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Chang BH, Thiel-Klare K, Tyner JW. In vivo Targeting MEK and TNK2/SRC pathways in PTPN11 driven leukemia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594555. [PMID: 38798550 PMCID: PMC11118393 DOI: 10.1101/2024.05.16.594555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
PTPN11 encodes for a tyrosine phosphatase implicated in the pathogenesis of hematologic malignancies such as Juvenile Myelomonocytic Leukemia (JMML), Acute Myeloid Leukemia (AML), and Acute Lymphoblastic Leukemia (ALL). Since activating mutations of PTPN11 increase proliferative signaling and cell survival through the RAS/MAPK proliferative pathway there is significant interest in using MEK inhibitors for clinical benefit. Yet, single agent clinical activity has been minimal. Previously, we showed that PTPN11 is further activated by upstream tyrosine kinases TNK2/SRC, and that PTPN11-mutant JMML and AML cells are sensitive to TNK2 inhibition using dasatinib. In order to validate these findings, we adopted a genetically engineered mouse model of PTPN11 driven leukemia using the mouse strain 129S/Sv- Ptpn11 tm6Bgn /Mmucd crossed with B6.129P2- Lyz2 tm1(cre)Ifo /J. The F1 progeny expressing Ptpn11 D61Y within hematopoietic cells destined along the granulocyte-monocyte progenitor lineage developed a fatal myeloproliferative disorder characterized by neutrophilia and monocytosis, and infiltration of myeloid cells into the liver and spleen. Cohorts of Ptpn11 D61Y expressing animals treated with combination of dasatinib and trametinib for an extended period of time was well tolerated and had a significant effect in mitigating disease parameters compared to single agents. Finally, a primary patient-derived xenograft model using a myeloid leukemia with PTPN11 F71L also displayed improved disease response to combination. Collectively, these studies point to combined therapies targeting MEK and TNK2/SRC as a promising therapeutic potential for PTPN11-mutant leukemias. Key Points Combining MEK and TNK2/SRC inhibitors has therapeutic potential in PTPN11 mutant JMML and AML.
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Strullu M, Leblanc T, Lainey E. [Juvenile myelomonocytic leukemia and pediatric myelodysplastic syndromes]. Bull Cancer 2023; 110:1183-1195. [PMID: 37453833 DOI: 10.1016/j.bulcan.2023.03.026] [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: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 07/18/2023]
Abstract
Juvenile myelomonocytic leukemia (JMML) and myelodysplastic syndromes (MDS) of children are rare and aggressive diseases. They both have the particularity of being very frequently associated with an underlying predisposition syndrome, which must be systematically investigated by meticulous clinical exam completed by molecular analysis on fibroblasts, in order to guarantee the best therapeutic management. New generation sequencing techniques have made it possible to better define the landscape of constitutional predisposing pathologies, to understand the clonal evolution that leads to the development of hematological malignancies and to identify new prognostic markers. In these two diseases, the only curative treatment is allogeneic hematopoietic stem cell transplantation, for which the appropriate timeframe, the type of donor and the conditioning must be decided in consultation with the expert teams in each entity.
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Affiliation(s)
- Marion Strullu
- AP-HP, hôpital Robert-Debré, service d'hémato-immunologie pédiatrique, Paris, France; Université Paris-Cité, institut universitaire d'hématologie, Inserm UMR1131, Paris, France.
