospital NHS Foundation Trust, London, UK
| | - Michelle Furtado
- Department of Haematology, Royal Cornwall Hospitals NHS Foundation Trust, Cornwall, Truro, UK
| | - Jonathan Cullis
- Department of Haematology, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Liz Grey-Davies
- Department of Haematology, Royal Surrey County Hospital NHS Foundation Trust, Guildford, UK
| | | | - Andrew McGregor
- Department of Haematology, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Mari Kilner
- Department of Haematology, Northumbria Healthcare NHS Foundation Trust, Tyneside, UK
| | - Jenny Bosworth
- Department of Haematology, St Helier Hospital, London, UK
- Department of Haematology, Royal Marsden Hospital NHS Trust, London, UK
| | | | - Thomas Coats
- Department of Haematology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | | | - Jamie Cavenagh
- Department of Haematology, St Bartholomew's Hospital, London, UK
| | - Jenny Byrne
- Department of Haematology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Sunil Iyengar
- Department of Haematology, Royal Marsden Hospital NHS Trust, London, UK
| | - Kabir Mohammed
- Department of Statistics, Royal Marsden Hospital NHS Trust, London, UK
| | - Nicholas Cross
- Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Genomics Laboratory Service, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Mike Hubank
- Department of Translational Research, Royal Marsden Hospital Sutton, London, UK
- Division of Molecular Pathology, Clinical Genomics (Research), Institute of Cancer Research, London, UK
| | - Sara Ribeiro
- Department of Molecular Pathology, Royal Marsden Hospital Sutton, London, UK
| | - Jamshid Khorashad
- Department of Molecular Pathology, Royal Marsden Hospital Sutton, London, UK
| | - Dorte Wren
- Department of Molecular Pathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Simon O'Connor
- Department of Histopathology, Royal Marsden NHS Foundation Trust, London, UK
| | - David Taussig
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Department of Haematology, Royal Marsden Hospital NHS Trust, London, UK
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Auger N, Douet-Guilbert N, Quessada J, Theisen O, Lafage-Pochitaloff M, Troadec MB. Cytogenetics in the management of myelodysplastic neoplasms (myelodysplastic syndromes, MDS): Guidelines from the groupe francophone de cytogénétique hématologique (GFCH). Curr Res Transl Med 2023; 71:103409. [PMID: 38091642 DOI: 10.1016/j.retram.2023.103409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 12/26/2023]
Abstract
Myelodysplastic neoplasms (MDS) are clonal hematopoietic neoplasms. Chromosomal abnormalities (CAs) are detected in 40-45% of de novo MDS and up to 80% of post-cytotoxic therapy MDS (MDS-pCT). Lately, several changes appeared in World Health Organization (WHO) classification and International Consensus Classification (ICC). The novel 'biallelic TP53 inactivation' (also called 'multi-hit TP53') MDS entity requires systematic investigation of TP53 locus (17p13.1). The ICC maintains CA allowing the diagnosis of MDS without dysplasia (del(5q), del(7q), -7 and complex karyotype). Deletion 5q is the only CA, still representing a low blast class of its own, if isolated or associated with one additional CA other than -7 or del(7q) and without multi-hit TP53. It represents one of the most frequent aberrations in adults' MDS, with chromosome 7 aberrations, and trisomy 8. Conversely, translocations are rarer in MDS. In children, del(5q) is very rare while -7 and del(7q) are predominant. Identification of a germline predisposition is key in childhood MDS. Aberrations of chromosomes 5, 7 and 17 are the most frequent in MDS-pCT, grouped in complex karyotypes. Despite the ever-increasing importance of molecular features, cytogenetics remains a major part of diagnosis and prognosis. In 2022, a molecular international prognostic score (IPSS-M) was proposed, combining the prognostic value of mutated genes to the previous scoring parameters (IPSS-R) including cytogenetics, still essential. A karyotype on bone marrow remains mandatory at diagnosis of MDS with complementary molecular analyses now required. Analyses with FISH or other technologies providing similar information can be necessary to complete and help in case of karyotype failure, for doubtful CA, for clonality assessment, and for detection of TP53 deletion to assess TP53 biallelic alterations.
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Affiliation(s)
- Nathalie Auger
- Gustave Roussy, Génétique des tumeurs, 144 rue Edouard Vaillant, Villejuif 94805, France
| | - Nathalie Douet-Guilbert
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest F-29200, France; CHRU Brest, Laboratoire de Génétique Chromosomique, Service de génétique, Brest, France
| | - Julie Quessada
- Laboratoire de Cytogénétique Hématologique, CHU Timone Aix Marseille University, Marseille, France
| | - Olivier Theisen
- Hematology Biology, Nantes University Hospital, Nantes, France
| | | | - Marie-Bérengère Troadec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest F-29200, France; CHRU Brest, Laboratoire de Génétique Chromosomique, Service de génétique, Brest, France.
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Yu ZP, Jian ZY, Sun AN, Chen BA, Ge Z. The CSN5/HSF/SPI1/PU.1 Axis Regulates Cell Proliferation in Hypocellular Myelodysplastic Syndrome Patients. J Pediatr Hematol Oncol 2023; 45:e873-e878. [PMID: 37526438 PMCID: PMC10521780 DOI: 10.1097/mph.0000000000002712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 05/20/2023] [Indexed: 08/02/2023]
Abstract
OBJECTIVE This study explored the relationship between the activation of the jak/stat3 signaling pathway and the CSN5 gene transcript and protein expression levels in the hematopoietic stem cells of patients with myelodysplastic syndromes (MDSs). This study also aimed to investigate the correlation between the expression level of CSN5 and the deubiquitination of HSF1, as well as the transcript level of the spi1/pu.1 genes to explore the pathogenesis of MDS. MATERIALS AND METHODS We isolated cells from normal individuals and MDS patients, and the mRNA and protein expression levels of spi1/pu.1 in cd34+ cells (hematopoietic stem cells) were measured by PCR and western blotting, respectively. A ChIP assay was used to detect the binding of HSF1 to the spi1/pu.1 promoter in cd34+ cells. The ubiquitination of HSF1 in cd34+ cells was detected by CO-IP. The binding of HSF1 and Fbxw7α was detected in in cd34+ cells by CO-IP. The binding of HSF1 and CSN5 was evaluated. A luciferase reporter assay was used to detect the effect of STAT3 on CSN5 promoter activation in cd34+ cells. Western blotting was used to detect the phosphorylation of STAT3 in cd34+ cells of MDS patients. The binding of STAT3 and C/EBP beta in cd34+ cells was detected by CO-IP. RESULTS Inhibition of SPI1/PU.1 expression was observed in MDS samples with low proliferation ability. Further experiments proved that phosphorylation of STAT3 affected CSN5 function and mediated the ubiquitination of HSF, the upstream regulator of SPI1/PU.1 transcription, which led to the inhibition of SPI1/PU.1 expression. Restoration of CSN5 rescued the inhibition of HSF1 ubiquitination, causing SPI1/PU.1 transcription to resume and increasing SPI1/PU.1 expression, promoting the recovery of cell proliferation in hypocellular MDS. CONCLUSIONS Our research revealed the regulatory role of the CSN5/HSF/SPI1/PU.1 axis in hypocellular MDS, providing a probable target for clinical intervention.
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Affiliation(s)
- Zheng-Ping Yu
- Department of Hematology (Key Department of Jiangsu Medicine), Zhong Da Hospital, Southeast University, Nanjing
| | - Zi-Ying Jian
- Department of Hematology (Key Department of Jiangsu Medicine), Zhong Da Hospital, Southeast University, Nanjing
| | - Ai-Ning Sun
- Hematology Division, Suzhou Medical University, Suzhou, China
| | - Bao-An Chen
- Department of Hematology (Key Department of Jiangsu Medicine), Zhong Da Hospital, Southeast University, Nanjing
| | - Zheng Ge
- Department of Hematology (Key Department of Jiangsu Medicine), Zhong Da Hospital, Southeast University, Nanjing
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Osman AEG, Mencia-Trinchant N, Saygin C, Moma L, Kim A, Housman G, Pozsgai M, Sinha E, Chandra P, Hassane DC, Sboner A, Sangani K, DiNardi N, Johnson C, Wallace SS, Jabri B, Luu H, Guzman ML, Desai P, Godley LA. Paired bone marrow and peripheral blood samples demonstrate lack of widespread dissemination of some CH clones. Blood Adv 2023; 7:1910-1914. [PMID: 36453641 PMCID: PMC10172868 DOI: 10.1182/bloodadvances.2022008521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/05/2022] [Accepted: 10/29/2022] [Indexed: 12/05/2022] Open
Abstract
Clonal hematopoiesis (CH) represents clonal expansion of mutated hematopoietic stem cells detectable in the peripheral blood or bone marrow through next generation sequencing. The current prevailing model posits that CH mutations detected in the peripheral blood mirror bone marrow mutations with clones widely disseminated across hematopoietic compartments. We sought to test the hypothesis that all clones are disseminated throughout hematopoietic tissues by comparing CH in hip vs peripheral blood specimens collected at the time of hip replacement surgery. Here, we show that patients with osteoarthritis have a high prevalence of CH, which involve genes encoding epigenetic modifiers and DNA damage repair pathway proteins. Importantly, we illustrate that CH, including clones with variant allele frequencies >10%, can be confined to specific bone marrow spaces and may be eliminated through surgical excision. Future work will define whether clones with somatic mutations in particular genes or clonal fractions of certain sizes are either more likely to be localized or are slower to disseminate into the peripheral blood and other bony sites.
