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O'Neill C, Nwachukwu N, Vergara-Lluri M, Hagiya A, O'Connell CL. Clinical and pathological features of clonal cytopenia of undetermined significance presenting with isolated thrombocytopenia (CCUS-IT). Eur J Haematol 2024; 112:594-600. [PMID: 38088145 DOI: 10.1111/ejh.14149] [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: 08/14/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 03/19/2024]
Abstract
BACKGROUND Clonal cytopenia of undetermined significance (CCUS) is defined as somatic mutations of myeloid malignancy-associated genes in the blood or bone marrow with one or more persistent unexplained cytopenias that do not meet diagnostic criteria for a defined myeloid neoplasm. CCUS with isolated thrombocytopenia (CCUS-IT) is rare. METHODS This is a retrospective case series of patients with prolonged isolated thrombocytopenia, a pathogenic mutation on a myeloid molecular panel, and a bone marrow biopsy with morphologic atypia below the WHO-defined diagnostic threshold for dysplasia. RESULTS Five male patients were identified with a median age at CCUS-IT diagnosis of 61 years (56-74). Median duration of thrombocytopenia prior to CCUS-IT diagnosis was 4 years (3-12), and median platelet count at CCUS-IT diagnosis was 41 × 103 /μL (26-80). All patients had megakaryocytic hyperplasia and megakaryocytes with hyperchromasia and high nuclear-cytoplasmic ratio. Pathogenic SRSF2 mutations were identified in all 5 patients with median variant allele frequency of 36% (28%-50%). Three patients were treated with IVIg and/or steroids with no response; one of three responded to thrombopoietin receptor agonists. Three patients progressed to MDS and one to AML. DISCUSSION We describe the clinicopathological features of CCUS-IT which can mimic immune thrombocytopenia.
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Affiliation(s)
- Caitlin O'Neill
- Jane Anne Nohl Division of Hematology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Nneka Nwachukwu
- Jane Anne Nohl Division of Hematology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Maria Vergara-Lluri
- Department of Pathology, Hematopathology Section, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Ashley Hagiya
- Department of Pathology, Hematopathology Section, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Casey L O'Connell
- Jane Anne Nohl Division of Hematology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
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2
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Hasserjian RP, Germing U, Malcovati L. Diagnosis and classification of myelodysplastic syndromes. Blood 2023; 142:2247-2257. [PMID: 37774372 DOI: 10.1182/blood.2023020078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/08/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023] Open
Abstract
ABSTRACT Myelodysplastic syndromes (MDSs) are neoplastic myeloid proliferations characterized by ineffective hematopoiesis resulting in peripheral blood cytopenias. MDS is distinguished from nonneoplastic clonal myeloid proliferations by the presence of morphologic dysplasia and from acute myeloid leukemia by a blast threshold of 20%. The diagnosis of MDS can be challenging because of the myriad other causes of cytopenias: accurate diagnosis requires the integration of clinical features with bone marrow and peripheral blood morphology, immunophenotyping, and genetic testing. MDS has historically been subdivided into several subtypes by classification schemes, the most recent of which are the International Consensus Classification and World Health Organization Classification (fifth edition), both published in 2022. The aim of MDS classification is to identify entities with shared genetic underpinnings and molecular pathogenesis, and the specific subtype can inform clinical decision-making alongside prognostic risk categorization. The current MDS classification schemes incorporate morphologic features (bone marrow and blood blast percentage, degree of dysplasia, ring sideroblasts, bone marrow fibrosis, and bone marrow hypocellularity) and also recognize 3 entities defined by genetics: isolated del(5q) cytogenetic abnormality, SF3B1 mutation, and TP53 mutation. It is anticipated that with advancing understanding of the genetic basis of MDS pathogenesis, future MDS classification will be based increasingly on genetic classes. Nevertheless, morphologic features in MDS reflect the phenotypic expression of the underlying abnormal genetic pathways and will undoubtedly retain importance to inform prognosis and guide treatment.
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Affiliation(s)
| | - Ulrich Germing
- Department of Hematology, Oncology, and Clinical Immunology, Heinrich-Heine University, Dusseldorf, Germany
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology, Fondazione IRCCS Policlinico S. Matteo, Pavia, Italy
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3
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Bhattacharya SA, Dias E, Nieto-Aliseda A, Buschbeck M. The consequences of cohesin mutations in myeloid malignancies. Front Mol Biosci 2023; 10:1319804. [PMID: 38033389 PMCID: PMC10684907 DOI: 10.3389/fmolb.2023.1319804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Recurrent somatic mutations in the genes encoding the chromatin-regulatory cohesin complex and its modulators occur in a wide range of human malignancies including a high frequency in myeloid neoplasms. The cohesin complex has a ring-like structure which can enclose two strands of DNA. A first function for the complex was described in sister chromatid cohesion during metaphase avoiding defects in chromosome segregation. Later studies identified additional functions of the cohesin complex functions in DNA replication, DNA damage response, 3D genome organisation, and transcriptional regulation through chromatin looping. In this review, we will focus on STAG2 which is the most frequently mutated cohesin subunit in myeloid malignancies. STAG2 loss of function mutations are not associated with chromosomal aneuploidies or genomic instability. We hypothesize that this points to changes in gene expression as disease-promoting mechanism and summarize the current state of knowledge on affected genes and pathways. Finally, we discuss potential strategies for targeting cohesion-deficient disease cells.
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Affiliation(s)
- Shubhra Ashish Bhattacharya
- Program of Myeloid Neoplasms, Program of Applied Epigenetics, Josep Carreras Leukaemia Research Institute, Badalona, Spain
- PhD Program of Cell Biology, Autonomous University of Barcelona, Barcelona, Spain
| | - Eve Dias
- Program of Myeloid Neoplasms, Program of Applied Epigenetics, Josep Carreras Leukaemia Research Institute, Badalona, Spain
- PhD Program of Cell Biology, Autonomous University of Barcelona, Barcelona, Spain
| | - Andrea Nieto-Aliseda
- Program of Myeloid Neoplasms, Program of Applied Epigenetics, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Marcus Buschbeck
- Program of Myeloid Neoplasms, Program of Applied Epigenetics, Josep Carreras Leukaemia Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
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4
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Gómez‐Rojas S, Segura GP, Ollé J, Carreño Gómez‐Tarragona G, Medina JG, Aguado JM, Guerrero EV, Santaella MP, Martínez‐López J. A machine learning tool for the diagnosis of SARS-CoV-2 infection from hemogram parameters. J Cell Mol Med 2023; 27:3423-3430. [PMID: 37882471 PMCID: PMC10660618 DOI: 10.1111/jcmm.17864] [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: 01/12/2023] [Revised: 06/20/2023] [Accepted: 07/05/2023] [Indexed: 10/27/2023] Open
Abstract
Monocytes and neutrophils play key roles in the cytokine storm triggered by SARS-CoV-2 infection, which changes their conformation and function. These changes are detectable at the cellular and molecular level and may be different to what is observed in other respiratory infections. Here, we applied machine learning (ML) to develop and validate an algorithm to diagnose COVID-19 using blood parameters. In this retrospective single-center study, 49 hemogram parameters from 12,321 patients with clinical suspicion of COVID-19 and tested by RT-PCR (4239 positive and 8082 negative) were analysed. The dataset was randomly divided into training and validation sets. Blood cell parameters and patient age were used to construct the predictive model with the support vector machine (SVM) tool. The model constructed from the training set (5936 patients) achieved an accuracy for diagnosis of SARS-CoV-2 infection of 0.952 (95% CI: 0.875-0.892). Test sensitivity and specificity was 0.868 and 0.899, respectively, with a positive (PPV) and negative (NPV) predictive value of 0.896 and 0.872, respectively (prevalence 0.50). The validation set model (4964 patients) achieved an accuracy of 0.894 (95% CI: 0.883-0.903). Test sensitivity and specificity was 0.8922 and 0.8951, respectively, with a positive (PPV) and negative (NPV) predictive value of 0.817 and 0.94, respectively (prevalence 0.34). The area under the receiver operating characteristic curve was 0.952 for the algorithm performance. This algorithm may allow to rule out COVID-19 diagnosis with 94% of probability. This represents a great advance for early diagnostic orientation and guiding clinical decisions.
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Affiliation(s)
- S. Gómez‐Rojas
- Department of HematologyHospital Universitario 12 octubreMadridSpain
| | - G. Pérez Segura
- Department of HematologyHospital Universitario 12 octubreMadridSpain
| | - J. Ollé
- Conceptos Claros CoBarcelonaSpain
| | | | - J. González Medina
- Department of HematologyHospital Universitario Fundación Jiménez DíazMadridSpain
| | - J. M. Aguado
- Unit of Infectious DiseasesHospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (i+12), CIBERINFEC, ISCIIIMadridSpain
- Department of Medicine, School of MedicineUniversidad ComplutenseMadridSpain
| | - E. Vera Guerrero
- Department of HematologyHospital Universitario 12 octubreMadridSpain
| | - M. Poza Santaella
- Department of HematologyHospital Universitario 12 octubreMadridSpain
| | - J. Martínez‐López
- Department of HematologyHospital Universitario 12 octubreMadridSpain
- Department of Medicine, School of MedicineUniversidad ComplutenseMadridSpain
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5
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Todisco G, Creignou M, Bernard E, Björklund AC, Moura PL, Tesi B, Mortera-Blanco T, Sander B, Jansson M, Walldin G, Barbosa I, Reinsbach SE, Hofman IJ, Nilsson C, Yoshizato T, Dimitriou M, Chang D, Olafsdottir S, Venckute Larsson S, Tobiasson M, Malcovati L, Woll P, Jacobsen SEW, Papaemmanuil E, Hellström-Lindberg E. Integrated Genomic and Transcriptomic Analysis Improves Disease Classification and Risk Stratification of MDS with Ring Sideroblasts. Clin Cancer Res 2023; 29:4256-4267. [PMID: 37498312 PMCID: PMC10570683 DOI: 10.1158/1078-0432.ccr-23-0538] [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: 02/20/2023] [Revised: 05/12/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE Ring sideroblasts (RS) define the low-risk myelodysplastic neoplasm (MDS) subgroup with RS but may also reflect erythroid dysplasia in higher risk myeloid neoplasm. The benign behavior of MDS with RS (MDSRS+) is limited to SF3B1-mutated cases without additional high-risk genetic events, but one third of MDSRS+ carry no SF3B1 mutation, suggesting that different molecular mechanisms may underlie RS formation. We integrated genomic and transcriptomic analyses to evaluate whether transcriptome profiles may improve current risk stratification. EXPERIMENTAL DESIGN We studied a prospective cohort of MDSRS+ patients irrespective of World Health Organization (WHO) class with regard to somatic mutations, copy-number alterations, and bone marrow CD34+ cell transcriptomes to assess whether transcriptome profiles add to prognostication and provide input on disease classification. RESULTS SF3B1, SRSF2, or TP53 multihit mutations were found in 89% of MDSRS+ cases, and each mutation category was associated with distinct clinical outcome, gene expression, and alternative splicing profiles. Unsupervised clustering analysis identified three clusters with distinct hemopoietic stem and progenitor (HSPC) composition, which only partially overlapped with mutation groups. IPSS-M and the transcriptome-defined proportion of megakaryocyte/erythroid progenitors (MEP) independently predicted survival in multivariable analysis. CONCLUSIONS These results provide essential input on the molecular basis of SF3B1-unmutated MDSRS+ and propose HSPC quantification as a prognostic marker in myeloid neoplasms with RS.
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Affiliation(s)
- Gabriele Todisco
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Unit of Precision Hematology Oncology, IRCCS S. Matteo Hospital Foundation, Pavia, Italy
| | - Maria Creignou
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Phase I Unit, Center for Clinical Cancer Studies, Karolinska University Hospital, Stockholm, Sweden
| | - Elsa Bernard
- Computational Oncology Service, Department of Epidemiology & Biostatistics and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ann-Charlotte Björklund
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Pedro Luis Moura
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Bianca Tesi
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Teresa Mortera-Blanco
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Birgitta Sander
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Monika Jansson
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Gunilla Walldin
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Indira Barbosa
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Susanne E. Reinsbach
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Gothenburg, Sweden
| | - Isabel Juliana Hofman
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Christer Nilsson
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Tetsuichi Yoshizato
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marios Dimitriou
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - David Chang
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Svannildur Olafsdottir
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sigita Venckute Larsson
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Tobiasson
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Unit of Precision Hematology Oncology, IRCCS S. Matteo Hospital Foundation, Pavia, Italy
| | - Petter Woll
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sten Eirik W. Jacobsen
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Elli Papaemmanuil
- Computational Oncology Service, Department of Epidemiology & Biostatistics and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eva Hellström-Lindberg
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
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6
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Kaseb H, Visconte V, Socha DS, Crane GM, Durkin L, Cook JR, Maciejewski JP, Hsi ED, Rogers HJ. The clinicopathologic significance of NPM1 mutation and ability to detect mutated NPM1 by immunohistochemistry in non-AML myeloid neoplasms. Genes Chromosomes Cancer 2023; 62:573-580. [PMID: 36959701 PMCID: PMC11104021 DOI: 10.1002/gcc.23139] [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: 12/02/2022] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/25/2023] Open
Abstract
NPM1 mutated non-AML myeloid neoplasms (MN; <20% blasts) are characterized by an aggressive clinical course in a few studies. In this retrospective study, we evaluate the clinicopathologic and immunohistochemical features of non-AML MN patients with NPM1 mutations. We assessed NPM1 mutation by targeted next generation sequencing (NGS). Cytoplasmic NPM1 expression was assessed by immunohistochemistry (IHC) on formalin-fixed, formic acid-decalcified bone marrow biopsy specimens. We evaluated 34 non-AML MN patients with NPM1 mutations comprising MDS (22), MPN (3) and MDS/MPN (9). They commonly presented with anemia (88%), thrombocytopenia (58%) and leukopenia (50%). Bone marrow dysplasia was common (79%). The karyotype was often normal (64%). NGS for MN-associated mutations performed in a subset of the patients showed a median of 3 mutations. NPM1 mutations were more often missense (c.859C > T p. L287F; 65%) than frameshift insertion/duplication (35%) with median variant allele frequency (VAF; 9.7%, range 5.1%-49.8%). Mutated NPM1 by IHC showed cytoplasmic positivity in 48% and positivity was associated with higher VAF. The median overall survival (OS) in this cohort was 70 months. Nine patients (26%) progressed to AML. OS in patients who progressed to AML was significantly shorter than the one of patients without progression to AML (OS 20 vs. 128 months, respectively, log rank p = 0.05). NPM1 mutated non-AML MN patients commonly had cytopenias, dysplasia, normal karyotype, mutations in multiple genes, and an unfavorable clinical outcome, including progression to AML. Our data demonstrated that IHC for NPM1 can be a useful supplementary tool to predict NPM1 mutation in some non-AML MN; however, genetic testing cannot be replaced by IHC assessment.