| | - Thierry Leblanc
- AP-HP, hôpital Robert-Debré, service d'hémato-immunologie pédiatrique, Paris, France
| | - Elodie Lainey
- Université Paris-Cité, institut universitaire d'hématologie, Inserm UMR1131, Paris, France; AP-HP, hôpital Robert-Debré, service d'hématologie biologique, Paris, France
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Sinha R, Dvorak M, Ganesan A, Kalesinskas L, Niemeyer CM, Flotho C, Sakamoto KM, Lacayo N, Patil RV, Perriman R, Cepika AM, Liu YL, Kuo A, Utz PJ, Khatri P, Bertaina A. Epigenetic Profiling of PTPN11 Mutant JMML Hematopoietic Stem and Progenitor Cells Reveals an Aberrant Histone Landscape. Cancers (Basel) 2023; 15:5204. [PMID: 37958378 PMCID: PMC10650722 DOI: 10.3390/cancers15215204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is a deadly pediatric leukemia driven by RAS pathway mutations, of which >35% are gain-of-function in PTPN11. Although DNA hypermethylation portends severe clinical phenotypes, the landscape of histone modifications and chromatin profiles in JMML patient cells have not been explored. Using global mass cytometry, Epigenetic Time of Flight (EpiTOF), we analyzed hematopoietic stem and progenitor cells (HSPCs) from five JMML patients with PTPN11 mutations. These data revealed statistically significant changes in histone methylation, phosphorylation, and acetylation marks that were unique to JMML HSPCs when compared with healthy controls. Consistent with these data, assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis revealed significant alterations in chromatin profiles at loci encoding post-translational modification enzymes, strongly suggesting their mis-regulated expression. Collectively, this study reveals histone modification pathways as an additional epigenetic abnormality in JMML patient HSPCs, thereby uncovering a new family of potential druggable targets for the treatment of JMML.
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Affiliation(s)
- Roshani Sinha
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
| | - Mai Dvorak
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Ananthakrishnan Ganesan
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Larry Kalesinskas
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Charlotte M. Niemeyer
- Department of Pediatric Hematology and Oncology, University of Freiburg Medical Centre, 79098 Freiburg im Breisgau, Germany; (C.M.N.); (C.F.)
| | - Christian Flotho
- Department of Pediatric Hematology and Oncology, University of Freiburg Medical Centre, 79098 Freiburg im Breisgau, Germany; (C.M.N.); (C.F.)
| | - Kathleen M. Sakamoto
- Bass Center for Childhood Cancer and Blood Disorders at Lucile Packard Children’s Hospital, Palo Alto, CA 94304, USA; (K.M.S.); (N.L.)
| | - Norman Lacayo
- Bass Center for Childhood Cancer and Blood Disorders at Lucile Packard Children’s Hospital, Palo Alto, CA 94304, USA; (K.M.S.); (N.L.)
| | - Rachana Vinay Patil
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
| | - Rhonda Perriman
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
| | - Alma-Martina Cepika
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
| | - Yunying Lucy Liu
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
| | - Alex Kuo
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Paul J. Utz
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Purvesh Khatri
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Alice Bertaina
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
- Bass Center for Childhood Cancer and Blood Disorders at Lucile Packard Children’s Hospital, Palo Alto, CA 94304, USA; (K.M.S.); (N.L.)
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Volchkov EV, Khozyainova AA, Gurzhikhanova MK, Larionova IV, Matveev VE, Evseev DA, Ignatova AK, Menyailo ME, Venyov DA, Vorobev RS, Semchenkova AA, Olshanskaya YV, Denisov EV, Maschan MA. Potential value of high-throughput single-cell DNA sequencing of Juvenile myelomonocytic leukemia: report of two cases. NPJ Syst Biol Appl 2023; 9:41. [PMID: 37684264 PMCID: PMC10491583 DOI: 10.1038/s41540-023-00303-7] [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: 02/27/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is a rare myeloproliferative disease of early childhood that develops due to mutations in the genes of the RAS-signaling pathway. Next-generation high throughput sequencing (NGS) enables identification of various secondary molecular genetic events that can facilitate JMML progression and transformation into secondary acute myeloid leukemia (sAML). The methods of single-cell DNA sequencing (scDNA-seq) enable overcoming limitations of bulk NGS and exploring genetic heterogeneity at the level of individual cells, which can help in a better understanding of the mechanisms leading to JMML progression and provide an opportunity to evaluate the response of leukemia to therapy. In the present work, we applied a two-step droplet microfluidics approach to detect DNA alterations among thousands of single cells and to analyze clonal dynamics in two JMML patients with sAML transformation before and after hematopoietic stem cell transplantation (HSCT). At the time of diagnosis both of our patients harbored only "canonical" mutations in the RAS signaling pathway genes detected by targeted DNA sequencing. Analysis of samples from the time of transformation JMML to sAML revealed additional genetic events that are potential drivers for disease progression in both patients. ScDNA-seq was able to measure of chimerism level and detect a residual tumor clone in the second patient after HSCT (sensitivity of less than 0.1% tumor cells). The data obtained demonstrate the value of scDNA-seq to assess the clonal evolution of JMML to sAML, response to therapy and engraftment monitoring.