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Affiliation(s)
- Afaf E. G. Osman
- Division of Hematology and Hematologic Malignancies, The University of Utah, Salt Lake City, UT
| | | | - Caner Saygin
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, Chicago, IL
| | - Luke Moma
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, Chicago, IL
| | - Aelin Kim
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, Chicago, IL
| | - Genevieve Housman
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL
| | - Matthew Pozsgai
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, Chicago, IL
| | - Eti Sinha
- Division of Hematology and Oncology, Weill Cornell Medical College, New York, NY
| | - Pooja Chandra
- Division of Hematology and Oncology, Weill Cornell Medical College, New York, NY
| | - Duane C. Hassane
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL
| | - Andrea Sboner
- Division of Hematology and Oncology, Weill Cornell Medical College, New York, NY
| | - Kishan Sangani
- Departments of Pathology and Pediatrics, Committee on Immunology, University of Chicago, Chicago, IL
| | - Nick DiNardi
- Departments of Pathology and Pediatrics, Committee on Immunology, University of Chicago, Chicago, IL
| | | | - Sara S. Wallace
- Department of Orthopedic Surgery, University of Chicago, Chicago, IL
| | - Bana Jabri
- Departments of Pathology and Pediatrics, Committee on Immunology, University of Chicago, Chicago, IL
| | - Hue Luu
- Department of Orthopedic Surgery, University of Chicago, Chicago, IL
| | - Monica L. Guzman
- Division of Hematology and Oncology, Weill Cornell Medical College, New York, NY
| | - Pinkal Desai
- Division of Hematology and Oncology, Weill Cornell Medical College, New York, NY
| | - Lucy A. Godley
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, Chicago, IL
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6
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Tsekoura G, Agathangelidis A, Kontandreopoulou CN, Taliouraki A, Mporonikola G, Stavropoulou M, Diamantopoulos PT, Viniou NA, Aleporou V, Papassideri I, Kollia P. Deregulation of Autophagy and Apoptosis in Patients with Myelodysplastic Syndromes: Implications for Disease Development and Progression. Curr Issues Mol Biol 2023; 45:4135-4150. [PMID: 37232732 DOI: 10.3390/cimb45050263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
(1) Background: Myelodysplastic neoplasms (MDSs) consist of a group of blood malignancies with a complex biological background. In this context, we investigated the role of autophagy and apoptosis in the pathogenesis and progression of MDSs. (2) Methods: To address this issue, we performed a systematic expression analysis on a total of 84 genes in patients with different types of MDSs (low/high risk of malignancy) versus healthy individuals. Furthermore, real-time quantitative PCR (qRT-PCR) was used to validate significantly upregulated or downregulated genes in a separate cohort of MDS patients and healthy controls. (3) Results: MDS patients were characterized by lower expression levels for a large series of genes involved in both processes compared to healthy individuals. Of importance, deregulation was more pronounced in patients with higher-risk MDS. Results from the qRT-PCR experiments displayed a high level of concordance with the PCR array, strengthening the relevance of our findings. (4) Conclusions: Our results indicate a clear effect of autophagy and apoptosis on MDS development, which becomes more pronounced as the disease progresses. The results from the present study are expected to assist in our understanding of the biological background of MDSs as well as in the identification of novel therapeutic targets.
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Affiliation(s)
- Georgia Tsekoura
- Division of Genetics & Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece
| | - Andreas Agathangelidis
- Division of Genetics & Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece
| | - Christina-Nefeli Kontandreopoulou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Angeliki Taliouraki
- Division of Genetics & Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece
| | - Georgia Mporonikola
- Division of Genetics & Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece
| | - Maria Stavropoulou
- Division of Genetics & Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece
| | - Panagiotis T Diamantopoulos
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Nora-Athina Viniou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Vassiliki Aleporou
- Division of Genetics & Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece
| | - Issidora Papassideri
- Division of Cell Biology and Biophysics, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece
| | - Panagoula Kollia
- Division of Genetics & Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece
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Jansko-Gadermeir B, Leisch M, Gassner FJ, Zaborsky N, Dillinger T, Hutter S, Risch A, Melchardt T, Egle A, Drost M, Larcher-Senn J, Greil R, Pleyer L. Myeloid NGS Analyses of Paired Samples from Bone Marrow and Peripheral Blood Yield Concordant Results: A Prospective Cohort Analysis of the AGMT Study Group. Cancers (Basel) 2023; 15:cancers15082305. [PMID: 37190237 DOI: 10.3390/cancers15082305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Background: Next generation sequencing (NGS) has become indispensable for diagnosis, risk stratification, prognostication, and monitoring of response in patients with myeloid neoplasias. Guidelines require bone marrow evaluations for the above, which are often not performed outside of clinical trials, indicating a need for surrogate samples. Methods: Myeloid NGS analyses (40 genes and 29 fusion drivers) of 240 consecutive, non-selected, prospectively collected, paired bone marrow/peripheral blood samples were compared. Findings: Very strong correlation (r = 0.91, p < 0.0001), high concordance (99.6%), sensitivity (98.8%), specificity (99.9%), positive predictive value (99.8%), and negative predictive value (99.6%) between NGS analyses of paired samples was observed. A total of 9/1321 (0.68%) detected mutations were discordant, 8 of which had a variant allele frequency (VAF) ≤ 3.7%. VAFs between peripheral blood and bone marrow samples were very strongly correlated in the total cohort (r = 0.93, p = 0.0001) and in subgroups without circulating blasts (r = 0.92, p < 0.0001) or with neutropenia (r = 0.88, p < 0.0001). There was a weak correlation between the VAF of a detected mutation and the blast count in either the peripheral blood (r = 0.19) or the bone marrow (r = 0.11). Interpretation: Peripheral blood samples can be used to molecularly classify and monitor myeloid neoplasms via NGS without loss of sensitivity/specificity, even in the absence of circulating blasts or in neutropenic patients.
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Affiliation(s)
- Bettina Jansko-Gadermeir
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Laboratory of Immunological and Molecular Cancer Research (LIMCR), 5020 Salzburg, Austria
- Laboratory for Molecular Cytology (MZL), 5020 Salzburg, Austria
- Department of Biosciences and Medical Biology, Allergy-Cancer-BioNano Research Centre, University of Salzburg, 5020 Salzburg, Austria
| | - Michael Leisch
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Austrian Group for Medical Tumor Therapy (AGMT) Study Group, 1180 Vienna, Austria
| | - Franz J Gassner
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Laboratory of Immunological and Molecular Cancer Research (LIMCR), 5020 Salzburg, Austria
| | - Nadja Zaborsky
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Laboratory of Immunological and Molecular Cancer Research (LIMCR), 5020 Salzburg, Austria
| | - Thomas Dillinger
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Laboratory for Molecular Cytology (MZL), 5020 Salzburg, Austria
| | - Sonja Hutter
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Laboratory for Molecular Cytology (MZL), 5020 Salzburg, Austria
| | - Angela Risch
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Department of Biosciences and Medical Biology, Allergy-Cancer-BioNano Research Centre, University of Salzburg, 5020 Salzburg, Austria
| | - Thomas Melchardt
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Austrian Group for Medical Tumor Therapy (AGMT) Study Group, 1180 Vienna, Austria
| | - Alexander Egle
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Laboratory of Immunological and Molecular Cancer Research (LIMCR), 5020 Salzburg, Austria
- Austrian Group for Medical Tumor Therapy (AGMT) Study Group, 1180 Vienna, Austria
| | - Manuel Drost
- Assign Data Management and Biostatistics GmbH, 6020 Innsbruck, Austria
| | | | - Richard Greil
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Laboratory of Immunological and Molecular Cancer Research (LIMCR), 5020 Salzburg, Austria
- Laboratory for Molecular Cytology (MZL), 5020 Salzburg, Austria
- Austrian Group for Medical Tumor Therapy (AGMT) Study Group, 1180 Vienna, Austria
| | - Lisa Pleyer
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Laboratory of Immunological and Molecular Cancer Research (LIMCR), 5020 Salzburg, Austria
- Laboratory for Molecular Cytology (MZL), 5020 Salzburg, Austria
- Austrian Group for Medical Tumor Therapy (AGMT) Study Group, 1180 Vienna, Austria
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8
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Duncavage EJ, Bagg A, Hasserjian RP, DiNardo CD, Godley LA, Iacobucci I, Jaiswal S, Malcovati L, Vannucchi AM, Patel KP, Arber DA, Arcila ME, Bejar R, Berliner N, Borowitz MJ, Branford S, Brown AL, Cargo CA, Döhner H, Falini B, Garcia-Manero G, Haferlach T, Hellström-Lindberg E, Kim AS, Klco JM, Komrokji R, Lee-Cheun Loh M, Loghavi S, Mullighan CG, Ogawa S, Orazi A, Papaemmanuil E, Reiter A, Ross DM, Savona M, Shimamura A, Skoda RC, Solé F, Stone RM, Tefferi A, Walter MJ, Wu D, Ebert BL, Cazzola M. Genomic profiling for clinical decision making in myeloid neoplasms and acute leukemia. Blood 2022; 140:2228-2247. [PMID: 36130297 PMCID: PMC10488320 DOI: 10.1182/blood.2022015853] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/27/2022] [Indexed: 11/20/2022] Open
Abstract
Myeloid neoplasms and acute leukemias derive from the clonal expansion of hematopoietic cells driven by somatic gene mutations. Although assessment of morphology plays a crucial role in the diagnostic evaluation of patients with these malignancies, genomic characterization has become increasingly important for accurate diagnosis, risk assessment, and therapeutic decision making. Conventional cytogenetics, a comprehensive and unbiased method for assessing chromosomal abnormalities, has been the mainstay of genomic testing over the past several decades and remains relevant today. However, more recent advances in sequencing technology have increased our ability to detect somatic mutations through the use of targeted gene panels, whole-exome sequencing, whole-genome sequencing, and whole-transcriptome sequencing or RNA sequencing. In patients with myeloid neoplasms, whole-genome sequencing represents a potential replacement for both conventional cytogenetic and sequencing approaches, providing rapid and accurate comprehensive genomic profiling. DNA sequencing methods are used not only for detecting somatically acquired gene mutations but also for identifying germline gene mutations associated with inherited predisposition to hematologic neoplasms. The 2022 International Consensus Classification of myeloid neoplasms and acute leukemias makes extensive use of genomic data. The aim of this report is to help physicians and laboratorians implement genomic testing for diagnosis, risk stratification, and clinical decision making and illustrates the potential of genomic profiling for enabling personalized medicine in patients with hematologic neoplasms.