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Affiliation(s)
- Hatem Kaseb
- Department of Pathology, University of Central Florida College of Medicine, Orlando, Florida, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Daniel S. Socha
- Department of Pathology, OhioHealth, Riverside Methodist Hospital, Columbus, Ohio, USA
| | - Genevieve M. Crane
- Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Lisa Durkin
- Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - James R. Cook
- Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jaroslaw P. Maciejewski
- Department of Translational Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Eric D. Hsi
- Department of Pathology and Laboratory Medicine, Wake Forest School of Medicine, Wake Forest Baptist Health, Winston-Salem, North Carolina, USA
| | - Heesun J. Rogers
- Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
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7
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Clichet V, Lebon D, Chapuis N, Zhu J, Bardet V, Marolleau JP, Garçon L, Caulier A, Boyer T. Artificial intelligence to empower diagnosis of myelodysplastic syndromes by multiparametric flow cytometry. Haematologica 2023; 108:2435-2443. [PMID: 36924240 PMCID: PMC10483367 DOI: 10.3324/haematol.2022.282370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/07/2023] [Indexed: 03/18/2023] Open
Abstract
The diagnosis of myelodysplastic syndromes (MDS) might be challenging and relies on the convergence of cytological, cytogenetic, and molecular factors. Multiparametric flow cytometry (MFC) helps diagnose MDS, especially when other features do not contribute to the decision-making process, but its usefulness remains underestimated, mostly due to a lack of standardization of cytometers. We present here an innovative model integrating artificial intelligence (AI) with MFC to improve the diagnosis and the classification of MDS. We develop a machine learning model through an elasticnet algorithm directed on a cohort of 191 patients, only based on flow cytometry parameters selected by the Boruta algorithm, to build a simple but reliable prediction score with five parameters. Our AI-assisted MDS prediction score greatly improves the sensitivity of the Ogata score while keeping an excellent specificity validated on an external cohort of 89 patients with an Area Under the Curve of 0.935. This model allows the diagnosis of both high- and low-risk MDS with 91.8% sensitivity and 92.5% specificity. Interestingly, it highlights a progressive evolution of the score from clonal hematopoiesis of indeterminate potential (CHIP) to highrisk MDS, suggesting a linear evolution between these different stages. By significantly decreasing the overall misclassification of 52% for patients with MDS and of 31.3% for those without MDS (P=0.02), our AI-assisted prediction score outperforms the Ogata score and positions itself as a reliable tool to help diagnose MDS.
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Affiliation(s)
- Valentin Clichet
- Service d’Hématologie Biologique, CHU Amiens-Picardie, Amiens, France
| | - Delphine Lebon
- Service d’Hématologie Clinique et de Thérapie Cellulaire, CHU Amiens-Picardie, Amiens, France
- HEMATIM, EA 4666, Université Picardie Jules Verne, Amiens, France
| | - Nicolas Chapuis
- Assistance Publique-Hôpitaux de Paris, Centre-Université Paris Cité, Service d’Hématologie Biologique, Hôpital Cochin, Paris, France
| | - Jaja Zhu
- Service d’Hématologie-Immunologie-Transfusion, CHU Ambroise Paré, INSERM UMR 1184, AP-HP, Université Paris Saclay, 92100 Boulogne Billancourt, France
| | - Valérie Bardet
- Service d’Hématologie-Immunologie-Transfusion, CHU Ambroise Paré, INSERM UMR 1184, AP-HP, Université Paris Saclay, 92100 Boulogne Billancourt, France
| | - Jean-Pierre Marolleau
- Service d’Hématologie Clinique et de Thérapie Cellulaire, CHU Amiens-Picardie, Amiens, France
- HEMATIM, EA 4666, Université Picardie Jules Verne, Amiens, France
| | - Loïc Garçon
- Service d’Hématologie Biologique, CHU Amiens-Picardie, Amiens, France
- HEMATIM, EA 4666, Université Picardie Jules Verne, Amiens, France
| | - Alexis Caulier
- Service d’Hématologie Clinique et de Thérapie Cellulaire, CHU Amiens-Picardie, Amiens, France
- HEMATIM, EA 4666, Université Picardie Jules Verne, Amiens, France
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Thomas Boyer
- Service d’Hématologie Biologique, CHU Amiens-Picardie, Amiens, France
- HEMATIM, EA 4666, Université Picardie Jules Verne, Amiens, France
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8
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de Almeida JG, Gudgin E, Besser M, Dunn WG, Cooper J, Haferlach T, Vassiliou GS, Gerstung M. Computational analysis of peripheral blood smears detects disease-associated cytomorphologies. Nat Commun 2023; 14:4378. [PMID: 37474506 PMCID: PMC10359268 DOI: 10.1038/s41467-023-39676-y] [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: 04/27/2022] [Accepted: 06/22/2023] [Indexed: 07/22/2023] Open
Abstract
Many hematological diseases are characterized by altered abundance and morphology of blood cells and their progenitors. Myelodysplastic syndromes (MDS), for example, are a group of blood cancers characterised by cytopenias, dysplasia of hematopoietic cells and blast expansion. Examination of peripheral blood slides (PBS) in MDS often reveals changes such as abnormal granulocyte lobulation or granularity and altered red blood cell (RBC) morphology; however, some of these features are shared with conditions such as haematinic deficiency anemias. Definitive diagnosis of MDS requires expert cytomorphology analysis of bone marrow smears and complementary information such as blood counts, karyotype and molecular genetics testing. Here, we present Haemorasis, a computational method that detects and characterizes white blood cells (WBC) and RBC in PBS. Applied to over 300 individuals with different conditions (SF3B1-mutant and SF3B1-wildtype MDS, megaloblastic anemia, and iron deficiency anemia), Haemorasis detected over half a million WBC and millions of RBC and characterized their morphology. These large sets of cell morphologies can be used in diagnosis and disease subtyping, while identifying novel associations between computational morphotypes and disease. We find that hypolobulated neutrophils and large RBC are characteristic of SF3B1-mutant MDS. Additionally, while prevalent in both iron deficiency and megaloblastic anemia, hyperlobulated neutrophils are larger in the latter. By integrating cytomorphological features using machine learning, Haemorasis was able to distinguish SF3B1-mutant MDS from other MDS using cytomorphology and blood counts alone, with high predictive performance. We validate our findings externally, showing that they generalize to other centers and scanners. Collectively, our work reveals the potential for the large-scale incorporation of automated cytomorphology into routine diagnostic workflows.
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Affiliation(s)
- José Guilherme de Almeida
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Champalimaud Foundation-Centre for the Unknown, Lisbon, Portugal
| | - Emma Gudgin
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Martin Besser
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - William G Dunn
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Jonathan Cooper
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - George S Vassiliou
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.
- Division of AI in Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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9
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Jain T, Ware AD, Dalton WB, Pasca S, Tsai HL, Gocke CD, Gondek LP, Xian RR, Borowitz MJ, Levis MJ. Co-occurring mutations in ASXL1, SRSF2, and SETBP1 define a subset of myelodysplastic/ myeloproliferative neoplasm with neutrophilia. Leuk Res 2023; 131:107345. [PMID: 37354804 DOI: 10.1016/j.leukres.2023.107345] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/12/2023] [Accepted: 06/19/2023] [Indexed: 06/26/2023]
Abstract
Identification of genomic signatures with consistent clinicopathological features in myelodysplastic/myeloproliferative neoplasm (MDS/MPN) is critical for improved diagnosis, elucidation of biology, inclusion in clinical trials, and development of therapies. We describe clinical and pathological features with co-existence of mutations in ASXL1 (missense or nonsense), SRSF2, and SKI homologous region of SETBP1, in 18 patients. Median age was 68 years with a male predominance (83%). Leukocytosis and neutrophilia were common at presentation. Marrow features included hypercellularity, granulocytic hyperplasia with megakaryocytic atypia, while the majority had myeloid hyperplasia and/or erythroid hypoplasia, myeloid dysplasia, and aberrant CD7 expression on blasts. Mutations in growth signaling pathways (RAS or JAK2) were noted at diagnosis or acquired during the disease course in 83% of patients. Two patients progressed upon acquisition of FLT3-TKD (acute myeloid leukemia) or KIT (aggressive systemic mastocytosis) mutations. The prognosis is poor with only two long-term survivors, thus far, who underwent blood or marrow transplantation. We propose that the presence of co-occurring ASXL1, SRSF2, and SETBP1 mutations can be diagnostic of a subtype of MDS/MPN with neutrophilia if clinical and morphological findings align. Our report underscores the association between genotype and phenotype within MDS/MPN and that genomic signatures should guide categorization of these entities.
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Affiliation(s)
- Tania Jain
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
| | - Alisha D Ware
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD, USA; Department of Pathology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - William Brian Dalton
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Sergiu Pasca
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Hua-Ling Tsai
- Division of Biostatistics and Bioinformatics, Johns Hopkins/Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | | | - Lukasz P Gondek
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Rena R Xian
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD, USA
| | | | - Mark J Levis
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
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10
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Pagliuca S, Gurnari C, Hercus C, Hergalant S, Hong S, Dhuyser A, D'Aveni M, Aarnink A, Rubio MT, Feugier P, Ferraro F, Carraway HE, Sobecks R, Hamilton BK, Majhail NS, Visconte V, Maciejewski JP. Leukemia relapse via genetic immune escape after allogeneic hematopoietic cell transplantation. Nat Commun 2023; 14:3153. [PMID: 37258544 PMCID: PMC10232425 DOI: 10.1038/s41467-023-38113-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 04/13/2023] [Indexed: 06/02/2023] Open
Abstract
Graft-versus-leukemia (GvL) reactions are responsible for the effectiveness of allogeneic hematopoietic cell transplantation as a treatment modality for myeloid neoplasia, whereby donor T- effector cells recognize leukemia neoantigens. However, a substantial fraction of patients experiences relapses because of the failure of the immunological responses to control leukemic outgrowth. Here, through a broad immunogenetic study, we demonstrate that germline and somatic reduction of human leucocyte antigen (HLA) heterogeneity enhances the risk of leukemic recurrence. We show that preexistent germline-encoded low evolutionary divergence of class II HLA genotypes constitutes an independent factor associated with disease relapse and that acquisition of clonal somatic defects in HLA alleles may lead to escape from GvL control. Both class I and II HLA genes are targeted by somatic mutations as clonal selection factors potentially impairing cellular immune responses and response to immunomodulatory strategies. These findings define key molecular modes of post-transplant leukemia escape contributing to relapse.