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Affiliation(s)
- E V Volchkov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia.
- Laboratory of Single Cell Biology, Research Institute of Molecular and Cellular Medicine, RUDN University, Moscow, 117198, Russia.
| | - A A Khozyainova
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - M Kh Gurzhikhanova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia
| | - I V Larionova
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - V E Matveev
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia
| | - D A Evseev
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia
| | - A K Ignatova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia
| | - M E Menyailo
- Laboratory of Single Cell Biology, Research Institute of Molecular and Cellular Medicine, RUDN University, Moscow, 117198, Russia
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - D A Venyov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia
| | - R S Vorobev
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - A A Semchenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia
| | - Yu V Olshanskaya
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia
| | - E V Denisov
- Laboratory of Single Cell Biology, Research Institute of Molecular and Cellular Medicine, RUDN University, Moscow, 117198, Russia
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - M A Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia.
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Yuan T, Edelmann D, Fan Z, Alwers E, Kather JN, Brenner H, Hoffmeister M. Machine learning in the identification of prognostic DNA methylation biomarkers among patients with cancer: A systematic review of epigenome-wide studies. Artif Intell Med 2023; 143:102589. [PMID: 37673571 DOI: 10.1016/j.artmed.2023.102589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 04/19/2023] [Accepted: 04/30/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND DNA methylation biomarkers have great potential in improving prognostic classification systems for patients with cancer. Machine learning (ML)-based analytic techniques might help overcome the challenges of analyzing high-dimensional data in relatively small sample sizes. This systematic review summarizes the current use of ML-based methods in epigenome-wide studies for the identification of DNA methylation signatures associated with cancer prognosis. METHODS We searched three electronic databases including PubMed, EMBASE, and Web of Science for articles published until 2 January 2023. ML-based methods and workflows used to identify DNA methylation signatures associated with cancer prognosis were extracted and summarized. Two authors independently assessed the methodological quality of included studies by a seven-item checklist adapted from 'A Tool to Assess Risk of Bias and Applicability of Prediction Model Studies (PROBAST)' and from the 'Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK). Different ML methods and workflows used in included studies were summarized and visualized by a sunburst chart, a bubble chart, and Sankey diagrams, respectively. RESULTS Eighty-three studies were included in this review. Three major types of ML-based workflows were identified. 1) unsupervised clustering, 2) supervised feature selection, and 3) deep learning-based feature transformation. For the three workflows, the most frequently used ML techniques were consensus clustering, least absolute shrinkage and selection operator (LASSO), and autoencoder, respectively. The systematic review revealed that the performance of these approaches has not been adequately evaluated yet and that methodological and reporting flaws were common in the identified studies using ML techniques. CONCLUSIONS There is great heterogeneity in ML-based methodological strategies used by epigenome-wide studies to identify DNA methylation markers associated with cancer prognosis. In theory, most existing workflows could not handle the high multi-collinearity and potentially non-linearity interactions in epigenome-wide DNA methylation data. Benchmarking studies are needed to compare the relative performance of various approaches for specific cancer types. Adherence to relevant methodological and reporting guidelines are urgently needed.