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Affiliation(s)
- Eric J. Duncavage
- Department of Pathology and Immunology, Washington University, St. Louis, MO
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - Courtney D. DiNardo
- Division of Cancer Medicine, Department of Leukemia, MD Anderson Cancer Center, Houston, TX
| | - Lucy A. Godley
- Section of Hematology and Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | | | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia & Fondazione IRCCS Policlinico S. Matteo, Pavia, Italy
| | - Alessandro M. Vannucchi
- Department of Hematology, Center Research and Innovation of Myeloproliferative Neoplasms, University of Florence and Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Keyur P. Patel
- Division of Pathology/Lab Medicine, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Lettering Cancer Center, New York, NY
| | - Rafael Bejar
- Division of Hematology and Oncology, University of California San Diego, La Jolla, CA
| | - Nancy Berliner
- Division of Hematology, Brigham and Women’s Hospital, Harvard University, Boston, MA
| | - Michael J. Borowitz
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Susan Branford
- Department of Genetics and Molecular Pathology, Center for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Anna L. Brown
- Department of Pathology, South Australia Heath Alliance, Adelaide, Australia
| | - Catherine A. Cargo
- Haematological Malignancy Diagnostic Service, St James’s University Hospital, Leeds, United Kingdom
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University Hospital, Ulm, Germany
| | - Brunangelo Falini
- Department of Hematology, CREO, University of Perugia, Perugia, Italy
| | | | | | - Eva Hellström-Lindberg
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Annette S. Kim
- Department of Pathology, Brigham and Women’s Hospital, Harvard University, Boston, MA
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Rami Komrokji
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL
| | - Mignon Lee-Cheun Loh
- Department of Pediatrics, Ben Towne Center for Childhood Cancer Research, Seattle Children’s Hospital, University of Washington, Seattle, WA
| | - Sanam Loghavi
- Division of Pathology/Lab Medicine, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Seishi Ogawa
- University of Kyoto School of Medicine, Kyoto, Japan
| | - Attilio Orazi
- Department of Pathology, Texas Tech University Health Sciences Center, El Paso, TX
| | | | - Andreas Reiter
- University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - David M. Ross
- Haematology Directorate, SA Pathology, Adelaide, Australia
| | - Michael Savona
- Department of Medicine, Vanderbilt University, Nashville, TN
| | - Akiko Shimamura
- Dana Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Radek C. Skoda
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Francesc Solé
- MDS Group, Institut de Recerca contra la Leucèmia Josep Carreras, Barcelona, Spain
| | - Richard M. Stone
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | - David Wu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Mario Cazzola
- Division of Hematology, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
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9
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Concordance of Peripheral Blood and Bone Marrow Next-Generation Sequencing in Hematologic Neoplasms. Adv Hematol 2022; 2022:8091746. [PMID: 35378848 PMCID: PMC8976630 DOI: 10.1155/2022/8091746] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/02/2022] [Indexed: 11/17/2022] Open
Abstract
Objective. Mutational analysis by next-generation sequencing (NGS) obtained by peripheral blood NGS has been of clinical interest to use as a minimally invasive screening tool. Our study evaluates the correlation between NGS results on peripheral blood and bone marrow in hematolymphoid disease. Method. We evaluated patients who had NGS for presumed hematologic malignancy performed on peripheral blood and bone marrow within a 1-year interval of each other. We excluded cases in which chemotherapy or bone marrow transplant occurred in the interval between the two tests. The concordance across peripheral blood and bone marrow NGS results was assessed by kappa coefficient analysis. Results. A total of 163 patients were studied. Concordance of peripheral blood and bone marrow NGS found in 150 patients (92.0%) with a kappa coefficient of 0.794 (kappa standard error 0.054) and
value for testing kappa <0.0001. Myeloid neoplasms showed concordant results in 77/78 cases (98.7%) with a kappa coefficient of 0.916. Lymphoid neoplasms showed concordant results in 26/31 cases (83.9%) with a kappa coefficient of 0.599. Nonneoplastic cases showed concordant results in 47/54 cases (87.0%) with a kappa coefficient of 0.743. Conclusion. Peripheral blood NGS is a reliable tool for mutational analysis and provides a less invasive method for screening and monitoring of the molecular profile.
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10
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Keel S. The clinical and laboratory evaluation of patients with suspected hypocellular marrow failure. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2021; 2021:134-142. [PMID: 34889426 PMCID: PMC8791137 DOI: 10.1182/hematology.2021000244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The overlap in clinical presentation and bone marrow features of acquired and inherited causes of hypocellular marrow failure poses a significant diagnostic challenge in real case scenarios, particularly in nonsevere disease. The distinction between acquired aplastic anemia (aAA), hypocellular myelodysplastic syndrome (MDS), and inherited bone marrow failure syndromes presenting with marrow hypocellularity is critical to inform appropriate care. Here, we review the workup of hypocellular marrow failure in adolescents through adults. Given the limitations of relying on clinical stigmata or family history to identify patients with inherited etiologies, we outline a diagnostic approach incorporating comprehensive genetic testing in patients with hypocellular marrow failure that does not require immediate therapy and thus allows time to complete the evaluation. We also review the clinical utility of marrow array to detect acquired 6p copy number-neutral loss of heterozygosity to support a diagnosis of aAA, the complexities of telomere length testing in patients with aAA, short telomere syndromes, and other inherited bone marrow failure syndromes, as well as the limitations of somatic mutation testing for mutations in myeloid malignancy genes for discriminating between the various diagnostic possibilities.
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Affiliation(s)
- Siobán Keel
- University of Washington, Seattle, WA
- Correspondence Siobán Keel, University of Washington, Division of Hematology, Seattle, WA 98105; e-mail:
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11
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Mikkelsen SU, Safavi S, Dimopoulos K, O'Rourke CJ, Andersen MK, Holm MS, Marcher CW, Andersen JB, Hansen JW, Grønbæk K. Structural aberrations are associated with poor survival in patients with clonal cytopenia of undetermined significance. Haematologica 2021; 106:1762-1766. [PMID: 33179473 PMCID: PMC8168501 DOI: 10.3324/haematol.2020.263319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Indexed: 11/09/2022] Open
Affiliation(s)
- Stine U Mikkelsen
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen
| | - Setareh Safavi
- Department of Clinical Genetics, Rigshospitalet, Copenhagen
| | | | - Colm J O'Rourke
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen
| | | | - Mette S Holm
- Department of Hematology, Aarhus University Hospital, Aarhus
| | - Claus W Marcher
- Department of Hematology, Odense University Hospital, Odense
| | - Jesper B Andersen
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen
| | - Jakob W Hansen
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; DanStem, University of Copenhagen, Copenhagen
| | - Kirsten Grønbæk
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; DanStem, University of Copenhagen, Copenhagen.
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12
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Wang W, Auer P, Zhang T, Spellman S, Carlson KS, Nazha A, Bolon YT, Saber W. Impact of Epigenomic Hypermethylation at TP53 on Allogeneic Hematopoietic Cell Transplantation Outcomes for Myelodysplastic Syndromes. Transplant Cell Ther 2021; 27:659.e1-659.e6. [PMID: 33992829 PMCID: PMC8421055 DOI: 10.1016/j.jtct.2021.04.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/03/2021] [Accepted: 04/29/2021] [Indexed: 01/25/2023]
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic stem cell disorders for which allogeneic hematopoietic cell transplantation (HCT) is currently the sole curative treatment. Epigenetic lesions are considered a major pathogenetic determinant in many cancers, and in MDS, epigenetic-based interventions have emerged as life-prolonging therapies. However, the impact of epigenomic aberrations on HCT outcomes among patients with MDS are not well understood. We hypothesized that epigenomic signatures in MDS patients before undergoing HCT serve as a novel prognostic indicator of the risk of post-HCT MDS relapse. To evaluate these epigenomic signatures in MDS patients, we analyzed reduced representation bisulfite sequencing profiles in a matched case-control population of 94 patients. Among these HCT recipients, 47 patients with MDS who relapsed post-HCT (cases) were matched 1:1 to patients with MDS who did not relapse (controls). Only patients with wild-type TP53, RAS pathway, and JAK2 mutations were included in this study to promote the discovery of novel factors. Cases were matched with controls based on conditioning regimen intensity, age, sex, Revised International Prognostic Scoring System, Karnofsky Performance Status, graft type, and donor type. Pre-HCT whole-blood samples from cases and matched controls were obtained from the Center for International Blood and Marrow Transplant Research repository. We comprehensively identified differentially methylated regions (DMRs) by comparing the methylation patterns among matched cases and controls. Our findings show that cases displayed more hyper-DMRs pretransplantation compared with controls, even after adjusting for pre-HCT use of hypomethylating agents. Hyper-DMRs specific to cases were mapped to the transcription start site of 218 unique genes enriched in 5 different signaling pathways that may serve as regions of interest and factors to consider as prognostic determinants of post-HCT relapse in MDS patients. Interestingly, although patients selected for this cohort were wild-type for the TP53 gene, cases showed significantly greater levels of methylation at TP53 compared with controls. These findings indicate that previously identified prognostic genes for MDS, such as TP53, may affect disease relapse not only through genetic mutation, but also through epigenetic methylation mechanisms.
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Affiliation(s)
- Wei Wang
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | - Paul Auer
- National Marrow Donor Program/Be the Match, Minneapolis, Minnesota
| | - Tao Zhang
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | - Stephen Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | | | - Aziz Nazha
- Leukemia Program, Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Avon Lake, Ohio
| | - Yung-Tsi Bolon
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, Minnesota.
| | - Wael Saber
- Center for International Blood and Marrow Transplant Research, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
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13
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Ai X, Li B, Xu Z, Liu J, Qin T, Li Q, Xiao Z. Multiplex ligation-dependent probe amplification and fluorescence in situ hybridization for detecting chromosome abnormalities in myelodysplastic syndromes: A retrospective study. Medicine (Baltimore) 2021; 100:e25768. [PMID: 33950965 PMCID: PMC8104212 DOI: 10.1097/md.0000000000025768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/10/2021] [Indexed: 01/04/2023] Open
Abstract
This study aimed to compare interphase fluorescence in situ hybridization (iFISH) and multiplex ligation dependent probe amplification (MLPA) for identifying genetic changes in myelodysplastic syndromes (MDS).The frequencies of cytogenetic changes in MDS patients treated at the Institute of Hematology and Blood Disease Hospital (China) in 2009 to 2018 were assessed by iFISH based on bone marrow samples. Then, the effectiveness of MLPA in detecting these anomalies was evaluated.Specimens from 287 MDS patients were assessed. A total of 36.9% (103/279) of MDS cases had chromosomal abnormalities detected by iFISH; meanwhile, 44.1% (123/279) harbored ≥1 copy-number variation (CNV) based on MLPA: +8 (n=46), -5 (n = 39), -7 (n = 27), del 20 (n = 32) and del 17 (n = 17). Overall, 0 to 4 aberrations/case were detected by MLPA, suggesting the heterogeneous and complex nature of MDS cytogenetics. There were 29 cases detected by MLPA, which were undetected by FISH or showed low signals. Sixteen of these cases had their risk classification changed due to MLPA detection, including 9 reassigned to the high-risk IPSS-R group. These findings demonstrated that MLPA is highly efficient in assessing cytogenetic anomalies, with data remarkably corroborating FISH findings (overall consistency of 97.1%). The sensitivities of MLPA in detecting +8, -5, -7, del 20 and del 17 were 92.3%, 97.1%, 100%, 100%, and 90%, respectively, with specificities of 95.8%, 97.6%, 97.7%, 97.6%, and 97%, respectively.MLPA represents a reliable approach, with greater efficiency, accuracy, and speed than iFISH in identifying cytogenetic aberrations in MDS.