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Affiliation(s)
- Simona Pagliuca
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Hematology, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- CNRS UMR 7365, IMoPA, Biopole of University of Lorraine, Vandœuvre-lès-Nancy, France
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Colin Hercus
- Novocraft Technologies Sdn Bhd, Kuala Lumpur, Malaysia
| | - Sébastien Hergalant
- Inserm UMR-S 1256 Nutrition-Genetics-Environmental Risk Exposure, University of Lorraine, 54500, Vandœuvre-lès-Nancy, France
| | - Sanghee Hong
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Adele Dhuyser
- CNRS UMR 7365, IMoPA, Biopole of University of Lorraine, Vandœuvre-lès-Nancy, France
- Histocompatibility Department, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Maud D'Aveni
- Department of Hematology, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- CNRS UMR 7365, IMoPA, Biopole of University of Lorraine, Vandœuvre-lès-Nancy, France
| | - Alice Aarnink
- CNRS UMR 7365, IMoPA, Biopole of University of Lorraine, Vandœuvre-lès-Nancy, France
- Histocompatibility Department, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Marie Thérèse Rubio
- Department of Hematology, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- CNRS UMR 7365, IMoPA, Biopole of University of Lorraine, Vandœuvre-lès-Nancy, France
| | - Pierre Feugier
- Department of Hematology, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Francesca Ferraro
- Division of Oncology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Hetty E Carraway
- Leukemia Program, Hematology Department, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ronald Sobecks
- Blood and Marrow Transplant Program, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Betty K Hamilton
- Blood and Marrow Transplant Program, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Navneet S Majhail
- Sarah Cannon Transplant and Cellular Therapy Network, Nashville, TN, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
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11
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Kewan T, Durmaz A, Bahaj W, Gurnari C, Terkawi L, Awada H, Ogbue OD, Ahmed R, Pagliuca S, Awada H, Kubota Y, Mori M, Ponvilawan B, Al-Share B, Patel BJ, Carraway HE, Scott J, Balasubramanian SK, Bat T, Madanat Y, Sekeres MA, Haferlach T, Visconte V, Maciejewski JP. Molecular patterns identify distinct subclasses of myeloid neoplasia. Nat Commun 2023; 14:3136. [PMID: 37253784 PMCID: PMC10229666 DOI: 10.1038/s41467-023-38515-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/03/2023] [Indexed: 06/01/2023] Open
Abstract
Genomic mutations drive the pathogenesis of myelodysplastic syndromes and acute myeloid leukemia. While morphological and clinical features have dominated the classical criteria for diagnosis and classification, incorporation of molecular data can illuminate functional pathobiology. Here we show that unsupervised machine learning can identify functional objective molecular clusters, irrespective of anamnestic clinico-morphological features, despite the complexity of the molecular alterations in myeloid neoplasia. Our approach reflects disease evolution, informed classification, prognostication, and molecular interactions. We apply machine learning methods on 3588 patients with myelodysplastic syndromes and secondary acute myeloid leukemia to identify 14 molecularly distinct clusters. Remarkably, our model shows clinical implications in terms of overall survival and response to treatment even after adjusting to the molecular international prognostic scoring system (IPSS-M). In addition, the model is validated on an external cohort of 412 patients. Our subclassification model is available via a web-based open-access resource ( https://drmz.shinyapps.io/mds_latent ).
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Affiliation(s)
- Tariq Kewan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
- Department of Hematology and Medical Oncology, Yale University, New Haven, CT, USA.
| | - Arda Durmaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Systems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Waled Bahaj
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedicine and Prevention, Ph.D. in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Laila Terkawi
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hussein Awada
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Olisaemeka D Ogbue
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ramsha Ahmed
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Simona Pagliuca
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Clinical Hematology, CHRU de Nancy, Nancy, France
| | - Hassan Awada
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Yasuo Kubota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Minako Mori
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ben Ponvilawan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Bayan Al-Share
- Department of Hematology and Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Bhumika J Patel
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hetty E Carraway
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jacob Scott
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Systems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Suresh K Balasubramanian
- Department of Hematology and Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Taha Bat
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yazan Madanat
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mikkael A Sekeres
- Division of Hematology, Sylvester Cancer Center, University of Miami, Miami, FL, USA
| | | | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
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12
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Gutierrez-Rodrigues F, Munger E, Ma X, Groarke EM, Tang Y, Patel BA, Catto LFB, Clé DV, Niewisch MR, Alves-Paiva RM, Donaires FS, Pinto AL, Borges G, Santana BA, McReynolds LJ, Giri N, Altintas B, Fan X, Shalhoub R, Siwy CM, Diamond C, Raffo DQ, Craft K, Kajigaya S, Summers RM, Liu P, Cunningham L, Hickstein DD, Dunbar CE, Pasquini R, De Oliveira MM, Velloso EDRP, Alter BP, Savage SA, Bonfim C, Wu CO, Calado RT, Young NS. Differential diagnosis of bone marrow failure syndromes guided by machine learning. Blood 2023; 141:2100-2113. [PMID: 36542832 PMCID: PMC10163315 DOI: 10.1182/blood.2022017518] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/10/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
The choice to postpone treatment while awaiting genetic testing can result in significant delay in definitive therapies in patients with severe pancytopenia. Conversely, the misdiagnosis of inherited bone marrow failure (BMF) can expose patients to ineffectual and expensive therapies, toxic transplant conditioning regimens, and inappropriate use of an affected family member as a stem cell donor. To predict the likelihood of patients having acquired or inherited BMF, we developed a 2-step data-driven machine-learning model using 25 clinical and laboratory variables typically recorded at the initial clinical encounter. For model development, patients were labeled as having acquired or inherited BMF depending on their genomic data. Data sets were unbiasedly clustered, and an ensemble model was trained with cases from the largest cluster of a training cohort (n = 359) and validated with an independent cohort (n = 127). Cluster A, the largest group, was mostly immune or inherited aplastic anemia, whereas cluster B comprised underrepresented BMF phenotypes and was not included in the next step of data modeling because of a small sample size. The ensemble cluster A-specific model was accurate (89%) to predict BMF etiology, correctly predicting inherited and likely immune BMF in 79% and 92% of cases, respectively. Our model represents a practical guide for BMF diagnosis and highlights the importance of clinical and laboratory variables in the initial evaluation, particularly telomere length. Our tool can be potentially used by general hematologists and health care providers not specialized in BMF, and in under-resourced centers, to prioritize patients for genetic testing or for expeditious treatment.
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Affiliation(s)
- Fernanda Gutierrez-Rodrigues
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD
| | - Eric Munger
- Department of Bioinformatics and Computational Biology, George Mason University, Fairfax, VA
| | - Xiaoyang Ma
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD
| | - Emma M. Groarke
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD
| | - Youbao Tang
- Imaging Biomarkers and Computer-Aided Diagnosis Laboratory, NIH Clinical Center, Bethesda, MD
| | - Bhavisha A. Patel
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD
| | - Luiz Fernando B. Catto
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Diego V. Clé
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Marena R. Niewisch
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute (NCI), NIH, Bethesda, MD
| | | | - Flávia S. Donaires
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - André Luiz Pinto
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Gustavo Borges
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Barbara A. Santana
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Lisa J. McReynolds
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute (NCI), NIH, Bethesda, MD
| | - Neelam Giri
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute (NCI), NIH, Bethesda, MD
| | - Burak Altintas
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute (NCI), NIH, Bethesda, MD
| | - Xing Fan
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, MD
| | - Ruba Shalhoub
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD
| | - Christopher M. Siwy
- Department of Clinical Reseach Infomatics, NIH Clinical Center, Bethesda, MD
| | - Carrie Diamond
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD
| | - Diego Quinones Raffo
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD
| | - Kathleen Craft
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD
| | - Ronald M. Summers
- Imaging Biomarkers and Computer-Aided Diagnosis Laboratory, NIH Clinical Center, Bethesda, MD
| | - Paul Liu
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD
| | - Lea Cunningham
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD
| | | | | | - Ricardo Pasquini
- Bone Marrow Transplantation Unit, Federal University of Parana, Curitiba, PR
| | | | - Elvira D. R. P. Velloso
- Hemotherapy and Cell Therapy Branch, Albert Einstein Hospital, São Paulo, Brazil
- Service of Hematology, Transfusion and Cell Therapy and Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31) HCFMUSP, University of Sao Paulo Medical School, São Paulo, Brazil
| | - Blanche P. Alter
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute (NCI), NIH, Bethesda, MD
| | - Sharon A. Savage
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute (NCI), NIH, Bethesda, MD
| | - Carmem Bonfim
- Bone Marrow Transplantation Unit, Federal University of Parana, Curitiba, PR
- Instituto de Pesquisa Pele Pequeno Principe, Curitiba, PR
| | - Colin O. Wu
- Office of Biostatistics Research, NHLBI, NIH, Bethesda, MD
| | - Rodrigo T. Calado
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Neal S. Young
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD
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13
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Kewan T, Bahaj W, Durmaz A, Aly M, Ogbue OD, Carraway HE, Sekeres MA, Visconte V, Gurnari C, Maciejewski JP. Validation of the Molecular International Prognostic Scoring System in patients with myelodysplastic syndromes. Blood 2023; 141:1768-1772. [PMID: 36720101 PMCID: PMC10933698 DOI: 10.1182/blood.2022018896] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 02/02/2023] Open
Affiliation(s)
- Tariq Kewan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
- Department of Hematology and Oncology, Yale University, New Haven, CT
| | - Waled Bahaj
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Arda Durmaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
- Systems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH
| | - Mai Aly
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
- Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Olisaemeka D Ogbue
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Hetty E Carraway
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Mikkael A Sekeres
- Department of Hematology and Oncology, University of Miami, Miami, FL
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
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14
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Pagliuca S, Gurnari C, Hercus C, Hergalant S, Hong S, Dhuyser A, D'Aveni M, Aarnink A, Rubio MT, Feugier P, Ferraro F, Carraway HE, Sobecks R, Hamilton BK, Majhail NS, Visconte V, Maciejewski JP. Leukemia relapse via genetic immune escape after allogeneic hematopoietic cell transplantation. RESEARCH SQUARE 2023:rs.3.rs-2773498. [PMID: 37066269 PMCID: PMC10104200 DOI: 10.21203/rs.3.rs-2773498/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Graft-versus-leukemia (GvL) reactions are responsible for the effectiveness of allogeneic hematopoietic cell transplantation as a treatment modality for myeloid neoplasia, whereby donor T- effector cells recognize leukemia neoantigens. However, a substantial fraction of patients experience relapses because of the failure of the immunological responses to control leukemic outgrowth. Here, through a broad immunogenetic study, we demonstrate that germline and somatic reduction of human leucocyte antigen (HLA) heterogeneity enhances the risk of leukemic recurrence. We show that preexistent germline-encoded low evolutionary divergence of class II HLA genotypes constitutes an independent factor associated with disease relapse and that acquisition of clonal somatic defects in HLA alleles may lead to escape from GvL control. Both class I and II HLA genes are targeted by somatic mutations as clonal selection factors potentially impairing cellular immune reactions and response to immunomodulatory strategies. These findings define key molecular modes of post-transplant leukemia escape contributing to relapse.
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15
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Durmaz A, Gurnari C, Hershberger CE, Pagliuca S, Daniels N, Awada H, Awada H, Adema V, Mori M, Ponvilawan B, Kubota Y, Kewan T, Bahaj WS, Barnard J, Scott J, Padgett RA, Haferlach T, Maciejewski JP, Visconte V. A multimodal analysis of genomic and RNA splicing features in myeloid malignancies. iScience 2023; 26:106238. [PMID: 36926651 PMCID: PMC10011742 DOI: 10.1016/j.isci.2023.106238] [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: 11/02/2022] [Revised: 01/12/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
RNA splicing dysfunctions are more widespread than what is believed by only estimating the effects resulting by splicing factor mutations (SFMT) in myeloid neoplasia (MN). The genetic complexity of MN is amenable to machine learning (ML) strategies. We applied an integrative ML approach to identify co-varying features by combining genomic lesions (mutations, deletions, and copy number), exon-inclusion ratio as measure of RNA splicing (percent spliced in, PSI), and gene expression (GE) of 1,258 MN and 63 normal controls. We identified 15 clusters based on mutations, GE, and PSI. Different PSI levels were present at various extents regardless of SFMT suggesting that changes in RNA splicing were not strictly related to SFMT. Combination of PSI and GE further distinguished the features and identified PSI similarities and differences, common pathways, and expression signatures across clusters. Thus, multimodal features can resolve the complex architecture of MN and help identifying convergent molecular and transcriptomic pathways amenable to therapies.
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Affiliation(s)
- Arda Durmaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Systems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | | | - Simona Pagliuca
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Clinical Hematology, CHRU de Nancy, Nancy, France
| | - Noah Daniels
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Hassan Awada
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Hussein Awada
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Vera Adema
- MD Anderson Cancer Center, Houston, TX, USA
| | - Minako Mori
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ben Ponvilawan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yasuo Kubota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Tariq Kewan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Waled S. Bahaj
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - John Barnard
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Jacob Scott
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Systems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Richard A. Padgett
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | | | - Jaroslaw P. Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Corresponding author
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16
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Falini B, Martelli MP. Comparison of the International Consensus and 5th WHO edition classifications of adult myelodysplastic syndromes and acute myeloid leukemia. Am J Hematol 2023; 98:481-492. [PMID: 36606297 DOI: 10.1002/ajh.26812] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 01/07/2023]
Abstract
Several editions of the World Health Organization (WHO) classifications of lympho-hemopoietic neoplasms in 2001, 2008, and 2016 served as the international standard for diagnosis. Since the 4th WHO edition, here referred as WHO-HAEM4, significant clinico-pathological, immunophenotypic, and molecular advances have been made in the field of myeloid neoplasms, which have contributed to refine diagnostic criteria, to upgrade entities previously defined as provisional and to identify new entities. This process has resulted in two recent classification proposals of myeloid neoplasms: the International Consensus Classification (ICC) and the 5th edition of the WHO classification (WHO-HAEM5). In this paper, we review and compare the two classifications in terms of diagnostic criteria and entity definition, with a focus on adult myelodysplastic syndromes/neoplasms (MDS) and acute myeloid leukemia (AML). The goal is to provide a tool to facilitate the work of pathologists, hematologists and researchers involved in the diagnosis and treatment of these hematological malignancies.