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Affiliation(s)
- Tanwei Yuan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Dominic Edelmann
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ziwen Fan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elizabeth Alwers
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jakob Nikolas Kather
- Else Kroener Fresenius Center for Digital Health, Technical University Dresden, Dresden, Germany; Medical Oncology, National Center of Tumour Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Park S, Rehman MU, Ullah F, Tayara H, Chong KT. iCpG-Pos: an accurate computational approach for identification of CpG sites using positional features on single-cell whole genome sequence data. Bioinformatics 2023; 39:btad474. [PMID: 37555812 PMCID: PMC10444964 DOI: 10.1093/bioinformatics/btad474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/11/2023] [Accepted: 08/08/2023] [Indexed: 08/10/2023] Open
Abstract
MOTIVATION The investigation of DNA methylation can shed light on the processes underlying human well-being and help determine overall human health. However, insufficient coverage makes it challenging to implement single-stranded DNA methylation sequencing technologies, highlighting the need for an efficient prediction model. Models are required to create an understanding of the underlying biological systems and to project single-cell (methylated) data accurately. RESULTS In this study, we developed positional features for predicting CpG sites. Positional characteristics of the sequence are derived using data from CpG regions and the separation between nearby CpG sites. Multiple optimized classifiers and different ensemble learning approaches are evaluated. The OPTUNA framework is used to optimize the algorithms. The CatBoost algorithm followed by the stacking algorithm outperformed existing DNA methylation identifiers. AVAILABILITY AND IMPLEMENTATION The data and methodologies used in this study are openly accessible to the research community. Researchers can access the positional features and algorithms used for predicting CpG site methylation patterns. To achieve superior performance, we employed the CatBoost algorithm followed by the stacking algorithm, which outperformed existing DNA methylation identifiers. The proposed iCpG-Pos approach utilizes only positional features, resulting in a substantial reduction in computational complexity compared to other known approaches for detecting CpG site methylation patterns. In conclusion, our study introduces a novel approach, iCpG-Pos, for predicting CpG site methylation patterns. By focusing on positional features, our model offers both accuracy and efficiency, making it a promising tool for advancing DNA methylation research and its applications in human health and well-being.
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Affiliation(s)
- Sehi Park
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Mobeen Ur Rehman
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Farman Ullah
- College of Information Technology in the United Arab Emirates University (UAEU), Abu Dhabi 15551, UAE
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
- Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea
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Liu YC, Geyer JT. Pediatric Hematopathology in the Era of Advanced Molecular Diagnostics: What We Know and How We Can Apply the Updated Classifications. Pathobiology 2023; 91:30-44. [PMID: 37311434 PMCID: PMC10857803 DOI: 10.1159/000531480] [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: 02/02/2023] [Accepted: 05/30/2023] [Indexed: 06/15/2023] Open
Abstract
Pediatric hematologic malignancies often show genetic features distinct from their adult counterparts, which reflect the differences in their pathogenesis. Advances in the molecular diagnostics including the widespread use of next-generation sequencing technology have revolutionized the diagnostic workup for hematologic disorders and led to the identification of new disease subgroups as well as prognostic information that impacts the clinical treatment. The increasing recognition of the importance of germline predisposition in various hematologic malignancies also shapes the disease models and management. Although germline predisposition variants can occur in patients with myelodysplastic syndrome/neoplasm (MDS) of all ages, the frequency is highest in the pediatric patient population. Therefore, evaluation for germline predisposition in the pediatric group can have significant clinical impact. This review discusses the recent advances in juvenile myelomonocytic leukemia, pediatric acute myeloid leukemia, B-lymphoblastic leukemia/lymphoma, and pediatric MDS. This review also includes a brief discussion of the updated classifications from the International Consensus Classification (ICC) and the 5th edition World Health Organization (WHO) classification regarding these disease entities.