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Affiliation(s)
| | - Bing Li
- MDS and MPN Centre, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Zefeng Xu
- MDS and MPN Centre, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Jinqin Liu
- MDS and MPN Centre, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Tiejun Qin
- MDS and MPN Centre, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | | | - Zhijian Xiao
- Department of Pathology
- MDS and MPN Centre, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
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14
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Miller PG, Sperling AS, Gibson CJ, Pozdnyakova O, Wong WJ, Manos MP, Buchbinder EI, Hodi FS, Ebert BL, Davids MS. A deep molecular response of splenic marginal zone lymphoma to front-line checkpoint blockade. Haematologica 2021; 106:651-654. [PMID: 33054119 PMCID: PMC7849751 DOI: 10.3324/haematol.2020.258426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Peter G Miller
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Adam S Sperling
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | | | - Olga Pozdnyakova
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Waihay J Wong
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Michael P Manos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | | | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215; Howard Hughes Medical Institute, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Matthew S Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215.
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15
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Miller PG, Steensma DP. Implications of Clonal Hematopoiesis for Precision Oncology. JCO Precis Oncol 2020; 4:639-646. [PMID: 35050749 DOI: 10.1200/po.20.00144] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clonal hematopoiesis (CH) is common in middle-aged and elderly populations and confers a risk of hematological malignancy and also death due to cardiovascular disease. Prior therapy with cytotoxic chemotherapy or radiation increases the risk of CH, especially that associated with TP53 or PPM1D mutations. CH can complicate interpretation of cell-free or circulating tumor DNA assays, since most blood DNA is derived from hematopoietic cells. The specific determinants of clonal progression are unclear, but the gene carrying the mutation, size of the mutant clone, and presence of multiple mutations appear to increase risk of evolution to myeloid leukemia. While CH is not yet modifiable, specific mutations such as TET2 or IDH1/IDH2 confer vulnerabilities to established drugs or developmental compounds, and investigators are developing clinical trials to try to exploit these vulnerabilities.
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Affiliation(s)
- Peter G Miller
- Dana-Farber Cancer Institute, Boston MA.,Harvard Medical School, Boston MA
| | - David P Steensma
- Dana-Farber Cancer Institute, Boston MA.,Harvard Medical School, Boston MA
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16
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Lee S, Wang F, Trujillo‐Ocampo A, Ruiz‐Vasquez W, Cho H, Takahashi K, Molldrem JJ, Futreal A, Garcia‐Manero G, Im JS. Fidelity of peripheral blood for monitoring genomics and tumor immune‐microenvironment in myelodysplastic syndromes. EJHAEM 2020; 1:552-557. [PMID: 35844984 PMCID: PMC9175915 DOI: 10.1002/jha2.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 11/29/2022]
Abstract
The aim of this study is to investigate whether the peripheral blood (PB) can serve as a surrogate immune‐microenvironment to bone marrow for genetic and immune monitoring in myelodysplastic syndrome (MDS). We compared the composition of T cell subsets and somatic mutation burden in 36 pairs of PB and matching bone marrow aspirate (BMA) using multi‐parameter flow cytometry and NGS‐based targeted sequencing analysis, respectively. Our immune‐subset and NGS‐based mutation analysis of BMA showed significant concordance with those of PB in MDS. Therefore, PB can provide easily accessible tumor immune‐microenvironment for monitoring in the immune and genetic landscapes for MDS patients.
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Affiliation(s)
- Sung‐Eun Lee
- Department of Stem Cell Transplantation and Cellular Therapy, Division of Cancer Medicine The University of Texas M.D. Anderson Cancer Center Houston Texas USA
- Department of Hematology, Seoul St. Mary's Hospital, College of Medicine The Catholic University of Korea Seoul South Korea
| | - Feng Wang
- Department of Genomic Medicine, Division of Cancer Medicine The University of Texas M.D. Anderson Cancer Center Houston Texas USA
| | - Abel Trujillo‐Ocampo
- Department of Stem Cell Transplantation and Cellular Therapy, Division of Cancer Medicine The University of Texas M.D. Anderson Cancer Center Houston Texas USA
| | - Wilfredo Ruiz‐Vasquez
- Department of Stem Cell Transplantation and Cellular Therapy, Division of Cancer Medicine The University of Texas M.D. Anderson Cancer Center Houston Texas USA
| | - Hyun‐Woo Cho
- Department of Stem Cell Transplantation and Cellular Therapy, Division of Cancer Medicine The University of Texas M.D. Anderson Cancer Center Houston Texas USA
| | - Koichi Takahashi
- Department of Genomic Medicine, Division of Cancer Medicine The University of Texas M.D. Anderson Cancer Center Houston Texas USA
- Department of Leukemia, Division of Cancer Medicine The University of Texas M.D. Anderson Cancer Center Houston Texas USA
| | - Jeffrey J. Molldrem
- Department of Stem Cell Transplantation and Cellular Therapy, Division of Cancer Medicine The University of Texas M.D. Anderson Cancer Center Houston Texas USA
- Department of Hematopoietic Biology and Malignancy, Division of Cancer Medicine The University of Texas M.D. Anderson Cancer Center Houston Texas USA
| | - Andrew Futreal
- Department of Genomic Medicine, Division of Cancer Medicine The University of Texas M.D. Anderson Cancer Center Houston Texas USA
| | - Guillermo Garcia‐Manero
- Department of Leukemia, Division of Cancer Medicine The University of Texas M.D. Anderson Cancer Center Houston Texas USA
| | - Jin S. Im
- Department of Stem Cell Transplantation and Cellular Therapy, Division of Cancer Medicine The University of Texas M.D. Anderson Cancer Center Houston Texas USA
- Department of Hematopoietic Biology and Malignancy, Division of Cancer Medicine The University of Texas M.D. Anderson Cancer Center Houston Texas USA
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17
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Jamali A, Kenyon B, Ortiz G, Abou-Slaybi A, Sendra VG, Harris DL, Hamrah P. Plasmacytoid dendritic cells in the eye. Prog Retin Eye Res 2020; 80:100877. [PMID: 32717378 DOI: 10.1016/j.preteyeres.2020.100877] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/28/2020] [Accepted: 06/05/2020] [Indexed: 02/07/2023]
Abstract
Plasmacytoid dendritic cells (pDCs) are a unique subpopulation of immune cells, distinct from classical dendritic cells. pDCs are generated in the bone marrow and following development, they typically home to secondary lymphoid tissues. While peripheral tissues are generally devoid of pDCs during steady state, few tissues, including the lung, kidney, vagina, and in particular ocular tissues harbor resident pDCs. pDCs were originally appreciated for their potential to produce large quantities of type I interferons in viral immunity. Subsequent studies have now unraveled their pivotal role in mediating immune responses, in particular in the induction of tolerance. In this review, we summarize our current knowledge on pDCs in ocular tissues in both mice and humans, in particular in the cornea, limbus, conjunctiva, choroid, retina, and lacrimal gland. Further, we will review our current understanding on the significance of pDCs in ameliorating inflammatory responses during herpes simplex virus keratitis, sterile inflammation, and corneal transplantation. Moreover, we describe their novel and pivotal neuroprotective role, their key function in preserving corneal angiogenic privilege, as well as their potential application as a cell-based therapy for ocular diseases.
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Affiliation(s)
- Arsia Jamali
- Center for Translational Ocular Immunology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA; Department of Ophthalmology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA
| | - Brendan Kenyon
- Center for Translational Ocular Immunology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA; Program in Neuroscience, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA
| | - Gustavo Ortiz
- Center for Translational Ocular Immunology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA; Department of Ophthalmology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA
| | - Abdo Abou-Slaybi
- Center for Translational Ocular Immunology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA; Program in Immunology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA
| | - Victor G Sendra
- Center for Translational Ocular Immunology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA; Department of Ophthalmology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA
| | - Deshea L Harris
- Center for Translational Ocular Immunology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA; Department of Ophthalmology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA
| | - Pedram Hamrah
- Center for Translational Ocular Immunology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA; Department of Ophthalmology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA; Program in Neuroscience, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA; Program in Immunology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA; Cornea Service, Tufts New England Eye Center, Boston, MA, USA.
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18
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Sun L, Babushok DV. Secondary myelodysplastic syndrome and leukemia in acquired aplastic anemia and paroxysmal nocturnal hemoglobinuria. Blood 2020; 136:36-49. [PMID: 32430502 PMCID: PMC7332901 DOI: 10.1182/blood.2019000940] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/09/2019] [Indexed: 02/06/2023] Open
Abstract
Acquired aplastic anemia (AA) and paroxysmal nocturnal hemoglobinuria (PNH) are pathogenically related nonmalignant bone marrow failure disorders linked to T-cell-mediated autoimmunity; they are associated with an increased risk of secondary myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Approximately 15% to 20% of AA patients and 2% to 6% of PNH patients go on to develop secondary MDS/AML by 10 years of follow-up. Factors determining an individual patient's risk of malignant transformation remain poorly defined. Recent studies identified nearly ubiquitous clonal hematopoiesis (CH) in AA patients. Similarly, CH with additional, non-PIGA, somatic alterations occurs in the majority of patients with PNH. Factors associated with progression to secondary MDS/AML include longer duration of disease, increased telomere attrition, presence of adverse prognostic mutations, and multiple mutations, particularly when occurring early in the disease course and at a high allelic burden. Here, we will review the prevalence and characteristics of somatic alterations in AA and PNH and will explore their prognostic significance and mechanisms of clonal selection. We will then discuss the available data on post-AA and post-PNH progression to secondary MDS/AML and provide practical guidance for approaching patients with PNH and AA who have CH.