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Affiliation(s)
- Brunangelo Falini
- Institute of Hematology and Center for Hemato-Oncological research (CREO), University of Perugia and Santa Maria della Misericordia Hospital, Perugia, Italy
| | - Maria Paola Martelli
- Institute of Hematology and Center for Hemato-Oncological research (CREO), University of Perugia and Santa Maria della Misericordia Hospital, Perugia, Italy
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17
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Walter W, Pohlkamp C, Meggendorfer M, Nadarajah N, Kern W, Haferlach C, Haferlach T. Artificial intelligence in hematological diagnostics: Game changer or gadget? Blood Rev 2023; 58:101019. [PMID: 36241586 DOI: 10.1016/j.blre.2022.101019] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 09/21/2022] [Accepted: 10/03/2022] [Indexed: 11/30/2022]
Abstract
The future of clinical diagnosis and treatment of hematologic diseases will inevitably involve the integration of artificial intelligence (AI)-based systems into routine practice to support the hematologists' decision making. Several studies have shown that AI-based models can already be used to automatically differentiate cells, reliably detect malignant cell populations, support chromosome banding analysis, and interpret clinical variants, contributing to early disease detection and prognosis. However, even the best tool can become useless if it is misapplied or the results are misinterpreted. Therefore, in order to comprehensively judge and correctly apply newly developed AI-based systems, the hematologist must have a basic understanding of the general concepts of machine learning. In this review, we provide the hematologist with a comprehensive overview of various machine learning techniques, their current implementations and approaches in different diagnostic subfields (e.g., cytogenetics, molecular genetics), and the limitations and unresolved challenges of the systems.
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Affiliation(s)
- Wencke Walter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 München, Germany.
| | - Christian Pohlkamp
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 München, Germany.
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 München, Germany.
| | - Niroshan Nadarajah
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 München, Germany.
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 München, Germany.
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 München, Germany.
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 München, Germany.
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18
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The Heterogeneous Complexity of Myeloid Neoplasm: Multi-Level Approaches to Study the Disease. Cancers (Basel) 2023; 15:cancers15051449. [PMID: 36900241 PMCID: PMC10000814 DOI: 10.3390/cancers15051449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
Myeloid neoplasms (MNs) include a spectrum of bone marrow malignancies that result from the clonal expansion and arrest of differentiation of myeloid progenitor cells [...].
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19
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Wang X, Wang Y, Qi C, Qiao S, Yang S, Wang R, Jin H, Zhang J. The Application of Morphogo in the Detection of Megakaryocytes from Bone Marrow Digital Images with Convolutional Neural Networks. Technol Cancer Res Treat 2023; 22:15330338221150069. [PMID: 36700246 PMCID: PMC9896096 DOI: 10.1177/15330338221150069] [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] [Indexed: 01/27/2023] Open
Abstract
The evaluation of megakaryocytes is an important part of the work up on bone marrow smear examination. It has significance in the differential diagnosis, therapeutic efficacy assessment, and predication of prognosis of many hematologic diseases. The process of manual identification of megakaryocytes are tedious and lack of reproducibility; therefore, a reliable method of automated megakaryocytic identification is urgently needed. Three hundred and thirty-three bone marrow aspirate smears were digitized by Morphogo system. Pathologists annotated megakaryocytes on the digital images of marrow smears are applied to construct a large dataset for testing the system's predictive performance. Subsequently, we obtained megakaryocyte count and classification for each sample by different methods (system-automated analysis, system-assisted analysis, and microscopic examination) to study the correlation between different counting and classification methods. Morphogo system localized cells likely to be megakaryocytes on digital smears, which were later annotated by pathologists and the system, respectively. The system showed outstanding performance in identifying megakaryocytes in bone marrow smears with high sensitivity (96.57%) and specificity (89.71%). The overall correlation between the different methods was confirmed the high consistency (r ≥ 0.7218, R2 ≥ 0.5211) with microscopic examination in classifying megakaryocytes. Morphogo system was proved as a reliable screen tool for analyzing megakaryocytes. The application of Morphogo system shows promises to advance the automation and standardization of bone marrow smear examination.
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Affiliation(s)
- Xiaofen Wang
- Clinical Laboratory, Sir Run Run Shaw Hospital, School of Medicine,
Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Precision Medicine in Diagnosis and Monitoring
Research of Zhejiang Province, China
| | - Ying Wang
- Department of Medical Development, Hangzhou Zhiwei
Information&Technology Ltd., Hangzhou, China
| | - Chao Qi
- Clinical Laboratory, Sir Run Run Shaw Hospital, School of Medicine,
Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Precision Medicine in Diagnosis and Monitoring
Research of Zhejiang Province, China
| | - Sai Qiao
- Clinical Laboratory, Sir Run Run Shaw Hospital, School of Medicine,
Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Precision Medicine in Diagnosis and Monitoring
Research of Zhejiang Province, China
| | - Suwen Yang
- Clinical Laboratory, Sir Run Run Shaw Hospital, School of Medicine,
Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Precision Medicine in Diagnosis and Monitoring
Research of Zhejiang Province, China
| | - Rongrong Wang
- Department of Clinical Pharmacy, the First Affiliated Hospital,
Zhejiang University, Hangzhou, Zhejiang, China
| | - Hong Jin
- Clinical Laboratory, Sir Run Run Shaw Hospital, School of Medicine,
Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Precision Medicine in Diagnosis and Monitoring
Research of Zhejiang Province, China
| | - Jun Zhang
- Clinical Laboratory, Sir Run Run Shaw Hospital, School of Medicine,
Zhejiang University, Hangzhou, Zhejiang, China,Key Laboratory of Precision Medicine in Diagnosis and Monitoring
Research of Zhejiang Province, China,Jun Zhang, Clinical Laboratory, Sir Run Run
Shaw Hospital, School of Medicine, Zhejiang University, No.3, Qingchun East
Road, Shangcheng District, Hangzhou, Zhejiang 310016, China.
Hong Jin, Clinical Laboratory, Sir
Run Run Shaw Hospital, School of Medicine, Zhejiang University, No.3, Qingchun
East Road, Shangcheng District, Hangzhou, Zhejiang 310016, China.
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20
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Hasserjian RP, Orazi A, Orfao A, Rozman M, Wang SA. The International Consensus Classification of myelodysplastic syndromes and related entities. Virchows Arch 2023; 482:39-51. [PMID: 36287260 DOI: 10.1007/s00428-022-03417-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The International Consensus Classification (ICC) of myeloid neoplasms and acute leukemia has updated the classification of myelodysplastic syndromes (MDSs) and placed MDS in a broader group of clonal cytopenias that includes clonal cytopenia of undetermined significance (CCUS) and related entities. Although subject to some interobserver variability and lack of specificity, morphologic dysplasia remains the main feature that distinguishes MDS from other clonal cytopenias and defines MDS as a hematologic malignancy. The ICC has introduced some changes in the definition of MDS whereby some cases categorized as MDS based on cytogenetic abnormalities are now classified as CCUS, while SF3B1 and multi-hit TP53 mutations are now considered to be MDS-defining in a cytopenic patient. The ICC has also recognized several cytogenetic and molecular abnormalities that reclassify some cases of MDS with excess blasts as acute myeloid leukemia (AML) and has introduced a new MDS/AML entity that encompasses cases with 10-19% blasts that lie on the continuum between MDS and AML. Two new genetically defined categories of MDS have been introduced: MDS with mutated SF3B1 and MDS with mutated TP53, the latter requiring bi-allelic aberrations in the TP53 gene. The entity MDS, unclassifiable has been eliminated. These changes have resulted in an overall simplification of the MDS classification scheme from 8 separate entities (including 1 that was genetically defined) in the revised 4th edition WHO classification to 7 separate entities (including 3 that are genetically defined) in the ICC.
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Affiliation(s)
- Robert P Hasserjian
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit St, Warren 244, Boston, MA, 02114, USA.
| | - Attilio Orazi
- Department of Pathology, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Alberto Orfao
- Department of Medicine, Cytometry Service, Cancer Research Center (IBMCC-CSIC/USAL), Institute for Biomedical Research of Salamanca (IBSAL) and CIBERONC, University of Salamanca, Salamanca, Spain
| | - Maria Rozman
- Hematopathology Section, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Sa A Wang
- Department of Hematopathology, MD Anderson Cancer Center, Houston, TX, USA
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21
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Madanat YF, Xie Z, Zeidan AM. Advances in myelodysplastic syndromes: promising novel agents and combination strategies. Expert Rev Hematol 2023; 16:51-63. [PMID: 36620919 DOI: 10.1080/17474086.2023.2166923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Myelodysplastic syndromes (MDS) are heterogeneous group of clonal hematopoietic stem cell neoplasms that have limited approved treatment options. Multiple novel agents are currently being tested in a clinical trial setting. From a therapeutic perspective, MDS is generally divided into lower-risk and higher-risk disease. In this review, we summarize some of the most prominent novel agents currently in development. AREAS COVERED This review focuses on select clinical trials in both lower- and higher-risk MDS, elucidating the mechanisms of action and rationale for drug combinations and summarizing early safety and efficacy data using novel agents in MDS. EXPERT OPINION Advances in understanding the innate immune system, telomere biology, as well as genomic drivers of the disease have led to the development of multiple novel agents that are currently in late stages of clinical development in MDS. Imetelstat is being tested in lower-risk disease and the phase III clinical trial recently completed accrual. Magrolimab, sabatolimab, and venetoclax in addition to novel oral hypomethylating agents (HMA) are being investigated in higher-risk MDS. These advances will hopefully bring better treatment options to patients and lead to a shift in the treatment paradigm. Post HMA therapy remains an area of dire unmet need.
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Affiliation(s)
- Yazan F Madanat
- Simmons Comprehensive Cancer Center, Division of Hematology/Oncology, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Zhuoer Xie
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, Florida, USA
| | - Amer M Zeidan
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, New Haven, Connecticut, USA
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22
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Polprasert C, Kongkiatkamon S, Niparuck P, Rattanathammethee T, Wudhikarn K, Chuncharunee S, Kobbuaklee S, Suksusut A, Lanamtieng T, Lawasut P, Asawapanumas T, Bunworasate U, Rojnuckarin P. Genetic mutations associated with blood count abnormalities in myeloid neoplasms. HEMATOLOGY (AMSTERDAM, NETHERLANDS) 2022; 27:765-771. [PMID: 35766510 DOI: 10.1080/16078454.2022.2094134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Myelodysplastic syndromes (MDS) predominantly present with varying degrees of cytopenia, while myelodysplastic syndromes/myeloproliferative neoplasms (MDS/MPN) exhibit proliferative features. Genetic defects underlying different complete blood count (CBC) alterations remain to be defined. OBJECTIVE We aimed to evaluate mutations and impacts on abnormal blood counts in MDS and MDS/MPN. METHOD MDS and MDS/MPN patients were recruited and sequenced by targeted next-generation sequencing. Clinical parameters, especially CBC, were evaluated for the association with genetic abnormalities and clinical outcomes. RESULTS A total of 168 patients with myeloid neoplasms were recruited (92 cases of low-risk MDS, 57 cases of high-risk MDS and 19 cases of MDS/MPN). Compared to low-risk MDS and MDS/MPN, patients with high-risk MDS were presented with more severe neutropenia with 17.5% showing absolute neutrophil counts (ANC) lower than 0.5 × 109/L. Patients with MDS/MPN more commonly harboured mutations and had a higher number of mutations per case than low-risk MDS (94.7% vs. 56.5%; p < 0.001 and 3 vs. 1; p < 0.001, respectively). Patients with SF3B1 mutations showed lower haemoglobin levels than wild-type (7.9 vs. 8.4 g/dL, p = 0.02), but were associated with normal platelet counts (286 vs. 93 × 109/L; p < 0.001). Patients with U2AF1 mutations were associated with more severe leukopenia than wild-type (3 vs. 4.18 × 109/L; p = 0.02). KRAS mutations were associated with monocytosis (p < 0.001). Multivariate analysis revealed high-risk MDS, MDS/MPN, severe neutropenia (ANC < 0.5 × 109/L), and mutations in ASXL1 and SETBP1 were associated with inferior survival outcomes. CONCLUSION Certain mutations were related to more severe anaemia, lower white blood cell count or monocytosis in Asian MDS and MDS/MPN patients.