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Affiliation(s)
- Yen-Chun Liu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Julia T. Geyer
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
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Li N, Chen M, Yin CC. Advances in molecular evaluation of myeloproliferative neoplasms. Semin Diagn Pathol 2023; 40:187-194. [PMID: 37087305 DOI: 10.1053/j.semdp.2023.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 04/24/2023]
Abstract
Myeloproliferative neoplasms (MPN) are a group of clonal hematopoietic stem cell disorders with uncontrolled proliferation of one or more hematopoietic cell types, including myeloid, erythroid and megakaryocytic lineages, and minimal defect in maturation. Most MPN are associated with well-defined molecular abnormalities involving genes that encode protein tyrosine kinases that lead to constitutive activation of the downstream signal transduction pathways and confer cells proliferative and survival advantage. Genome-wide sequencing analyses have discovered secondary cooperating mutations that are shared by most of the MPN subtypes as well as other myeloid neoplasms and play a major role in disease progression. Without appropriate management, the natural history of most MPN consists of an initial chronic phase and a terminal blast phase. Molecular aberrations involving protein tyrosine kinases have been used for the diagnosis, classification, detection of minimal/measurable residual disease, and target therapy. We review recent advances in molecular genetic aberrations in MPN with a focus on MPN associated with gene rearrangements or mutations involving tyrosine kinase pathways.
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Affiliation(s)
- Nianyi Li
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mingyi Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States.
| | - C Cameron Yin
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX, United States.
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9
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Mohanraj L, Lapato DM, Toor A, Swift-Scanlan T. DNA Methylation Research in Autologous Hematopoietic Stem Cell Transplant Population. Biol Res Nurs 2023; 25:220-226. [PMID: 36242509 DOI: 10.1177/10998004221132251] [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: 11/15/2022]
Abstract
Despite increased sophistication in DNA methylation (DNAm) measurement and methods, conducting studies in specific populations such as the hematopoietic stem cell transplant (HCT) population, presents unique challenges and study design considerations. In this article, we explain the motivation for investigating DNAm in the HCT population, highlighting important study design features and key findings in a longitudinal prospective pilot study of DNAm in 32 patients undergoing autologous HCT in Central Virginia, USA. We also discuss limitations and challenges to generating robust results. We observed that HCT does not prevent high-quality DNA from being extracted from whole blood for DNAm research and that longitudinal prospective studies that span pre- and 2-months post-HCT are feasible. Critically, we did not observe significant impacts of cancer diagnosis, time since transplant, age, or chromosomal sex on overall DNAm data dimensionality. These observations demonstrate that while extreme care is required to ensure generalizable, accurate, and interpretable results, researchers should not avoid HCT-DNAm research simply for fear that the transplant procedure or presence of a cancer diagnosis will prevent meaningful conclusions from being drawn. DNAm is an attractive biomarker that is understudied in patients undergoing HCT and needs to expand to improve precise prediction of HCT outcomes.
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Affiliation(s)
- Lathika Mohanraj
- Department of Adult Health and Nursing Systems, 16197VCU School of Nursing, Richmond, VA, USA
| | - Dana M Lapato
- Department of Human and Molecular Genetics, VCU School of Medicine, Richmond, VA, USA
| | - Amir Toor
- Department of Internal Medicine, VCU School of Medicine, Richmond, VA, USA
| | - Theresa Swift-Scanlan
- Endowed Professor and Director, Biobehavioral Research Lab, 16197VCU School of Nursing, Richmond, VA, USA
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10
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Yi ES, Baek HJ, Ju HY, Kim SK, Lee JW, Cho B, Kim BK, Kang HJ, Kook H, Yang EJ, Lim YT, Ahn WK, Hahn SM, Park SK, Yoo ES, Yoo KH. Response to chemotherapy in juvenile myelomonocytic leukemia and its clinical implications for survival: A retrospective registry-based study of the Korean Pediatric Hematology-Oncology Group. Leuk Res 2023; 129:107070. [PMID: 37019050 DOI: 10.1016/j.leukres.2023.107070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023]
Abstract
Juvenile myelomonocytic leukemia (JMML) is a life-threatening myeloproliferative neoplasm. The chemotherapeutic effect on survival remains unclear, and feasible standardized response criteria are yet to be established. We aimed to evaluate the chemotherapeutic response and its effect on survival in patients with JMML. A retrospective registry was reviewed for children diagnosed with JMML between 2000 and 2019. Response was assessed according to the criteria proposed by the International JMML Symposium in 2007 (criteria I) and the updated version in 2013 with its modifications (criteria II). A total of 73 patients were included in this study. Complete response (CR) rates were 46.6% and 28.8% using the criteria I and criteria II, respectively. A platelet count ≥ 40 × 109/L at diagnosis was associated with higher CR rates using the criteria II. Patients with criteria I-based CR had a better overall survival (OS) than those without CR (81.1% vs. 49.1% at 5 years). Patients with criteria II-based CR showed better OS (85.7% vs. 55.5% at 5 years) and event-free survival (EFS) (71.1% vs. 44.7% at 5 years) than those without CR. Additionally, a trend toward better EFS was observed in patients with criteria II-based CR than in those with criteria I-based CR but without criteria II-based CR (71.1% vs. 53.8% at 5 years). Chemotherapeutic response is associated with better survival outcomes. Along with splenomegaly, the addition of platelet count recovery, existence of extramedullary leukemic infiltration, and more stringent leukocyte counts to the response criteria allows for a more sensitive prediction of survival outcomes.