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MESH Headings
- Age of Onset
- Anemia, Aplastic/drug therapy
- Anemia, Aplastic/genetics
- Anemia, Aplastic/pathology
- Antibodies, Monoclonal, Humanized/adverse effects
- Antibodies, Monoclonal, Humanized/therapeutic use
- Benzoates/adverse effects
- Benzoates/therapeutic use
- Bone Marrow/pathology
- Chromosome Aberrations
- Chromosomes, Human, Pair 7/genetics
- Clonal Evolution/drug effects
- Clone Cells/drug effects
- Clone Cells/pathology
- Disease Progression
- Granulocyte Colony-Stimulating Factor/adverse effects
- Granulocyte Colony-Stimulating Factor/therapeutic use
- Hemoglobinuria, Paroxysmal/drug therapy
- Hemoglobinuria, Paroxysmal/genetics
- Hemoglobinuria, Paroxysmal/pathology
- Humans
- Hydrazines/adverse effects
- Hydrazines/therapeutic use
- Leukemia, Myeloid, Acute/epidemiology
- Leukemia, Myeloid, Acute/etiology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Models, Biological
- Monosomy
- Mutation
- Myelodysplastic Syndromes/epidemiology
- Myelodysplastic Syndromes/etiology
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/pathology
- Oncogene Proteins, Fusion/genetics
- Pyrazoles/adverse effects
- Pyrazoles/therapeutic use
- Selection, Genetic
- Telomere Shortening
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Affiliation(s)
- Lova Sun
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, PA; and
| | - Daria V Babushok
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, PA; and
- Comprehensive Bone Marrow Failure Center, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
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19
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Kawata E, Lazo-Langner A, Xenocostas A, Hsia CC, Howson-Jan K, Deotare U, Saini L, Yang P, Broadbent R, Levy M, Howlett C, Stuart A, Kerkhof J, Santos S, Lin H, Sadikovic B, Chin-Yee I. Clinical value of next-generation sequencing compared to cytogenetics in patients with suspected myelodysplastic syndrome. Br J Haematol 2020; 192:729-736. [PMID: 32588428 DOI: 10.1111/bjh.16891] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/25/2020] [Indexed: 12/21/2022]
Abstract
Next-generation sequencing (NGS) increasingly influences diagnosis, prognosis and management of myelodysplastic syndrome (MDS). In addition to marrow morphology and flow cytometry, our institution performs cytogenetics (CG) and NGS-based testing routinely in patients with suspected MDS. We evaluated the relative value of NGS in the assessment of patients with suspected MDS. We initially compared the diagnostic and prognostic information derived from CG and NGS in 134 patients. NGS enhanced the diagnostic yield compared to CG for clonal myeloid disorders (sensitivity 77% vs. 42·2%; specificity 90·2% vs. 78%; positive predictive value 92·8% vs. 76%; and negative predictive value 70·8% vs. 45·5%). The identification of poor prognosis mutations by NGS altered risk category in 27/39 (69·2%) patients with MDS with good/intermediate risk CG. Subsequently, we prospectively evaluated 70 patients with suspected MDS using an 'NGS-first approach' with CG restricted to samples with morphological abnormalities. We rarely identified mutations or CG abnormalities in patients without dysplastic features. NGS has a superior diagnostic performance compared to CG in patients with suspected MDS. We estimate that by using an 'NGS-first approach' we could reduce karyotyping by approximately 30%.
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Affiliation(s)
- Eri Kawata
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Department of Hematology, Matsushita Memorial Hospital, Moriguchi, Osaka, Japan.,Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, Japan
| | - Alejandro Lazo-Langner
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Division of Hematology, Department of Medicine, Schulish School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Anargyros Xenocostas
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Division of Hematology, Department of Medicine, Schulish School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Cyrus C Hsia
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Division of Hematology, Department of Medicine, Schulish School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Department of Pathology & Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Kang Howson-Jan
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Division of Hematology, Department of Medicine, Schulish School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Uday Deotare
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Division of Hematology, Department of Medicine, Schulish School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Lalit Saini
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Division of Hematology, Department of Medicine, Schulish School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Ping Yang
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Cytogenetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Robert Broadbent
- Cytogenetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Michael Levy
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Christopher Howlett
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Stephanie Santos
- Molecular Genetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Hanxin Lin
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Ian Chin-Yee
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Division of Hematology, Department of Medicine, Schulish School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Department of Pathology & Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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20
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Svobodova K, Lhotska H, Hodanova L, Pavlistova L, Vesela D, Belickova M, Vesela J, Brezinova J, Sarova I, Izakova S, Lizcova L, Siskova M, Jonasova A, Cermak J, Michalova K, Zemanova Z. Cryptic aberrations may allow more accurate prognostic classification of patients with myelodysplastic syndromes and clonal evolution. Genes Chromosomes Cancer 2020; 59:396-405. [PMID: 32170980 DOI: 10.1002/gcc.22841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/03/2020] [Accepted: 02/29/2020] [Indexed: 11/05/2022] Open
Abstract
The karyotype of bone-marrow cells at the time of diagnosis is one of the most important prognostic factors in patients with myelodysplastic syndromes (MDS). In some cases, the acquisition of additional genetic aberrations (clonal evolution [CE]) associated with clinical progression may occur during the disease. We analyzed a cohort of 469 MDS patients using a combination of molecular cytogenomic methods to identify cryptic aberrations and to assess their potential role in CE. We confirmed CE in 36 (8%) patients. The analysis of bone-marrow samples with a combination of cytogenomic methods at diagnosis and after CE identified 214 chromosomal aberrations. The early genetic changes in the diagnostic samples were frequently MDS specific (17 MDS-specific/57 early changes). Most progression-related aberrations identified after CE were not MDS specific (131 non-MDS-specific/155 progression-related changes). Copy number neutral loss of heterozygosity (CN-LOH) was detected in 19% of patients. MDS-specific CN-LOH (4q, 17p) was identified in three patients, and probably pathogenic homozygous mutations were found in TET2 (4q24) and TP53 (17p13.1) genes. We observed a statistically significant difference in overall survival (OS) between the groups of patients divided according to their diagnostic cytogenomic findings, with worse OS in the group with complex karyotypes (P = .021). A combination of cytogenomic methods allowed us to detect many cryptic genomic changes and identify genes and genomic regions that may represent therapeutic targets in patients with progressive MDS.
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Affiliation(s)
- Karla Svobodova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Halka Lhotska
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Lucie Hodanova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Lenka Pavlistova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Denisa Vesela
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Monika Belickova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jitka Vesela
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jana Brezinova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Iveta Sarova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Silvia Izakova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Libuse Lizcova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Magda Siskova
- First Medical Department, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Anna Jonasova
- First Medical Department, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Jaroslav Cermak
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Kyra Michalova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Zuzana Zemanova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
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21
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Sekeres MA, Gore SD, Stablein DM, DiFronzo N, Abel GA, DeZern AE, Troy JD, Rollison DE, Thomas JW, Waclawiw MA, Liu JJ, Al Baghdadi T, Walter MJ, Bejar R, Gorak EJ, Starczynowski DT, Foran JM, Cerhan JR, Moscinski LC, Komrokji RS, Deeg HJ, Epling-Burnette PK. The National MDS Natural History Study: design of an integrated data and sample biorepository to promote research studies in myelodysplastic syndromes. Leuk Lymphoma 2019; 60:3161-3171. [PMID: 31111762 DOI: 10.1080/10428194.2019.1616186] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Myelodysplastic syndromes (MDS), a spectrum of heterogeneous hematopoietic stem cell diseases, vary in clinical severity, response to therapy, and propensity toward progression to acute myeloid leukemia. These are acquired clonal disorders resulting from somatic mutations within the hematopoietic stem or progenitor cell population. Understanding the natural history and the risk of developing leukemia and other adverse outcomes is dependent on access to well-annotated biospecimens linked to robust clinical and molecular data. To facilitate the acquisition and distribution of MDS biospecimens to the wider scientific community and support scientific discovery in this disease, the National MDS Natural History study was initiated by the National Heart, Lung, and Blood Institute (NHLBI) and is being conducted in collaboration with community hospitals and academic medical centers supported by the National Cancer Institute (NCI). The study will recruit up to 2000 MDS patients or overlapping myeloproliferative neoplasms (MDS/MPN) and up to 500 cases of idiopathic cytopenia of undetermined significance (ICUS). The National MDS Natural History Study (NCT02775383) will offer the world's largest disease-focused tissue biobank linked to longitudinal clinical and molecular data in MDS. Here, we report on the study design features and describe the vanguard phase of 200 cases. The study assembles a comprehensive clinical database, quality of life results, laboratory data, histopathology slides and images, genetic information, hematopoietic and germline tissues representing high-quality biospecimens and data from diverse centers across the United States. These resources will be available to the scientific community for investigator-initiated research.