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Affiliation(s)
- Chantana Polprasert
- Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand.,Research Unit in Translational Hematology, Chulalongkorn University, Bangkok, Thailand
| | - Sunisa Kongkiatkamon
- Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand.,Research Unit in Translational Hematology, Chulalongkorn University, Bangkok, Thailand
| | - Pimjai Niparuck
- Department of Medicine, Faculty of Medicine, Mahidol University Ramathibodi hospital, Bangkok, Thailand
| | | | - Kitsada Wudhikarn
- Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand.,Research Unit in Translational Hematology, Chulalongkorn University, Bangkok, Thailand
| | - Suporn Chuncharunee
- Department of Medicine, Faculty of Medicine, Mahidol University Ramathibodi hospital, Bangkok, Thailand
| | - Sirorat Kobbuaklee
- Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand.,Research Unit in Translational Hematology, Chulalongkorn University, Bangkok, Thailand
| | - Amornchai Suksusut
- Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Theerin Lanamtieng
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Panisinee Lawasut
- Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand.,Research Unit in Translational Hematology, Chulalongkorn University, Bangkok, Thailand
| | - Thiti Asawapanumas
- Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand.,Research Unit in Translational Hematology, Chulalongkorn University, Bangkok, Thailand
| | - Udomsak Bunworasate
- Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand.,Research Unit in Translational Hematology, Chulalongkorn University, Bangkok, Thailand
| | - Ponlapat Rojnuckarin
- Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand.,Research Unit in Translational Hematology, Chulalongkorn University, Bangkok, Thailand
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23
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Abstract
PURPOSE OF REVIEW We review how understanding the fitness and comorbidity burden of patients, and molecular landscape of underlying acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) at the time of diagnosis is now integral to treatment. RECENT FINDINGS The upfront identification of patients' fitness and molecular profile facilitates selection of targeted and novel agents, enables risk stratification, allows consideration of allogeneic hematopoietic cell transplantation in high-risk patients, and provides treatment selection for older (age ≥ 75) or otherwise unfit patients who may not tolerate conventional treatment. The use of measurable residual disease (MRD) assessment improves outcome prediction and can also guide therapeutic strategies such as chemotherapy maintenance and transplant. In recent years, several novel drugs have received FDA approval for treating patients with AML with or without specific mutations. A doublet and triplet combination of molecular targeted and other novel treatments have resulted in high response rates in early trials. Following the initial success in AML, novel drugs are undergoing clinical trials in MDS. Unprecedented advances have been made in precision medicine approaches in AML and MDS. However, lack of durable responses and long-term disease control in many patients still present significant challenges, which can only be met, to some extent, with innovative combination strategies throughout the course of treatment from induction to consolidation and maintenance.
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24
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Abstract
Myelodysplastic syndromes (MDS) are a family of myeloid cancers with diverse genotypes and phenotypes characterized by ineffective haematopoiesis and risk of transformation to acute myeloid leukaemia (AML). Some epidemiological data indicate that MDS incidence is increasing in resource-rich regions but this is controversial. Most MDS cases are caused by randomly acquired somatic mutations. In some patients, the phenotype and/or genotype of MDS overlaps with that of bone marrow failure disorders such as aplastic anaemia, paroxysmal nocturnal haemoglobinuria (PNH) and AML. Prognostic systems, such as the revised International Prognostic Scoring System (IPSS-R), provide reasonably accurate predictions of survival at the population level. Therapeutic goals in individuals with lower-risk MDS include improving quality of life and minimizing erythrocyte and platelet transfusions. Therapeutic goals in people with higher-risk MDS include decreasing the risk of AML transformation and prolonging survival. Haematopoietic cell transplantation (HCT) can cure MDS, yet fewer than 10% of affected individuals receive this treatment. However, how, when and in which patients with HCT for MDS should be performed remains controversial, with some studies suggesting HCT is preferred in some individuals with higher-risk MDS. Advances in the understanding of MDS biology offer the prospect of new therapeutic approaches.
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25
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Hong S, Rybicki L, Gurnari C, Pagliuca S, Zhang A, Thomas D, Visconte V, Durrani J, Sobecks RM, Kalaycio M, Gerds AT, Carraway HE, Mukherjee S, Sekeres MA, Advani AS, Majhail NS, Hamilton BK, Patel BJ, Maciejewski JP. Pattern of somatic mutation changes after allogeneic hematopoietic cell transplantation for acute myeloid leukemia and myelodysplastic syndromes. Bone Marrow Transplant 2022; 57:1615-1619. [PMID: 35896698 PMCID: PMC10846350 DOI: 10.1038/s41409-022-01762-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/13/2022] [Accepted: 07/08/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Sanghee Hong
- Department of Hematology and Oncology, University Hospitals Cleveland Medical Center/ Case Western Reserve University, Cleveland, OH, USA
| | - Lisa Rybicki
- Department of Quantitative Health Science, Lerner Resesarch Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Simona Pagliuca
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
- Department of Clinical Hematology, CHRU de Nancy, Nancy, France
| | - Aiwen Zhang
- Allogen Laboratories, Cleveland Clinic, Cleveland, OH, USA
| | - Dawn Thomas
- Allogen Laboratories, Cleveland Clinic, Cleveland, OH, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Jibran Durrani
- Department of Hematology and Oncology, National Institute of Health, Bethesda, MD, USA
| | - Ronald M Sobecks
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Matt Kalaycio
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Aaron T Gerds
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hetty E Carraway
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Sudipto Mukherjee
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mikkael A Sekeres
- Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Anjali S Advani
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Betty K Hamilton
- Department of Hematology and Oncology, National Institute of Health, Bethesda, MD, USA
| | - Bhumika J Patel
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA.
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
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26
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Arber DA, Orazi A, Hasserjian RP, Borowitz MJ, Calvo KR, Kvasnicka HM, Wang SA, Bagg A, Barbui T, Branford S, Bueso-Ramos CE, Cortes JE, Dal Cin P, DiNardo CD, Dombret H, Duncavage EJ, Ebert BL, Estey EH, Facchetti F, Foucar K, Gangat N, Gianelli U, Godley LA, Gökbuget N, Gotlib J, Hellström-Lindberg E, Hobbs GS, Hoffman R, Jabbour EJ, Kiladjian JJ, Larson RA, Le Beau MM, Loh MLC, Löwenberg B, Macintyre E, Malcovati L, Mullighan CG, Niemeyer C, Odenike OM, Ogawa S, Orfao A, Papaemmanuil E, Passamonti F, Porkka K, Pui CH, Radich JP, Reiter A, Rozman M, Rudelius M, Savona MR, Schiffer CA, Schmitt-Graeff A, Shimamura A, Sierra J, Stock WA, Stone RM, Tallman MS, Thiele J, Tien HF, Tzankov A, Vannucchi AM, Vyas P, Wei AH, Weinberg OK, Wierzbowska A, Cazzola M, Döhner H, Tefferi A. International Consensus Classification of Myeloid Neoplasms and Acute Leukemias: integrating morphologic, clinical, and genomic data. Blood 2022; 140:1200-1228. [PMID: 35767897 PMCID: PMC9479031 DOI: 10.1182/blood.2022015850] [Citation(s) in RCA: 916] [Impact Index Per Article: 458.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/16/2022] [Indexed: 02/02/2023] Open
Abstract
The classification of myeloid neoplasms and acute leukemias was last updated in 2016 within a collaboration between the World Health Organization (WHO), the Society for Hematopathology, and the European Association for Haematopathology. This collaboration was primarily based on input from a clinical advisory committees (CACs) composed of pathologists, hematologists, oncologists, geneticists, and bioinformaticians from around the world. The recent advances in our understanding of the biology of hematologic malignancies, the experience with the use of the 2016 WHO classification in clinical practice, and the results of clinical trials have indicated the need for further revising and updating the classification. As a continuation of this CAC-based process, the authors, a group with expertise in the clinical, pathologic, and genetic aspects of these disorders, developed the International Consensus Classification (ICC) of myeloid neoplasms and acute leukemias. Using a multiparameter approach, the main objective of the consensus process was the definition of real disease entities, including the introduction of new entities and refined criteria for existing diagnostic categories, based on accumulated data. The ICC is aimed at facilitating diagnosis and prognostication of these neoplasms, improving treatment of affected patients, and allowing the design of innovative clinical trials.
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Affiliation(s)
| | - Attilio Orazi
- Texas Tech University Health Sciences Center El Paso, El Paso, TX
| | | | | | | | | | - Sa A Wang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Adam Bagg
- University of Pennsylvania, Philadelphia, PA
| | - Tiziano Barbui
- Clinical Research Foundation, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | | | | | | | | | | | - Hervé Dombret
- Université Paris Cité, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris, Paris, France
| | | | | | | | | | | | | | | | | | | | - Jason Gotlib
- Stanford University School of Medicine, Stanford, CA
| | | | | | | | | | - Jean-Jacques Kiladjian
- Université Paris Cité, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris, Paris, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Kimmo Porkka
- Helsinki University Central Hospital Comprehensive Cancer Center, Helsinki, Finland
| | | | | | | | | | | | | | | | | | - Akiko Shimamura
- Dana-Farber Cancer Institute, Boston, MA
- Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Jorge Sierra
- Hospital Santa Creu i Sant Pau, Barcelona, Spain
| | | | | | | | | | - Hwei-Fang Tien
- National Taiwan University Hospital, Taipei City, Taiwan
| | | | | | - Paresh Vyas
- University of Oxford, Oxford, United Kingdom
| | - Andrew H Wei
- Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia
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27
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El Alaoui Y, Elomri A, Qaraqe M, Padmanabhan R, Yasin Taha R, El Omri H, El Omri A, Aboumarzouk O. A Review of Artificial Intelligence Applications in Hematology Management: Current Practices and Future Prospects. J Med Internet Res 2022; 24:e36490. [PMID: 35819826 PMCID: PMC9328784 DOI: 10.2196/36490] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/14/2022] [Accepted: 05/29/2022] [Indexed: 12/23/2022] Open
Abstract
Background Machine learning (ML) and deep learning (DL) methods have recently garnered a great deal of attention in the field of cancer research by making a noticeable contribution to the growth of predictive medicine and modern oncological practices. Considerable focus has been particularly directed toward hematologic malignancies because of the complexity in detecting early symptoms. Many patients with blood cancer do not get properly diagnosed until their cancer has reached an advanced stage with limited treatment prospects. Hence, the state-of-the-art revolves around the latest artificial intelligence (AI) applications in hematology management. Objective This comprehensive review provides an in-depth analysis of the current AI practices in the field of hematology. Our objective is to explore the ML and DL applications in blood cancer research, with a special focus on the type of hematologic malignancies and the patient’s cancer stage to determine future research directions in blood cancer. Methods We searched a set of recognized databases (Scopus, Springer, and Web of Science) using a selected number of keywords. We included studies written in English and published between 2015 and 2021. For each study, we identified the ML and DL techniques used and highlighted the performance of each model. Results Using the aforementioned inclusion criteria, the search resulted in 567 papers, of which 144 were selected for review. Conclusions The current literature suggests that the application of AI in the field of hematology has generated impressive results in the screening, diagnosis, and treatment stages. Nevertheless, optimizing the patient’s pathway to treatment requires a prior prediction of the malignancy based on the patient’s symptoms or blood records, which is an area that has still not been properly investigated.
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Affiliation(s)
- Yousra El Alaoui
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Adel Elomri
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Marwa Qaraqe
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Regina Padmanabhan
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Ruba Yasin Taha
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Halima El Omri
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Abdelfatteh El Omri
- Surgical Research Section, Department of Surgery, Hamad Medical Corporation, Doha, Qatar
| | - Omar Aboumarzouk
- Surgical Research Section, Department of Surgery, Hamad Medical Corporation, Doha, Qatar.,College of Medicine, Qatar University, Doha, Qatar.,College of Medicine, University of Glasgow, Glasgow, United Kingdom
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Liu K, Hu J. Classification of acute myeloid leukemia M1 and M2 subtypes using machine learning. Comput Biol Med 2022; 147:105741. [PMID: 35738057 DOI: 10.1016/j.compbiomed.2022.105741] [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: 01/27/2022] [Revised: 05/24/2022] [Accepted: 06/11/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Classification of acute myeloid leukemia (AML) relies on manual analysis of bone marrow or peripheral blood smear images. We aimed to construct a machine learning model for automatic classification of AML-M1 and M2 subtypes in bone marrow smear images. METHODS Bone marrow smear images of AML patients were extracted from the Cancer Imaging Archive (TCIA) open database. Classification criteria of AML subtypes were based on the French-American-British (FAB) classification system. Random forest method and broad learning system (BLS) were used to develop the classification model. Morphological features, radiomics features, and clinical features were extracted. The performance of the classification model was evaluated by calculating accuracy, precision, recall, F1-score, and area under the curve (AUC). A total of 50 bone marrow smear images (AML-M1, 31 cases; AML-M2, 19 cases) with 500 slices were included in this study. RESULTS A total of 43 morphological features, 276 radiomics features, and 1 clinical feature were extracted. Finally, 9 variables including 2 morphological features, 6 radiomics features, and 1 clinical feature were selected into the classification model. The best classification performance was observed in the random forest model with 9 variables, with the average accuracy, AUC, F1-score, recall, and precision of the model being 0.998 ± 0.003, 0.998 ± 0.004, 0.998 ± 0.004, 0.996 ± 0.009, and 1 ± 0, respectively. CONCLUSION The random forest model performed well for the classification of AML-M1 and M2, which may provide a tool for clinicians to classify AML-M1 and M2.