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Cai Y, Zhang J, Yi M, Zhang W, Liu X, Zhang X, Wan Y, Chang L, Zhang L, Chen X, Guo Y, Zou Y, Chen Y, Li J, Zhang Y, Yang W, Zhu X. Short-term efficacy of decitabine-based therapy in JMML: a retrospective study from a single center in China. Int J Hematol 2023; 117:121-127. [PMID: 36182987 DOI: 10.1007/s12185-022-03457-y] [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: 07/14/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 01/07/2023]
Abstract
Juvenile myelomonocytic leukemia (JMML) is an aggressive pediatric myeloproliferative disease, and newly diagnosed patients frequently cannot tolerate hematopoietic stem cell transplantation (HSCT) at diagnosis due to their poor condition. This retrospective analysis aimed to explore the short-term effect of decitabine-dominant therapy on improving the condition of JMML patients before HSCT. The subjects were 10 JMML patients. All patients were treated with decitabine after low-dose chemotherapy with an interval of 4 weeks before bridging to HSCT. The median treatment course was 3 cycles, and the overall response rate (ORR) was 70.0% after one cycle and 71.4% after three cycles. White blood cell (WBC) and monocyte counts were significantly lower after treatment, and spleen volume was also lower, though not significantly lower. The 12 month progression-free survival rate (PFS) was 80.0 ± 12.6%. Decitabine-dominant therapy was beneficial for reducing tumor burden and improving clinical condition.
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Affiliation(s)
- Yuli Cai
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Jingliao Zhang
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Meihui Yi
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Wenfeng Zhang
- Division of Ultrosound, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology And Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Xiaoming Liu
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Xiaoyan Zhang
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Yang Wan
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Lixian Chang
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Li Zhang
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Xiaojuan Chen
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Ye Guo
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Yao Zou
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Yumei Chen
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Jun Li
- Division of Ultrosound, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology And Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Yingchi Zhang
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Wenyu Yang
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China.
| | - Xiaofan Zhu
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, National Clinical Research Center for Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China.