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Affiliation(s)
| | | | | | - Nancy DiFronzo
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | | | | | | | | | - John W Thomas
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Myron A Waclawiw
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Jane Jijun Liu
- Illinois CancerCare, PC/Heartland NCORP, Peoria, IL, USA
| | | | | | - Rafael Bejar
- Moores Cancer Center, University of California, San Diego, CA, USA
| | - Edward J Gorak
- Baptist MD Anderson Cancer Center, Jacksonville, FL, USA
| | | | | | | | | | | | - H Joachim Deeg
- Clinical Research Division, Fred Hutchison Cancer Research Center, Seattle, WA, USA
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22
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Kanagal-Shamanna R, Hodge JC, Tucker T, Shetty S, Yenamandra A, Dixon-McIver A, Bryke C, Huxley E, Lennon PA, Raca G, Xu X, Jeffries S, Quintero-Rivera F, Greipp PT, Slovak ML, Iqbal MA, Fang M. Assessing copy number aberrations and copy neutral loss of heterozygosity across the genome as best practice: An evidence based review of clinical utility from the cancer genomics consortium (CGC) working group for myelodysplastic syndrome, myelodysplastic/myeloproliferative and myeloproliferative neoplasms. Cancer Genet 2018; 228-229:197-217. [PMID: 30377088 DOI: 10.1016/j.cancergen.2018.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 12/16/2022]
Abstract
Multiple studies have demonstrated the utility of chromosomal microarray (CMA) testing to identify clinically significant copy number alterations (CNAs) and copy-neutral loss-of-heterozygosity (CN-LOH) in myeloid malignancies. However, guidelines for integrating CMA as a standard practice for diagnostic evaluation, assessment of prognosis and predicting treatment response are still lacking. CMA has not been recommended for clinical work-up of myeloid malignancies by the WHO 2016 or the NCCN 2017 guidelines but is a suggested test by the European LeukaemiaNet 2013 for the diagnosis of primary myelodysplastic syndrome (MDS). The Cancer Genomics Consortium (CGC) Working Group for Myeloid Neoplasms systematically reviewed peer-reviewed literature to determine the power of CMA in (1) improving diagnostic yield, (2) refining risk stratification, and (3) providing additional genomic information to guide therapy. In this manuscript, we summarize the evidence base for the clinical utility of array testing in the workup of MDS, myelodysplastic/myeloproliferative neoplasms (MDS/MPN) and myeloproliferative neoplasms (MPN). This review provides a list of recurrent CNAs and CN-LOH noted in this disease spectrum and describes the clinical significance of the aberrations and how they complement gene mutation findings by sequencing. Furthermore, for new or suspected diagnosis of MDS or MPN, we present suggestions for integrating genomic testing methods (CMA and mutation testing by next generation sequencing) into the current standard-of-care clinical laboratory testing (karyotype, FISH, morphology, and flow).
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Affiliation(s)
- Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston TX, USA.
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics, University of California Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tracy Tucker
- Department of Pathology and Laboratory Medicine, Cancer Genetics Laboratory, British Columbia Cancer Agency, Vancouver, BC Canada
| | - Shashi Shetty
- Department of Pathology, UHCMC, University Hospitals and Case Western Reserve University, Cleveland, OH, USA
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Christine Bryke
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Emma Huxley
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA, USA
| | - Xinjie Xu
- ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Sally Jeffries
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Genomics Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Marilyn L Slovak
- TriCore Reference Laboratories, University of New Mexico, Albuquerque, NM, USA
| | - M Anwar Iqbal
- University of Rochester Medical Center, Rochester, NY, USA
| | - Min Fang
- Fred Hutchinson Cancer Research Center and University of Washington, Seattle, WA, USA.
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23
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Hwang SM, Im K, Chang YH, Park HS, Kim JA, Kim SM, Lee DS. Are clonal cells circulating in the peripheral blood of myelodysplastic syndrome?: Quantitative comparison between bone marrow and peripheral blood by targeted gene sequencing and fluorescence in situ hybridization. Leuk Res 2018; 71:92-94. [PMID: 30041080 DOI: 10.1016/j.leukres.2018.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 10/28/2022]
Affiliation(s)
- Sang Mee Hwang
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Kyongok Im
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoon Hwan Chang
- Department of Laboratory Medicine, Korea Cancer Center Hospital, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Hee Sue Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jung-Ah Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung Min Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong Soon Lee
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
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24
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Asadi Fakhr Z, Mehrzad V, Izaditabar A, Salehi M. Evaluation of the utility of peripheral blood vs bone marrow in karyotype and fluorescence in situ hybridization for myelodysplastic syndrome diagnosis. J Clin Lab Anal 2018; 32:e22586. [PMID: 29893006 DOI: 10.1002/jcla.22586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 05/19/2018] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVE To clear the role of peripheral blood as a substitution for bone marrow in myelodysplastic syndrome and to evaluate the concordance between peripheral blood and bone marrow using karyotype and fluorescence in situ hybridization (FISH) methods. METHODS We examined 35 bone marrow (BM) and peripheral blood (PB) samples from myelodysplastic syndrome (MDS) patient using karyotype and FISH. Karyotype method for BM and PB samples performed using the standard protocol with an exception for peripheral blood in which growth factor for cultivation was not used. FISH testing was performed using a panel of MDS-associated probes to detect 20q12, 20qter, 5q31, 5q33, 5p15 and chromosome 7 and 8 centromeres. RESULTS Our results showed karyotypes of BM and PB are concordant in 74% of cases, while about 53% of these concordances were achieved from cases with normal karyotypes. However, the results of BM FISH were completely concordant with PB FISH. CONCLUSION Although peripheral blood karyotype is not trustworthy for MDS diagnosis, examining peripheral blood, using the FISH method, could be useful for clinical monitoring.
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Affiliation(s)
- Zhaleh Asadi Fakhr
- Department of Genetics and Molecular Biology, Medical School, Isfahan University of Medical Science, Isfahan, Iran
| | - Valiollah Mehrzad
- Department of Hematology and Oncology, Medical School, Omid Hospital, Isfahan University of Medical Science, Isfahan, Iran
| | | | - Mansoor Salehi
- Department of Genetics and Molecular Biology, Medical School, Isfahan University of Medical Science, Isfahan, Iran.,Medical Genetics Center of Genome, Isfahan, Iran
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25
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Martin R, Acha P, Ganster C, Palomo L, Dierks S, Fuster‐Tormo F, Mallo M, Ademà V, Gómez‐Marzo P, De Haro N, Solanes N, Zamora L, Xicoy B, Shirneshan K, Flach J, Braulke F, Schanz J, Kominowski A, Stromburg M, Brockmann A, Trümper L, Solé F, Haase D. Targeted deep sequencing of CD34+ cells from peripheral blood can reproduce bone marrow molecular profile in myelodysplastic syndromes. Am J Hematol 2018; 93:E152-E154. [PMID: 29575088 PMCID: PMC6001632 DOI: 10.1002/ajh.25089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Roman Martin
- Clinics of Haematology and Medical OncologyUniversity Medical Center GöttingenGöttingen Germany
| | - Pamela Acha
- MDS Research Group, Josep Carreras Leukaemia Research Institute, ICO‐Hospital Germans Trias i Pujol, Universitat Autònoma de BarcelonaBadalona Barcelona Spain
- Departament de Biomedicina, Facultat de MedicinaUniversitat de BarcelonaBarcelona Spain
| | - Christina Ganster
- Clinics of Haematology and Medical OncologyUniversity Medical Center GöttingenGöttingen Germany
| | - Laura Palomo
- MDS Research Group, Josep Carreras Leukaemia Research Institute, ICO‐Hospital Germans Trias i Pujol, Universitat Autònoma de BarcelonaBadalona Barcelona Spain
| | - Sascha Dierks
- Clinics of Haematology and Medical OncologyUniversity Medical Center GöttingenGöttingen Germany
| | - Francisco Fuster‐Tormo
- MDS Research Group, Josep Carreras Leukaemia Research Institute, ICO‐Hospital Germans Trias i Pujol, Universitat Autònoma de BarcelonaBadalona Barcelona Spain
| | - Mar Mallo
- MDS Research Group, Josep Carreras Leukaemia Research Institute, ICO‐Hospital Germans Trias i Pujol, Universitat Autònoma de BarcelonaBadalona Barcelona Spain
| | - Vera Ademà
- MDS Research Group, Josep Carreras Leukaemia Research Institute, ICO‐Hospital Germans Trias i Pujol, Universitat Autònoma de BarcelonaBadalona Barcelona Spain
| | - Paula Gómez‐Marzo
- MDS Research Group, Josep Carreras Leukaemia Research Institute, ICO‐Hospital Germans Trias i Pujol, Universitat Autònoma de BarcelonaBadalona Barcelona Spain
| | - Nuri De Haro
- MDS Research Group, Josep Carreras Leukaemia Research Institute, ICO‐Hospital Germans Trias i Pujol, Universitat Autònoma de BarcelonaBadalona Barcelona Spain
| | - Neus Solanes
- MDS Research Group, Josep Carreras Leukaemia Research Institute, ICO‐Hospital Germans Trias i Pujol, Universitat Autònoma de BarcelonaBadalona Barcelona Spain
| | - Lurdes Zamora
- Hematology Service, ICO‐Hospital Germans Trias i Pujol, Josep Carreras Leukaemia Research Institute (IJC), Universitat Autònoma de BarcelonaBadalona Barcelona Spain
| | - Blanca Xicoy
- Hematology Service, ICO‐Hospital Germans Trias i Pujol, Josep Carreras Leukaemia Research Institute (IJC), Universitat Autònoma de BarcelonaBadalona Barcelona Spain
| | - Katayoon Shirneshan
- Clinics of Haematology and Medical OncologyUniversity Medical Center GöttingenGöttingen Germany
| | - Johanna Flach
- Clinics of Haematology and Medical OncologyUniversity Medical Center GöttingenGöttingen Germany
| | - Friederike Braulke
- Clinics of Haematology and Medical OncologyUniversity Medical Center GöttingenGöttingen Germany
| | - Julie Schanz
- Clinics of Haematology and Medical OncologyUniversity Medical Center GöttingenGöttingen Germany
| | - Arkadiusz Kominowski
- Clinics of Haematology and Medical OncologyUniversity Medical Center GöttingenGöttingen Germany
| | - Martin Stromburg
- Clinics of Haematology and Medical OncologyUniversity Medical Center GöttingenGöttingen Germany
| | - Alina Brockmann
- Clinics of Haematology and Medical OncologyUniversity Medical Center GöttingenGöttingen Germany
| | - Lorenz Trümper
- Clinics of Haematology and Medical OncologyUniversity Medical Center GöttingenGöttingen Germany
| | - Francesc Solé
- MDS Research Group, Josep Carreras Leukaemia Research Institute, ICO‐Hospital Germans Trias i Pujol, Universitat Autònoma de BarcelonaBadalona Barcelona Spain
| | - Detlef Haase
- Clinics of Haematology and Medical OncologyUniversity Medical Center GöttingenGöttingen Germany
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26
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Germ line tissues for optimal detection of somatic variants in myelodysplastic syndromes. Blood 2018; 131:2402-2405. [PMID: 29661788 DOI: 10.1182/blood-2018-01-827881] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/03/2018] [Indexed: 12/27/2022] Open
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27
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Wu B, Ingersoll K, Jug R, Yang LH, Luedke C, Lo A, Su P, Liu X, Rehder C, Gong J, Lu CM, Wang E. Myeloid Neoplasms Following Solid Organ Transplantation: Clinicopathologic Studies of 23 Cases. Am J Clin Pathol 2017; 149:55-66. [PMID: 29228125 DOI: 10.1093/ajcp/aqx133] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVES Myeloid neoplasms (MNs) after solid organ transplant are rare, and their clinicopathologic features have not been well characterized. METHODS We retrospectively analyzed 23 such cases. RESULTS The ages ranged from 2 to 76 years, with a median of 59 years at the diagnosis. The median interval between the transplant and diagnosis was 56 months (range, 8-384 months). The transplanted organs included liver in five, kidney in six, lung in five, heart in six, and heart/lung in one case(s). The types of MN included acute myeloid leukemia (AML) in 12, myelodysplastic syndrome (MDS) in five, chronic myelogenous leukemia (CML) in four, and myeloproliferative neoplasms (MPNs) in two cases. Cytogenetics demonstrated clonal abnormalities in 18 (78.3%) cases, including unbalanced changes in 10 (55.6%), Philadelphia chromosome in four (22.2%), and other balanced aberrations in four (22.2%) cases. Thirteen (56.5%) patients died, with an estimated median survival of 9 months. With disease stratification, AML and MDS have short median survivals (3.5 and 7 months, respectively), with an initial precipitous decline of the survival curve. CONCLUSIONS Posttransplant MNs have a latency period between that seen in AML/MDS related to alkylators and that associated with topoisomerase II inhibitors. The cytogenetic profile suggests a mutagenic effect on leukemogenesis. The clinical outcome for AML/MDS is dismal, with death occurring at an early phase of treatment.