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Affiliation(s)
- Ke Liu
- Department of Hematology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, China.
| | - Jie Hu
- Department of Medical Record Management, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, China
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Kaisrlikova M, Vesela J, Kundrat D, Votavova H, Dostalova Merkerova M, Krejcik Z, Divoky V, Jedlicka M, Fric J, Klema J, Mikulenkova D, Stastna Markova M, Lauermannova M, Mertova J, Soukupova Maaloufova J, Jonasova A, Cermak J, Belickova M. RUNX1 mutations contribute to the progression of MDS due to disruption of antitumor cellular defense: a study on patients with lower-risk MDS. Leukemia 2022; 36:1898-1906. [PMID: 35505182 PMCID: PMC9252911 DOI: 10.1038/s41375-022-01584-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/12/2022] [Accepted: 04/21/2022] [Indexed: 11/18/2022]
Abstract
Patients with lower-risk myelodysplastic syndromes (LR-MDS) have a generally favorable prognosis; however, a small proportion of cases progress rapidly. This study aimed to define molecular biomarkers predictive of LR-MDS progression and to uncover cellular pathways contributing to malignant transformation. The mutational landscape was analyzed in 214 LR-MDS patients, and at least one mutation was detected in 137 patients (64%). Mutated RUNX1 was identified as the main molecular predictor of rapid progression by statistics and machine learning. To study the effect of mutated RUNX1 on pathway regulation, the expression profiles of CD34 + cells from LR-MDS patients with RUNX1 mutations were compared to those from patients without RUNX1 mutations. The data suggest that RUNX1-unmutated LR-MDS cells are protected by DNA damage response (DDR) mechanisms and cellular senescence as an antitumor cellular barrier, while RUNX1 mutations may be one of the triggers of malignant transformation. Dysregulated DDR and cellular senescence were also observed at the functional level by detecting γH2AX expression and β-galactosidase activity. Notably, the expression profiles of RUNX1-mutated LR-MDS resembled those of higher-risk MDS at diagnosis. This study demonstrates that incorporating molecular data improves LR-MDS risk stratification and that mutated RUNX1 is associated with a suppressed defense against LR-MDS progression.
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Affiliation(s)
- Monika Kaisrlikova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic.,First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jitka Vesela
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - David Kundrat
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Hana Votavova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | | | - Zdenek Krejcik
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Vladimir Divoky
- Department of Biology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Marek Jedlicka
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Fric
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Jiri Klema
- Czech Technical University, Prague, Czech Republic
| | - Dana Mikulenkova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | | | | | - Jolana Mertova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | | | - Anna Jonasova
- First Department of Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Jaroslav Cermak
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Monika Belickova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic. .,First Faculty of Medicine, Charles University, Prague, Czech Republic.
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30
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Shen Q, Feng Y, Gong X, Jia Y, Gao Q, Jiao X, Qi S, Liu X, Wei H, Huang B, Zhao N, Song X, Ma Y, Liang S, Zhang D, Qin L, Wang Y, Qu S, Zou Y, Chen Y, Guo Y, Yi S, An G, Jiao Z, Zhang S, Li L, Yan J, Wang H, Song Z, Mi Y, Qiu L, Zhu X, Wang J, Xiao Z, Chen J. A Phenogenetic Axis that Modulates Clinical Manifestation and Predicts Treatment Outcome in Primary Myeloid Neoplasms. CANCER RESEARCH COMMUNICATIONS 2022; 2:258-276. [PMID: 36873623 PMCID: PMC9981215 DOI: 10.1158/2767-9764.crc-21-0194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/02/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
Abstract
Although the concept of "myeloid neoplasm continuum" has long been proposed, few comparative genomics studies directly tested this hypothesis. Here we report a multi-modal data analysis of 730 consecutive newly diagnosed patients with primary myeloid neoplasm, along with 462 lymphoid neoplasm cases serving as the outgroup. Our study identified a "Pan-Myeloid Axis" along which patients, genes, and phenotypic features were all aligned in sequential order. Utilizing relational information of gene mutations along the Pan-Myeloid Axis improved prognostic accuracy for complete remission and overall survival in adult patients of de novo acute myeloid leukemia and for complete remission in adult patients of myelodysplastic syndromes with excess blasts. We submit that better understanding of the myeloid neoplasm continuum might shed light on how treatment should be tailored to individual diseases. Significance The current criteria for disease diagnosis treat myeloid neoplasms as a group of distinct, separate diseases. This work provides genomics evidence for a "myeloid neoplasm continuum" and suggests that boundaries between myeloid neoplastic diseases are much more blurred than previously thought.
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Affiliation(s)
- Qiujin Shen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yahui Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xiaowen Gong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yujiao Jia
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Qingyan Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | | | - Saibing Qi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xueou Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Hui Wei
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Bingqing Huang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Ningning Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xiaoqiang Song
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yueshen Ma
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | | | - Donglei Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Li Qin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Ying Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Shiqiang Qu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yao Zou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yumei Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Ye Guo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Shuhua Yi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Gang An
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | | | - Song Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Linfeng Li
- Yidu Cloud Technology Inc., Beijing, China
| | - Jun Yan
- Yidu Cloud Technology Inc., Beijing, China
| | - Huijun Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Zhen Song
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yingchang Mi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Lugui Qiu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Jianxiang Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Zhijian Xiao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Junren Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
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31
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Enjeti AK, Agarwal R, Blombery P, Chee L, Chua CC, Grigg A, Hamad N, Iland H, Lane S, Perkins A, Singhal D, Tate C, Tiong IS, Ross DM. Panel-based gene testing in myelodysplastic/myeloproliferative neoplasm- overlap syndromes: Australasian Leukaemia and Lymphoma Group (ALLG) consensus statement. Pathology 2022; 54:389-398. [DOI: 10.1016/j.pathol.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 11/30/2022]
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32
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Awada H, Gurnari C, Durmaz A, Awada H, Pagliuca S, Visconte V. Personalized Risk Schemes and Machine Learning to Empower Genomic Prognostication Models in Myelodysplastic Syndromes. Int J Mol Sci 2022; 23:2802. [PMID: 35269943 PMCID: PMC8911403 DOI: 10.3390/ijms23052802] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 02/04/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are characterized by variable clinical manifestations and outcomes. Several prognostic systems relying on clinical factors and cytogenetic abnormalities have been developed to help stratify MDS patients into different risk categories of distinct prognoses and therapeutic implications. The current abundance of molecular information poses the challenges of precisely defining patients' molecular profiles and their incorporation in clinically established diagnostic and prognostic schemes. Perhaps the prognostic power of the current systems can be boosted by incorporating molecular features. Machine learning (ML) algorithms can be helpful in developing more precise prognostication models that integrate complex genomic interactions at a higher dimensional level. These techniques can potentially generate automated diagnostic and prognostic models and assist in advancing personalized therapies. This review highlights the current prognostication models used in MDS while shedding light on the latest achievements in ML-based research.
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Affiliation(s)
- Hussein Awada
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (H.A.); (C.G.); (A.D.); (S.P.)
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (H.A.); (C.G.); (A.D.); (S.P.)
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Arda Durmaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (H.A.); (C.G.); (A.D.); (S.P.)
| | - Hassan Awada
- Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA;
| | - Simona Pagliuca
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (H.A.); (C.G.); (A.D.); (S.P.)
- Department of Clinical Hematology, CHRU Nancy, CEDEX, 54035 Nancy, France
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (H.A.); (C.G.); (A.D.); (S.P.)
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Duchmann M, Wagner-Ballon O, Boyer T, Cheok M, Fournier E, Guerin E, Fenwarth L, Badaoui B, Freynet N, Benayoun E, Lusina D, Garcia I, Gardin C, Fenaux P, Pautas C, Quesnel B, Turlure P, Terré C, Thomas X, Lambert J, Renneville A, Preudhomme C, Dombret H, Itzykson R, Cluzeau T. Machine learning identifies the independent role of dysplasia in the prediction of response to chemotherapy in AML. Leukemia 2022; 36:656-663. [PMID: 34615986 DOI: 10.1038/s41375-021-01435-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 12/17/2022]
Abstract
The independent prognostic impact of specific dysplastic features in acute myeloid leukemia (AML) remains controversial and may vary between genomic subtypes. We apply a machine learning framework to dissect the relative contribution of centrally reviewed dysplastic features and oncogenetics in 190 patients with de novo AML treated in ALFA clinical trials. One hundred and thirty-five (71%) patients achieved complete response after the first induction course (CR). Dysgranulopoiesis, dyserythropoiesis and dysmegakaryopoiesis were assessable in 84%, 83% and 63% patients, respectively. Multi-lineage dysplasia was present in 27% of assessable patients. Micromegakaryocytes (q = 0.01), hypolobulated megakaryocytes (q = 0.08) and hyposegmented granulocytes (q = 0.08) were associated with higher ELN-2017 risk. Using a supervised learning algorithm, the relative importance of morphological variables (34%) for the prediction of CR was higher than demographic (5%), clinical (2%), cytogenetic (25%), molecular (29%), and treatment (5%) variables. Though dysplasias had limited predictive impact on survival, a multivariate logistic regression identified the presence of hypolobulated megakaryocytes (p = 0.014) and micromegakaryocytes (p = 0.035) as predicting lower CR rates, independently of monosomy 7 (p = 0.013), TP53 (p = 0.004), and NPM1 mutations (p = 0.025). Assessment of these specific dysmegakarypoiesis traits, for which we identify a transcriptomic signature, may thus guide treatment allocation in AML.
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Affiliation(s)
- Matthieu Duchmann
- Laboratoire d'Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France.,Université de Paris, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, 75010, Paris, France
| | - Orianne Wagner-Ballon
- Département d'Hématologie et Immunologie biologiques, Hôpital Henri-Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France.,INSERM U955 IMRB, UPEC, Créteil, France
| | - Thomas Boyer
- Service d'Hématologie Biologique, CHU Lille, Lille, France.,Service d'Hématologie Biologique, CHU Amiens-Picardie, Amiens, France
| | | | - Elise Fournier
- Service d'Hématologie Biologique, CHU Lille, Lille, France
| | - Estelle Guerin
- Service d'Hématologie biologique, Hôpital Dupuytren, Limoges, France.,UMR CNRS 7276/INSERM 1262, CHU Limoges, Limoges, France
| | - Laurène Fenwarth
- Université Lille, CNRS, INSERM, CHU Lille, IRCL, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, 59000, Lille, France
| | - Bouchra Badaoui
- Département d'Hématologie et Immunologie biologiques, Hôpital Henri-Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
| | - Nicolas Freynet
- Département d'Hématologie et Immunologie biologiques, Hôpital Henri-Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
| | - Emmanuel Benayoun
- Département d'Hématologie et Immunologie biologiques, Hôpital Henri-Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
| | - Daniel Lusina
- Laboratoire d'Hématologie, Hôpital Avicenne, Assistance Publique-Hôpitaux de Paris, Université Sorbonne Paris Cité, Bobigny, France
| | - Isabel Garcia
- Laboratoire d'Hématologie, Hôpital André Mignot, Centre Hospitalier de Versailles, Le Chesnay, France
| | - Claude Gardin
- Département d'Hématologie Clinique, Hôpital Avicenne, Assistance Publique-Hôpitaux de Paris, Bobigny, France
| | - Pierre Fenaux
- Département d'Hématologie Clinique, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
| | - Cécile Pautas
- Département d'Hématologie clinique, Hôpital Henri-Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
| | - Bruno Quesnel
- CHU Lille, Service des Maladies du Sang, 59000, Lille, France
| | - Pascal Turlure
- Département d'Hématologie Clinique, CHU Limoges, Limoges, France
| | - Christine Terré
- Laboratoire de Cytogénétique, Hôpital André Mignot, Centre Hospitalier de Versailles, Le Chesnay, France
| | - Xavier Thomas
- Département d'Hématologie Clinique, Hospices Civils de Lyon, Hôpital Lyon-Sud, Pierre Bénite, France
| | - Juliette Lambert
- Département d'Hématologie Clinique, Hôpital André Mignot, Centre Hospitalier de Versailles, Le Chesnay, France
| | | | - Claude Preudhomme
- Université Lille, CNRS, INSERM, CHU Lille, IRCL, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, 59000, Lille, France
| | - Hervé Dombret
- Département d'Hématologie Clinique, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, EA-3518, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Raphael Itzykson
- Université de Paris, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, 75010, Paris, France. .,Département d'Hématologie Clinique, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France.
| | - Thomas Cluzeau
- Département d'Hématologie, Université Côte d'Azur, CHU de Nice, Nice, France.
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Bongrand P. Is There a Need for a More Precise Description of Biomolecule Interactions to Understand Cell Function? Curr Issues Mol Biol 2022; 44:505-525. [PMID: 35723321 PMCID: PMC8929073 DOI: 10.3390/cimb44020035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/15/2022] [Accepted: 01/17/2022] [Indexed: 11/16/2022] Open
Abstract
An important goal of biological research is to explain and hopefully predict cell behavior from the molecular properties of cellular components. Accordingly, much work was done to build extensive “omic” datasets and develop theoretical methods, including computer simulation and network analysis to process as quantitatively as possible the parameters contained in these resources. Furthermore, substantial effort was made to standardize data presentation and make experimental results accessible to data scientists. However, the power and complexity of current experimental and theoretical tools make it more and more difficult to assess the capacity of gathered parameters to support optimal progress in our understanding of cell function. The purpose of this review is to focus on biomolecule interactions, the interactome, as a specific and important example, and examine the limitations of the explanatory and predictive power of parameters that are considered as suitable descriptors of molecular interactions. Recent experimental studies on important cell functions, such as adhesion and processing of environmental cues for decision-making, support the suggestion that it should be rewarding to complement standard binding properties such as affinity and kinetic constants, or even force dependence, with less frequently used parameters such as conformational flexibility or size of binding molecules.