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MESH Headings
- Adult
- Aged
- Bone Marrow/pathology
- Child, Preschool
- Cytogenetics
- Humans
- Kaplan-Meier Estimate
- Kidney/pathology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/mortality
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Liver/pathology
- Lung/pathology
- Middle Aged
- Mutation
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/mortality
- Myelodysplastic Syndromes/pathology
- Myeloproliferative Disorders/genetics
- Myeloproliferative Disorders/mortality
- Myeloproliferative Disorders/pathology
- Myocardium/pathology
- Organ Transplantation/adverse effects
- Retrospective Studies
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Affiliation(s)
- Bin Wu
- Division of Hematology, Department of Medicine, Shengjing Hospital affiliated to China Medical University, Shenyang, China
- Department of Pathology, Duke University Medical Center, Durham, NC
| | | | - Rachel Jug
- Department of Pathology, Duke University Medical Center, Durham, NC
| | - Lian-He Yang
- Department of Pathology, Duke University Medical Center, Durham, NC
| | - Catherine Luedke
- Department of Pathology, Duke University Medical Center, Durham, NC
| | - Amanda Lo
- Department of Pathology, Duke University Medical Center, Durham, NC
| | - Pu Su
- Department of Pathology, Duke University Medical Center, Durham, NC
| | - Xin Liu
- Department of Pathology, Duke University Medical Center, Durham, NC
| | - Catherine Rehder
- Department of Pathology, Duke University Medical Center, Durham, NC
| | - Jerald Gong
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA
| | - Chuanyi Mark Lu
- Department of Laboratory Medicine, University of California, San Francisco
| | - Endi Wang
- Department of Pathology, Duke University Medical Center, Durham, NC
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28
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Jann JC, Nowak D, Nolte F, Fey S, Nowak V, Obländer J, Pressler J, Palme I, Xanthopoulos C, Fabarius A, Platzbecker U, Giagounidis A, Götze K, Letsch A, Haase D, Schlenk R, Bug G, Lübbert M, Ganser A, Germing U, Haferlach C, Hofmann WK, Mossner M. Accurate quantification of chromosomal lesions via short tandem repeat analysis using minimal amounts of DNA. J Med Genet 2017; 54:640-650. [PMID: 28600436 PMCID: PMC5574397 DOI: 10.1136/jmedgenet-2017-104528] [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: 01/10/2017] [Revised: 02/15/2017] [Accepted: 03/22/2017] [Indexed: 11/04/2022]
Abstract
Background Cytogenetic aberrations such as deletion of chromosome 5q (del(5q)) represent key elements in routine clinical diagnostics of haematological malignancies. Currently established methods such as metaphase cytogenetics, FISH or array-based approaches have limitations due to their dependency on viable cells, high costs or semi-quantitative nature. Importantly, they cannot be used on low abundance DNA. We therefore aimed to establish a robust and quantitative technique that overcomes these shortcomings. Methods For precise determination of del(5q) cell fractions, we developed an inexpensive multiplex-PCR assay requiring only nanograms of DNA that simultaneously measures allelic imbalances of 12 independent short tandem repeat markers. Results Application of this method to n=1142 samples from n=260 individuals revealed strong intermarker concordance (R²=0.77–0.97) and reproducibility (mean SD: 1.7%). Notably, the assay showed accurate quantification via standard curve assessment (R²>0.99) and high concordance with paired FISH measurements (R²=0.92) even with subnanogram amounts of DNA. Moreover, cytogenetic response was reliably confirmed in del(5q) patients with myelodysplastic syndromes treated with lenalidomide. While the assay demonstrated good diagnostic accuracy in receiver operating characteristic analysis (area under the curve: 0.97), we further observed robust correlation between bone marrow and peripheral blood samples (R²=0.79), suggesting its potential suitability for less-invasive clonal monitoring. Conclusions In conclusion, we present an adaptable tool for quantification of chromosomal aberrations, particularly in problematic samples, which should be easily applicable to further tumour entities.
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Affiliation(s)
- Johann-Christoph Jann
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Daniel Nowak
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Florian Nolte
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Stephanie Fey
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Verena Nowak
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Julia Obländer
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Jovita Pressler
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Iris Palme
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Christina Xanthopoulos
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Alice Fabarius
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Uwe Platzbecker
- Medizinische Klinik und Poliklinik I, Universitatsklinikum Carl Gustav Carus, Dresden, Germany
| | | | - Katharina Götze
- III. Medizinischen Klinik des Klinikums rechts der Isar, Technische Universitat Munchen, Munchen, Germany
| | - Anne Letsch
- Medizinische Klinik für Hämatologie, Onkologie, Campus Benjamin Franklin, Charite Universitatsmedizin Berlin, Berlin, Germany
| | - Detlef Haase
- Klinik für Hämatologie und Medizinische Onkologie, Georg-August-Universitat Gottingen Universitatsmedizin, Gottingen, Germany
| | - Richard Schlenk
- NCT Trial Center, Nationales Centrum für Tumorerkrankungen (NCT), Heidelberg, Gemany
| | - Gesine Bug
- Medizinische Klinik II, Abteilung für Hämatologie/Onkologie, Klinikum der Johann Wolfgang Goethe-Universitat Frankfurt, Frankfurt am Main, Germany
| | - Michael Lübbert
- Abteilung für Innere Medizin I, Hämatologie und Onkologie, Universitatsklinikum Freiburg, Freiburg, Germany
| | - Arnold Ganser
- Abteilung für Hämatologie, Hämostaseologie, Onkologie und Stammzelltransplantation, Medizinische Hochschule Hannover, Hannover, Germany
| | - Ulrich Germing
- Abteilung für Hämatologie, Onkologie und klinische Immunologie, Heinrich-Heine-Universitat Dusseldorf Medizinische Fakultat, Dusseldorf, Germany
| | | | - Wolf-Karsten Hofmann
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Maximilian Mossner
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
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29
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da Silva-Coelho P, Kroeze LI, Yoshida K, Koorenhof-Scheele TN, Knops R, van de Locht LT, de Graaf AO, Massop M, Sandmann S, Dugas M, Stevens-Kroef MJ, Cermak J, Shiraishi Y, Chiba K, Tanaka H, Miyano S, de Witte T, Blijlevens NMA, Muus P, Huls G, van der Reijden BA, Ogawa S, Jansen JH. Clonal evolution in myelodysplastic syndromes. Nat Commun 2017; 8:15099. [PMID: 28429724 PMCID: PMC5530598 DOI: 10.1038/ncomms15099] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 02/24/2017] [Indexed: 02/08/2023] Open
Abstract
Cancer development is a dynamic process during which the successive accumulation of mutations results in cells with increasingly malignant characteristics. Here, we show the clonal evolution pattern in myelodysplastic syndrome (MDS) patients receiving supportive care, with or without lenalidomide (follow-up 2.5–11 years). Whole-exome and targeted deep sequencing at multiple time points during the disease course reveals that both linear and branched evolutionary patterns occur with and without disease-modifying treatment. The application of disease-modifying therapy may create an evolutionary bottleneck after which more complex MDS, but also unrelated clones of haematopoietic cells, may emerge. In addition, subclones that acquired an additional mutation associated with treatment resistance (TP53) or disease progression (NRAS, KRAS) may be detected months before clinical changes become apparent. Monitoring the genetic landscape during the disease may help to guide treatment decisions. Myelodysplastic syndromes are a broad group of haematopoietic malignancies that often progress to acute myeloid leukaemia. Here, the authors show that linear and branched evolution occurs within myelodysplastic syndrome and these patterns can be impacted by treatment.
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Affiliation(s)
- Pedro da Silva-Coelho
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands.,Department of Haematology, Centro Hospitalar de São João and Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, Porto 4200-319, Portugal
| | - Leonie I Kroeze
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto-shi, Kyoto 606-8501, Japan
| | - Theresia N Koorenhof-Scheele
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Ruth Knops
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Louis T van de Locht
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Aniek O de Graaf
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Marion Massop
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Marian J Stevens-Kroef
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Jaroslav Cermak
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20 Prague 2, Czech Republic
| | - Yuichi Shiraishi
- Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639 Japan
| | - Kenichi Chiba
- Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639 Japan
| | - Hiroko Tanaka
- Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639 Japan
| | - Satoru Miyano
- Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639 Japan
| | - Theo de Witte
- Department of Tumor Immunology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Nicole M A Blijlevens
- Department of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Petra Muus
- Department of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Gerwin Huls
- Department of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands.,Department of Hematology, University Medical Centre Groningen, PO Box 30001, 9700 RB Groningen, The Netherlands
| | - Bert A van der Reijden
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto-shi, Kyoto 606-8501, Japan
| | - Joop H Jansen
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
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30
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Stevens-Kroef MJ, Olde Weghuis D, ElIdrissi-Zaynoun N, van der Reijden B, Cremers EMP, Alhan C, Westers TM, Visser-Wisselaar HA, Chitu DA, Cunha SM, Vellenga E, Klein SK, Wijermans P, de Greef GE, Schaafsma MR, Muus P, Ossenkoppele GJ, van de Loosdrecht AA, Jansen JH. Genomic array as compared to karyotyping in myelodysplastic syndromes in a prospective clinical trial. Genes Chromosomes Cancer 2017; 56:524-534. [DOI: 10.1002/gcc.22455] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/16/2017] [Accepted: 02/16/2017] [Indexed: 02/06/2023] Open
Affiliation(s)
| | - Daniel Olde Weghuis
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | | | - Bert van der Reijden
- Department of Laboratory Medicine; Radboud University Medical Center; Nijmegen The Netherlands
| | - Eline M. P. Cremers
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Canan Alhan
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Theresia M. Westers
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Heleen A. Visser-Wisselaar
- Department of Hematology; Erasmus MC Cancer Institute, HOVON Data Center, Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - Dana A. Chitu
- Department of Hematology; Erasmus MC Cancer Institute, HOVON Data Center, Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - Sonia M. Cunha
- Department of Hematology; Erasmus MC Cancer Institute, HOVON Data Center, Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - Edo Vellenga
- Department of Experimental Hematology; University Medical Center Groningen; Groningen The Netherlands
| | - Saskia K. Klein
- Department of Internal Medicine; Meander Medisch Centrum; Amersfoort The Netherlands
| | - Pierre Wijermans
- Department of Internal Medicine; Haga Ziekenhuis; The Hague The Netherlands
| | - Georgine E. de Greef
- Department of Hematology; Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - M. Ron Schaafsma
- Department of Internal Medicine; Medisch Centrum Twente; Enschede The Netherlands
| | - Petra Muus
- Department of Hematology; Radboud University Medical Center; Nijmegen The Netherlands
| | - Gert J. Ossenkoppele
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Arjan A. van de Loosdrecht
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Joop H. Jansen
- Department of Laboratory Medicine; Radboud University Medical Center; Nijmegen The Netherlands
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31
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Basha B, Smith J, Rogers HJ, Cook JR. What Is the Clinical Utility of Repeat SNP Array Testing in the Follow-up of Myeloid Neoplasms?: A Retrospective Analysis of 44 Patients With Serial SNP Arrays. Am J Clin Pathol 2017; 147:278-284. [PMID: 28395056 DOI: 10.1093/ajcp/aqx003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES Single-nucleotide polymorphism (SNP) arrays have been shown to identify cytogenetic abnormalities in myeloid neoplasms that may be missed by metaphase cytogenetics alone at initial diagnosis. This study examines the utility of serial SNP arrays in follow-up testing of myeloid neoplasms. METHODS We retrospectively reviewed results of SNP array testing in 44 patients with myeloid neoplasms and more than one SNP array study (n = 133 SNP arrays total; median, three per patient; range, two to eight per patient). RESULTS Baseline abnormalities were identified by SNP array in 35 (79%) of 44 (79%) compared with 18 (50%) of 36 by metaphase karyotype. In follow-up studies, clonal evolution was found by both SNP array and karyotyping in seven (15.9%), by metaphase karyotyping alone in six (13.6%), and SNP arrays alone in two (4.5%). Overall survival was not significantly different between patients with or without clonal evolution detected by SNP array. CONCLUSIONS This study, the first systematic examination of serial SNP arrays in myeloid neoplasms, confirms the clinical utility of SNP arrays at initial diagnosis but shows that clonal evolution of the karyotype can be detected by metaphase cytogenetics alone in most patients. Follow-up SNP array testing is not required in routine clinical use in most cases.
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Affiliation(s)
- Basma Basha
- From the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH
| | - Janice Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Heesun J Rogers
- From the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH
| | - James R Cook
- From the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH
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32
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Genetic abnormalities in myelodysplasia and secondary acute myeloid leukemia: impact on outcome of stem cell transplantation. Blood 2017; 129:2347-2358. [PMID: 28223278 DOI: 10.1182/blood-2016-12-754796] [Citation(s) in RCA: 244] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/08/2017] [Indexed: 12/17/2022] Open
Abstract
Genetic alterations, including mutations and copy-number alterations, are central to the pathogenesis of myelodysplastic syndromes and related diseases (myelodysplasia), but their roles in allogeneic stem cell transplantation have not fully been studied in a large cohort of patients. We enrolled 797 patients who had been diagnosed with myelodysplasia at initial presentation and received transplantation via the Japan Marrow Donor Program. Targeted-capture sequencing was performed to identify mutations in 69 genes, together with copy-number alterations, whose effects on transplantation outcomes were investigated. We identified 1776 mutations and 927 abnormal copy segments among 617 patients (77.4%). In multivariate modeling using Cox proportional-hazards regression, genetic factors explained 30% of the total hazards for overall survival; clinical characteristics accounted for 70% of risk. TP53 and RAS-pathway mutations, together with complex karyotype (CK) as detected by conventional cytogenetics and/or sequencing-based analysis, negatively affected posttransplant survival independently of clinical factors. Regardless of disease subtype, TP53-mutated patients with CK were characterized by unique genetic features and associated with an extremely poor survival with frequent early relapse, whereas outcomes were substantially better in TP53-mutated patients without CK. By contrast, the effects of RAS-pathway mutations depended on disease subtype and were confined to myelodysplastic/myeloproliferative neoplasms (MDS/MPNs). Our results suggest that TP53 and RAS-pathway mutations predicted a dismal prognosis, when associated with CK and MDS/MPNs, respectively. However, for patients with mutated TP53 or CK alone, long-term survival could be obtained with transplantation. Clinical sequencing provides vital information for accurate prognostication in transplantation.
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33
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Stanley N, Olson TS, Babushok DV. Recent advances in understanding clonal haematopoiesis in aplastic anaemia. Br J Haematol 2017; 177:509-525. [PMID: 28107566 DOI: 10.1111/bjh.14510] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Acquired aplastic anaemia (AA) is an immune-mediated bone marrow failure disorder inextricably linked to clonal haematopoiesis. The majority of AA patients have somatic mutations and/or structural chromosomal abnormalities detected as early as at diagnosis. In contrast to other conditions linked to clonal haematopoiesis, the clonal signature of AA reflects its immune pathophysiology. The most common alterations are clonal expansions of cells lacking glycophosphotidylinositol-anchored proteins, loss of human leucocyte antigen alleles, and mutations in BCOR/BCORL1, ASXL1 and DNMT3A. Here, we present the current knowledge of clonal haematopoiesis in AA as it relates to aging, inherited bone marrow failure, and the grey-zone overlap of AA and myelodysplastic syndrome (MDS). We conclude by discussing the significance of clonal haematopoiesis both for improved diagnosis of AA, as well as for a more precise, personalized approach to prognostication of outcomes and therapy choices.
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Affiliation(s)
- Natasha Stanley
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Timothy S Olson
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Blood and Marrow Transplant Program, Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA, USA
| | - Daria V Babushok
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Hematology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
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34
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Mutational landscape and response are conserved in peripheral blood of AML and MDS patients during decitabine therapy. Blood 2017; 129:1397-1401. [PMID: 28082444 DOI: 10.1182/blood-2016-10-745273] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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35
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Mutation allele burden remains unchanged in chronic myelomonocytic leukaemia responding to hypomethylating agents. Nat Commun 2016; 7:10767. [PMID: 26908133 PMCID: PMC4770084 DOI: 10.1038/ncomms10767] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 01/19/2016] [Indexed: 12/18/2022] Open
Abstract
The cytidine analogues azacytidine and 5-aza-2'-deoxycytidine (decitabine) are commonly used to treat myelodysplastic syndromes, with or without a myeloproliferative component. It remains unclear whether the response to these hypomethylating agents results from a cytotoxic or an epigenetic effect. In this study, we address this question in chronic myelomonocytic leukaemia. We describe a comprehensive analysis of the mutational landscape of these tumours, combining whole-exome and whole-genome sequencing. We identify an average of 14±5 somatic mutations in coding sequences of sorted monocyte DNA and the signatures of three mutational processes. Serial sequencing demonstrates that the response to hypomethylating agents is associated with changes in DNA methylation and gene expression, without any decrease in the mutation allele burden, nor prevention of new genetic alteration occurence. Our findings indicate that cytosine analogues restore a balanced haematopoiesis without decreasing the size of the mutated clone, arguing for a predominantly epigenetic effect.
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36
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Impact of TP53 mutation variant allele frequency on phenotype and outcomes in myelodysplastic syndromes. Leukemia 2015; 30:666-73. [PMID: 26514544 DOI: 10.1038/leu.2015.304] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/09/2015] [Accepted: 10/13/2015] [Indexed: 12/31/2022]
Abstract
Although next-generation sequencing has allowed for the detection of somatic mutations in myelodysplastic syndromes (MDS), the clinical relevance of variant allele frequency (VAF) for the majority of mutations is unknown. We profiled TP53 and 20 additional genes in our training set of 219 patients with MDS or secondary acute myeloid leukemia with findings confirmed in a validation cohort. When parsed by VAF, TP53 VAF predicted for complex cytogenetics in both the training (P=0.001) and validation set (P<0.0001). MDS patients with a TP53 VAF > 40% had a median overall survival (OS) of 124 days versus an OS that was not reached in patients with VAF <20% (hazard ratio (HR), 3.52; P=0.01) with validation in an independent cohort (HR, 4.94, P=0.01). TP53 VAF further stratified distinct prognostic groups independent of clinical prognostic scoring systems (P=0.0005). In multivariate analysis, only a TP53 VAF >40% was an independent covariate (HR, 1.61; P<0.0001). In addition, SRSF2 VAF predicted for monocytosis (P=0.003), RUNX1 VAF with thrombocytopenia (P=0.01) and SF3B1 with ringed sideroblasts (P=0.001). Together, our study indicates that VAF should be incorporated in patient management and risk stratification in MDS.
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