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Affiliation(s)
- Pierre Bongrand
- Lab Adhesion and Inflammation (LAI), Inserm UMR 1067, Cnrs UMR 7333, Aix-Marseille Université UM 61, Marseille 13009, France
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Ball S, Komrokji RS, Sallman DA. Prognostic scoring systems and risk stratification in myelodysplastic syndrome: focus on integration of molecular profile. Leuk Lymphoma 2021; 63:1281-1291. [PMID: 34933652 DOI: 10.1080/10428194.2021.2018579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Myelodysplastic syndromes (MDS) form a clinically and molecularly heterogeneous disease group. Precise risk stratification remains crucial for choosing optimal management strategies. Several conventional prognostic scoring systems have been developed and validated in the MDS population. These risk models divide patients into prognostic subgroups based on clinical and cytogenetic characteristics. Lack of dynamicity, variable risk estimate across models, and heterogeneity within intermediate-risk group are the limitations of traditional models like IPSS-R, with questionable relevance of these scoring systems in treated MDS patients. Recent progress in next-generation sequencing techniques has improved understanding of the distribution and prognostic importance of recurrent genetic mutations in MDS. Early studies have suggested that incorporating mutations in risk stratification could supplement IPSS-R in further refining the model's performance in predicting overall survival and risk of transformation to acute myeloid leukemia and should translate into a molecularly driven prognostication approach in the near future.
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Affiliation(s)
- Somedeb Ball
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Rami S Komrokji
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - David A Sallman
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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36
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Voso MT. Have we reached a molecular era in myelodysplastic syndromes? HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2021; 2021:418-427. [PMID: 34889424 PMCID: PMC8791166 DOI: 10.1182/hematology.2021000276] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Myelodysplastic syndromes (MDS) are characterized by heterogeneous biological and clinical characteristics, leading to variable outcomes. The availability of sophisticated platforms of genome sequencing allowed the discovery of recurrently mutated genes, which have led to a new era in MDS. This is reflected by the 2016 update of the World Health Organization classification, in which the criteria to define MDS with ringed sideroblasts include the presence of SF3B1 mutations. Further, the detection of somatic mutations in myeloid genes at high variant allele frequency guides the diagnostic algorithm in cases with cytopenias, unclear dysplastic changes, and normal karyotypes, supporting MDS over alternative diagnoses. SF3B1 mutations have been shown to play a positive prognostic role, while mutations in ASXL1, EZH2, RUNX1, and TP53 have been associated with a dismal prognosis. This is particularly relevant in lower- and intermediate-risk disease, in which a higher number of mutations and/or the presence of "unfavorable" somatic mutations may support the use of disease-modifying treatments. In the near future, the incorporation of mutation profiles in currently used prognostication systems, also taking into consideration the classical patient clinical variables (including age and comorbidities), will support a more precise disease stratification, eg, the assignment to targeted treatment approaches or to allogeneic stem cell transplantation in younger patients.
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Affiliation(s)
- Maria Teresa Voso
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Santa Lucia Foundation, IRCCS, Neuro-Oncohematology, Rome, Italy
- Correspondence Maria Teresa Voso, Department of Biomedicine and Prevention, University of Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; e-mail:
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TET2 mutations as a part of DNA dioxygenase deficiency in myelodysplastic syndromes. Blood Adv 2021; 6:100-107. [PMID: 34768283 PMCID: PMC8753204 DOI: 10.1182/bloodadvances.2021005418] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/26/2021] [Indexed: 11/25/2022] Open
Abstract
5-hydroxymethylcytosine and TET2 messenger RNA (mRNA) downregulation are common in myelodysplastic syndromes irrespective of TET2 mutations. TET3 mRNA expression levels are associated with distinct clinical outcomes in myelodysplastic syndromes with and without TET2 mutations.
Decrease in DNA dioxygenase activity generated by TET2 gene family is crucial in myelodysplastic syndromes (MDS). The general downregulation of 5-hydroxymethylcytosine (5-hmC) argues for a role of DNA demethylation in MDS beyond TET2 mutations, which albeit frequent, do not convey any prognostic significance. We investigated TETs expression to identify factors which can modulate the impact of mutations and thus 5-hmC levels on clinical phenotypes and prognosis of MDS patients. DNA/RNA-sequencing and 5-hmC data were collected from 1665 patients with MDS and 91 controls. Irrespective of mutations, a significant fraction of MDS patients exhibited lower TET2 expression, whereas 5-hmC levels were not uniformly decreased. In searching for factors explaining compensatory mechanisms, we discovered that TET3 was upregulated in MDS and inversely correlated with TET2 expression in wild-type cases. Although TET2 was reduced across all age groups, TET3 levels were increased in a likely feedback mechanism induced by TET2 dysfunction. This inverse relationship of TET2 and TET3 expression also corresponded to the expression of L-2-hydroxyglutarate dehydrogenase, involved in agonist/antagonist substrate metabolism. Importantly, elevated TET3 levels influenced the clinical phenotype of TET2 deficiency whereby the lack of compensation by TET3 (low TET3 expression) was associated with poor outcomes of TET2 mutant carriers.
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Gallì A, Todisco G, Catamo E, Sala C, Elena C, Pozzi S, Bono E, Ferretti VV, Rizzo E, Molteni E, Zibellini S, Sarchi M, Boveri E, Ferrari J, Fiorelli N, Camaschella C, Gasparini P, Toniolo D, Cazzola M, Malcovati L. Relationship between clone metrics and clinical outcome in clonal cytopenia. Blood 2021; 138:965-976. [PMID: 34255818 DOI: 10.1182/blood.2021011323] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/21/2021] [Indexed: 01/05/2023] Open
Abstract
Clonal cytopenia of undetermined significance (CCUS) is associated with an increased risk of developing a myeloid neoplasm with myelodysplasia (MN). To identify the features of the mutant clone(s) that is associated with clinical phenotype and progression, we studied the following cohorts of individuals: 311 patients with idiopathic cytopenia of undetermined significance (ICUS), 532 community-dwelling individuals without hematologic phenotype (n = 355) or with unexplained anemia (n = 177), and 592 patients with overt MN. Ninety-two of 311 (30%) patients with ICUS carried a somatic genetic lesion that signaled CCUS. Clonal hematopoiesis (CH) was detected in 19.7% and 27.7% of nonanemic and anemic community-dwelling individuals, respectively. Different mutation patterns and variant allele frequencies (VAFs) (clone metrics parameters) were observed in the conditions studied. Recurrent mutation patterns exhibited different VAFs associated with marrow dysplasia (0.17-0.48), indicating variable clinical expressivity of mutant clones. Unsupervised clustering analysis based on mutation profiles identified 2 major clusters, characterized by isolated DNMT3A mutations (CH-like cluster) or combinatorial mutation patterns (MN-like cluster), and showing different overall survival (HR, 1.8). In patients with CCUS, the 2 clusters had different risk of progression to MN (HR, 2.7). Within the MN-like cluster, distinct subsets with different risk of progression to MN were identified based on clone metrics. These findings unveil marked variability in the clinical expressivity of myeloid driver genes and underline the limitations of morphologic dysplasia for clinical staging of mutant hematopoietic clones. Clone metrics appears to be critical for informing clinical decision-making in patients with clonal cytopenia.
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Affiliation(s)
- Anna Gallì
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
| | - Gabriele Todisco
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Eulalia Catamo
- Department of Medicine, Surgery, and Health Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Cinzia Sala
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Elena
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
| | - Sara Pozzi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Elisa Bono
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | | | | | - Silvia Zibellini
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
| | - Martina Sarchi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Emanuela Boveri
- Department of Pathology, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| | - Jacqueline Ferrari
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Nicolas Fiorelli
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Clara Camaschella
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Paolo Gasparini
- Department of Medicine, Surgery, and Health Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Mario Cazzola
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Luca Malcovati
- Department of Hematology Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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Deep learning detects acute myeloid leukemia and predicts NPM1 mutation status from bone marrow smears. Leukemia 2021; 36:111-118. [PMID: 34497326 PMCID: PMC8727290 DOI: 10.1038/s41375-021-01408-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/12/2021] [Accepted: 08/27/2021] [Indexed: 12/02/2022]
Abstract
The evaluation of bone marrow morphology by experienced hematopathologists is essential in the diagnosis of acute myeloid leukemia (AML); however, it suffers from a lack of standardization and inter-observer variability. Deep learning (DL) can process medical image data and provides data-driven class predictions. Here, we apply a multi-step DL approach to automatically segment cells from bone marrow images, distinguish between AML samples and healthy controls with an area under the receiver operating characteristic (AUROC) of 0.9699, and predict the mutation status of Nucleophosmin 1 (NPM1)—one of the most common mutations in AML—with an AUROC of 0.92 using only image data from bone marrow smears. Utilizing occlusion sensitivity maps, we observed so far unreported morphologic cell features such as a pattern of condensed chromatin and perinuclear lightening zones in myeloblasts of NPM1-mutated AML and prominent nucleoli in wild-type NPM1 AML enabling the DL model to provide accurate class predictions.
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40
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A predictive algorithm using clinical and laboratory parameters may assist in ruling out and in diagnosing MDS. Blood Adv 2021; 5:3066-3075. [PMID: 34387647 DOI: 10.1182/bloodadvances.2020004055] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/08/2021] [Indexed: 02/08/2023] Open
Abstract
We present a noninvasive Web-based app to help exclude or diagnose myelodysplastic syndrome (MDS), a bone marrow (BM) disorder with cytopenias and leukemic risk, diagnosed by BM examination. A sample of 502 MDS patients from the European MDS (EUMDS) registry (n > 2600) was combined with 502 controls (all BM proven). Gradient-boosted models (GBMs) were used to predict/exclude MDS using demographic, clinical, and laboratory variables. Area under the receiver operating characteristic curve (AUC), sensitivity, and specificity were used to evaluate the models, and performance was validated using 100 times fivefold cross-validation. Model stability was assessed by repeating its fit using different randomly chosen groups of 502 EUMDS cases. AUC was 0.96 (95% confidence interval, 0.95-0.97). MDS is predicted/excluded accurately in 86% of patients with unexplained anemia. A GBM score (range, 0-1) of less than 0.68 (GBM < 0.68) resulted in a negative predictive value of 0.94, that is, MDS was excluded. GBM ≥ 0.82 provided a positive predictive value of 0.88, that is, MDS. The diagnosis of the remaining patients (0.68 ≤ GBM < 0.82) is indeterminate. The discriminating variables: age, sex, hemoglobin, white blood cells, platelets, mean corpuscular volume, neutrophils, monocytes, glucose, and creatinine. A Web-based app was developed; physicians could use it to exclude or predict MDS noninvasively in most patients without a BM examination. Future work will add peripheral blood cytogenetics/genetics, EUMDS-based prospective validation, and prognostication.
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41
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Myelodysplastic Syndromes in the Postgenomic Era and Future Perspectives for Precision Medicine. Cancers (Basel) 2021; 13:cancers13133296. [PMID: 34209457 PMCID: PMC8267785 DOI: 10.3390/cancers13133296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary With demographic ageing, improved cancer survivorship and increased diagnostic sensitivity, incident cases of patients with Myelodysplastic Syndromes (MDS) are continuously rising, leading to a relevant impact on health care resources. Disease heterogeneity and various comorbidities are challenges for the management of the generally elderly patients. Therefore, experienced physicians and multidisciplinary teams should be involved in the establishment of the correct diagnosis, risk-assessment and personalized treatment plan. Next-generation sequencing allows for early detection of clonal hematopoiesis and monitoring of clonal evolution, but also poses new challenges for its appropriate use. At present, allogeneic hematopoietic stem cell transplantation remains the only curative treatment option for a minority of fit MDS patients. All others receive palliative treatment and will eventually progress, having an unmet need for novel therapies. Targeting compounds are in prospect for precision medicine, however, abrogation of clonal evolution to acute myeloid leukemia remains actually out of reach. Abstract Myelodysplastic syndromes (MDS) represent a heterogeneous group of clonal disorders caused by sequential accumulation of somatic driver mutations in hematopoietic stem and progenitor cells (HSPCs). MDS is characterized by ineffective hematopoiesis with cytopenia, dysplasia, inflammation, and a variable risk of transformation into secondary acute myeloid leukemia. The advent of next-generation sequencing has revolutionized our understanding of the genetic basis of the disease. Nevertheless, the biology of clonal evolution remains poorly understood, and the stochastic genetic drift with sequential accumulation of genetic hits in HSPCs is individual, highly dynamic and hardly predictable. These continuously moving genetic targets pose substantial challenges for the implementation of precision medicine, which aims to maximize efficacy with minimal toxicity of treatments. In the current postgenomic era, allogeneic hematopoietic stem cell transplantation remains the only curative option for younger and fit MDS patients. For all unfit patients, regeneration of HSPCs stays out of reach and all available therapies remain palliative, which will eventually lead to refractoriness and progression. In this review, we summarize the recent advances in our understanding of MDS pathophysiology and its impact on diagnosis, risk-assessment and disease monitoring. Moreover, we present ongoing clinical trials with targeting compounds and highlight future perspectives for precision medicine.
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42
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Sidhom JW, Siddarthan IJ, Lai BS, Luo A, Hambley BC, Bynum J, Duffield AS, Streiff MB, Moliterno AR, Imus P, Gocke CB, Gondek LP, DeZern AE, Baras AS, Kickler T, Levis MJ, Shenderov E. Deep learning for diagnosis of acute promyelocytic leukemia via recognition of genomically imprinted morphologic features. NPJ Precis Oncol 2021; 5:38. [PMID: 33990660 PMCID: PMC8121867 DOI: 10.1038/s41698-021-00179-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/16/2021] [Indexed: 12/16/2022] Open
Abstract
Acute promyelocytic leukemia (APL) is a subtype of acute myeloid leukemia (AML), classified by a translocation between chromosomes 15 and 17 [t(15;17)], that is considered a true oncologic emergency though appropriate therapy is considered curative. Therapy is often initiated on clinical suspicion, informed by both clinical presentation as well as direct visualization of the peripheral smear. We hypothesized that genomic imprinting of morphologic features learned by deep learning pattern recognition would have greater discriminatory power and consistency compared to humans, thereby facilitating identification of t(15;17) positive APL. By applying both cell-level and patient-level classification linked to t(15;17) PML/RARA ground-truth, we demonstrate that deep learning is capable of distinguishing APL in both discovery and prospective independent cohort of patients. Furthermore, we extract learned information from the trained network to identify previously undescribed morphological features of APL. The deep learning method we describe herein potentially allows a rapid, explainable, and accurate physician-aid for diagnosing APL at the time of presentation in any resource-poor or -rich medical setting given the universally available peripheral smear.
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Affiliation(s)
- John-William Sidhom
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ingharan J Siddarthan
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bo-Shiun Lai
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Adam Luo
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bryan C Hambley
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer Bynum
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amy S Duffield
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael B Streiff
- Division of Hematology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alison R Moliterno
- Division of Hematology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Philip Imus
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christian B Gocke
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lukasz P Gondek
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amy E DeZern
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexander S Baras
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas Kickler
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mark J Levis
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eugene Shenderov
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Brück OE, Lallukka-Brück SE, Hohtari HR, Ianevski A, Ebeling FT, Kovanen PE, Kytölä SI, Aittokallio TA, Ramos PM, Porkka KV, Mustjoki SM. Machine Learning of Bone Marrow Histopathology Identifies Genetic and Clinical Determinants in Patients with MDS. Blood Cancer Discov 2021; 2:238-249. [PMID: 34661156 PMCID: PMC8513905 DOI: 10.1158/2643-3230.bcd-20-0162] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/18/2021] [Accepted: 03/05/2021] [Indexed: 12/30/2022] Open
Abstract
In myelodysplastic syndrome (MDS) and myeloproliferative neoplasm (MPN), bone marrow (BM) histopathology is assessed to identify dysplastic cellular morphology, cellularity, and blast excess. Yet, other morphologic findings may elude the human eye. We used convolutional neural networks to extract morphologic features from 236 MDS, 87 MDS/MPN, and 11 control BM biopsies. These features predicted genetic and cytogenetic aberrations, prognosis, age, and gender in multivariate regression models. Highest prediction accuracy was found for TET2 [area under the receiver operating curve (AUROC) = 0.94] and spliceosome mutations (0.89) and chromosome 7 monosomy (0.89). Mutation prediction probability correlated with variant allele frequency and number of affected genes per pathway, demonstrating the algorithms' ability to identify relevant morphologic patterns. By converting regression models to texture and cellular composition, we reproduced the classical del(5q) MDS morphology consisting of hypolobulated megakaryocytes. In summary, this study highlights the potential of linking deep BM histopathology with genetics and clinical variables. SIGNIFICANCE Histopathology is elementary in the diagnostics of patients with MDS, but its high-dimensional data are underused. By elucidating the association of morphologic features with clinical variables and molecular genetics, this study highlights the vast potential of convolutional neural networks in understanding MDS pathology and how genetics is reflected in BM morphology. See related commentary by Elemento, p. 195.
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Affiliation(s)
- Oscar E. Brück
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Helsinki University Hospital Comprehensive Cancer Center, Department of Hematology, Helsinki, Finland
| | - Susanna E. Lallukka-Brück
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Helena R. Hohtari
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Aleksandr Ianevski
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Freja T. Ebeling
- Helsinki University Hospital Comprehensive Cancer Center, Department of Hematology, Helsinki, Finland
| | - Panu E. Kovanen
- Department of Pathology, HUSLAB, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Soili I. Kytölä
- HUS Diagnostic Center, HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Tero A. Aittokallio
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, and Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Oslo, Norway
| | | | - Kimmo V. Porkka
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Helsinki University Hospital Comprehensive Cancer Center, Department of Hematology, Helsinki, Finland
| | - Satu M. Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
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44
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Elemento O. Towards artificial intelligence-driven pathology assessment for hematological malignancies. Blood Cancer Discov 2021; 2:195-197. [PMID: 34027414 PMCID: PMC8133372 DOI: 10.1158/2643-3230.bcd-21-0048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this issue of Blood Cancer Discovery, Brück et al applied unsupervised and supervised machine learning to bone marrow histopathology images from Myelodysplastic Syndrome (MDS) patients. Their study provides new insights into the pathobiology of MDS and paves the way for increased use of artificial intelligence for the assessment and diagnosis of hematological malignancies.
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Affiliation(s)
- Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York.
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45
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Palomo L, Acha P, Solé F. Genetic Aspects of Myelodysplastic/Myeloproliferative Neoplasms. Cancers (Basel) 2021; 13:cancers13092120. [PMID: 33925681 PMCID: PMC8124412 DOI: 10.3390/cancers13092120] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Myelodysplastic/myeloproliferative neoplasms (MDS/MPN) are clonal myeloid neoplasms characterized, at the time of their presentation, by the simultaneous presence of both myelodysplastic and myeloproliferative features. In MDS/MPN, the karyotype is often normal but mutations in genes that are common across myeloid neoplasms can be detected in a high proportion of cases by targeted sequencing. In this review, we intend to summarize the main genetic findings across all MDS/MPN overlap syndromes and discuss their relevance in the management of patients. Abstract Myelodysplastic/myeloproliferative neoplasms (MDS/MPN) are myeloid neoplasms characterized by the presentation of overlapping features from both myelodysplastic syndromes and myeloproliferative neoplasms. Although the classification of MDS/MPN relies largely on clinical features and peripheral blood and bone marrow morphology, studies have demonstrated that a large proportion of patients (~90%) with this disease harbor somatic mutations in a group of genes that are common across myeloid neoplasms. These mutations play a role in the clinical heterogeneity of these diseases and their clinical evolution. Nevertheless, none of them is specific to MDS/MPN and current diagnostic criteria do not include molecular data. Even when such alterations can be helpful for differential diagnosis, they should not be used alone as proof of neoplasia because some of these mutations may also occur in healthy older people. Here, we intend to review the main genetic findings across all MDS/MPN overlap syndromes and discuss their relevance in the management of the patients.
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Affiliation(s)
- Laura Palomo
- MDS Group, Institut de Recerca Contra la Leucèmia Josep Carreras, ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (L.P.); (P.A.)
- Experimental Hematology, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Pamela Acha
- MDS Group, Institut de Recerca Contra la Leucèmia Josep Carreras, ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (L.P.); (P.A.)
| | - Francesc Solé
- MDS Group, Institut de Recerca Contra la Leucèmia Josep Carreras, ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (L.P.); (P.A.)
- Correspondence: ; Tel.: +34-93-557-2806
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Royston D, Mead AJ, Psaila B. Application of Single-Cell Approaches to Study Myeloproliferative Neoplasm Biology. Hematol Oncol Clin North Am 2021; 35:279-293. [PMID: 33641869 PMCID: PMC7935666 DOI: 10.1016/j.hoc.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Philadelphia-negative myeloproliferative neoplasms (MPNs) are an excellent tractable disease model of a number of aspects of human cancer biology, including genetic evolution, tissue-associated fibrosis, and cancer stem cells. In this review, we discuss recent insights into MPN biology gained from the application of a number of new single-cell technologies to study human disease, with a specific focus on single-cell genomics, single-cell transcriptomics, and digital pathology.
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Affiliation(s)
- Daniel Royston
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine and NIHR Biomedical Research Centre, University of Oxford, Headley Way, Oxford OX39DS, UK
| | - Adam J Mead
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Biomedical Research Centre, University of Oxford, Headley Way, Oxford OX3 9DS, UK.
| | - Bethan Psaila
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Biomedical Research Centre, University of Oxford, Headley Way, Oxford OX3 9DS, UK
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Bewersdorf JP, Zeidan AM. Management of patients with higher-risk myelodysplastic syndromes after failure of hypomethylating agents: What is on the horizon? Best Pract Res Clin Haematol 2021; 34:101245. [PMID: 33762100 DOI: 10.1016/j.beha.2021.101245] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The hypomethylating agents (HMA) azacitidine (AZA) and decitabine (DAC) are the standard of care for frontline treatment of patients with higher-risk myelodysplastic syndromes (MDS). As complete responses to HMAs are rare and typically not durable, HMA failure is a common clinical dilemma and associated with very short survival in most patients. Salvage therapies with various agents such as novel HMAs (guadecitabine, CC-486), and CTLA-4/PD1-type immune checkpoint inhibitors (ICPIs) have yielded mixed and only modest results at best in MDS patients with HMA failure. Thanks to advances in the understanding of the molecular and biologic pathogenesis of MDS, several novel targeted agents such as the BCL-2 inhibitor venetoclax, TP-53 refolding agent APR-246, IDH1/2 inhibitors, and novel ICPIs such as magrolimab and sabatolimab have been developed and demonstrated activity in combination with HMA in the frontline setting. However, clinical testing of these agents post HMA failure has been limited to date. Furthermore, the biology of HMA failure remains poorly defined which significantly limits rationale drug development. This highlights the importance of optimization of frontline therapy to avoid/delay HMA failure in addition to development of more effective salvage therapies.
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Affiliation(s)
- Jan Philipp Bewersdorf
- Department of Internal Medicine, Section of Hematology, Yale University School of Medicine, New Haven, CT, USA
| | - Amer M Zeidan
- Department of Internal Medicine, Section of Hematology, Yale University School of Medicine, New Haven, CT, USA.
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Hasserjian RP, Buckstein R, Patnaik MM. Navigating Myelodysplastic and Myelodysplastic/Myeloproliferative Overlap Syndromes. Am Soc Clin Oncol Educ Book 2021; 41:328-350. [PMID: 34010050 DOI: 10.1200/edbk_320113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Myelodysplastic syndromes (MDS) and MDS/myeloproliferative neoplasms (MPNs) are clonal diseases that differ in morphologic diagnostic criteria but share some common disease phenotypes that include cytopenias, propensity to acute myeloid leukemia evolution, and a substantially shortened patient survival. MDS/MPNs share many clinical and molecular features with MDS, including frequent mutations involving epigenetic modifier and/or spliceosome genes. Although the current 2016 World Health Organization classification incorporates some genetic features in its diagnostic criteria for MDS and MDS/MPNs, recent accumulation of data has underscored the importance of the mutation profiles on both disease classification and prognosis. Machine-learning algorithms have identified distinct molecular genetic signatures that help refine prognosis and notable associations of these genetic signatures with morphologic and clinical features. Combined geno-clinical models that incorporate mutation data seem to surpass the current prognostic schemes. Future MDS classification and prognostication schema will be based on the portfolio of genetic aberrations and traditional features, such as blast count and clinical factors. Arriving at these systems will require studies on large patient cohorts that incorporate advanced computational analysis. The current treatment algorithm in MDS is based on patient risk as derived from existing prognostic and disease classes. Luspatercept is newly approved for patients with MDS and ring sideroblasts who are transfusion dependent after erythropoietic-stimulating agent failure. Other agents that address red blood cell transfusion dependence in patients with lower-risk MDS and the failure of hypomethylating agents in higher-risk disease are in advanced testing. Finally, a plethora of novel targeted agents and immune checkpoint inhibitors are being evaluated in combination with a hypomethylating agent backbone to augment the depth and duration of response and, we hope, improve overall survival.
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Affiliation(s)
| | - Rena Buckstein
- Division of Hematology/Oncology, Sunnybrook Odette Cancer Center, Toronto, Ontario, Canada
| | - Mrinal M Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, MN
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Iacobucci I, Mullighan C. Prognostic mutation constellations in acute myeloid leukaemia and myelodysplastic syndrome. Curr Opin Hematol 2021; 28:101-109. [PMID: 33427759 PMCID: PMC8174569 DOI: 10.1097/moh.0000000000000629] [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] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW In the past decade, numerous studies analysing the genome and transcriptome of large cohorts of acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS) patients have substantially improved our knowledge of the genetic landscape of these diseases with the identification of heterogeneous constellations of germline and somatic mutations with prognostic and therapeutic relevance. However, inclusion of integrated genetic data into classification schema is still far from a reality. The purpose of this review is to summarize recent insights into the prevalence, pathogenic role, clonal architecture, prognostic impact and therapeutic management of genetic alterations across the spectrum of myeloid malignancies. RECENT FINDINGS Recent multiomic-studies, including analysis of genetic alterations at the single-cell resolution, have revealed a high heterogeneity of lesions in over 200 recurrently mutated genes affecting disease initiation, clonal evolution and clinical outcome. Artificial intelligence and specifically machine learning approaches have been applied to large cohorts of AML and MDS patients to define in an unbiased manner clinically meaningful disease patterns including, disease classification, prognostication and therapeutic vulnerability, paving the way for future use in clinical practice. SUMMARY Integration of genomic, transcriptomic, epigenomic and clinical data coupled to conventional and machine learning approaches will allow refined leukaemia classification and risk prognostication and will identify novel therapeutic targets for these still high-risk leukaemia subtypes.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis (USA)
| | - Charles Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis (USA)
- Hematological Malignancies Program, St Jude Children’s Research Hospital, Memphis, TN, United States
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