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12
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Yi ES, Kim SK, Ju HY, Lee JW, Cho B, Kim BK, Kang HJ, Baek HJ, Kook H, Yang EJ, Lim YT, Ahn WK, Hahn SM, Park SK, Yoo ES, Yoo KH. Allogeneic hematopoietic cell transplantation in patients with juvenile myelomonocytic leukemia in Korea: a report of the Korean Pediatric Hematology-Oncology Group. Bone Marrow Transplant 2023; 58:20-29. [PMID: 36167906 DOI: 10.1038/s41409-022-01826-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/08/2022] [Accepted: 09/05/2022] [Indexed: 01/07/2023]
Abstract
Juvenile myelomonocytic leukemia (JMML) is a life-threatening myeloproliferative neoplasm. This multicenter study evaluated the characteristics, outcomes, and prognostic factors of allogeneic hematopoietic cell transplantation (HCT) in recipients with JMML who were diagnosed between 2000 and 2019 in Korea. Sixty-eight patients were retrospectively enrolled-28 patients (41.2%) received HCT during 2000-2010 and 40 patients (58.8%) during 2011-2020. The proportion of familial mismatched donors increased from 3.6 to 37.5%. The most common conditioning therapy was changed from Busulfan/Cyclophosphamide-based to Busulfan/Fludarabine-based therapy. The 5-year probabilities of event-free survival (EFS) and overall survival (OS) were 52.6% and 62.3%, respectively. The 5-year incidence of transplant-related mortality was 30.1%. Multivariate analysis revealed that the proportion of hemoglobin F ≥ 40%, abnormal cytogenetics, and matched sibling donors were independent risk factors for a higher relapse rate. Patients whose donor chimerism was below 99% had a significantly higher relapse rate. Better OS and lower treatment-related mortality were observed in patients with chronic graft-versus-host disease (GVHD), whereas grade III or IV acute GVHD was associated with worse EFS. In conclusion, the number of transplant increased along with the increase in alternative donor transplants, nevertheless, similar results were maintained. Alternative donor transplantation should be encouraged.
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Affiliation(s)
- Eun Sang Yi
- Department of Pediatrics, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Korea.,Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seong Koo Kim
- Department of Pediatrics, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hee Young Ju
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Wook Lee
- Department of Pediatrics, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Bin Cho
- Department of Pediatrics, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Bo Kyung Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Cancer Research Institute, Wide River Institute of Immunology, Seoul National University Children's Hospital, Seoul, Korea
| | - Hyoung Jin Kang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Cancer Research Institute, Wide River Institute of Immunology, Seoul National University Children's Hospital, Seoul, Korea
| | - Hee Jo Baek
- Department of Pediatrics, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Hwasun, Korea
| | - Hoon Kook
- Department of Pediatrics, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Hwasun, Korea
| | - Eu Jeen Yang
- Department of Pediatrics, Pusan National University School of Medicine, Pusan National University Children's Hospital, Yangsan, Korea
| | - Young Tak Lim
- Department of Pediatrics, Pusan National University School of Medicine, Pusan National University Children's Hospital, Yangsan, Korea
| | - Won Kee Ahn
- Department of Pediatrics, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Seung Min Hahn
- Department of Pediatrics, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Sang Kyu Park
- Department of Pediatrics, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, Korea
| | - Eun Sun Yoo
- Department of Pediatrics, Ewha Womans University College of Medicine, Ewha Womans University Seoul Hospital, Seoul, Korea
| | - Keon Hee Yoo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea. .,Department of Health Science and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea. .,Cell & Gene Therapy Institute, Samsung Medical Center, Seoul, Korea.
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13
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Ney G, Gross A, Livinski A, Kratz CP, Stewart DR. Cancer incidence and surveillance strategies in individuals with RASopathies. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:530-540. [PMID: 36533693 PMCID: PMC9825668 DOI: 10.1002/ajmg.c.32018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/15/2022] [Accepted: 11/20/2022] [Indexed: 12/24/2022]
Abstract
RASopathies are a set of clinical syndromes that have molecular and clinical overlap. Genetically, these syndromes are defined by germline pathogenic variants in RAS/MAPK pathway genes resulting in activation of this pathway. Clinically, their common molecular signature leads to comparable phenotypes, including cardiac anomalies, neurologic disorders and notably, elevated cancer risk. Cancer risk in individuals with RASopathies has been estimated from retrospective reviews and cohort studies. For example, in Costello syndrome, cancer incidence is significantly elevated over the general population, largely due to solid tumors. In some forms of Noonan syndrome, cancer risk is also elevated over the general population and is enriched for hematologic malignancies. Thus, cancer surveillance guidelines have been developed to monitor for the occurrence of such cancers in individuals with some RASopathies. These include abdominal ultrasound and urinalyses for individuals with Costello syndrome, while complete blood counts and splenic examination are recommended in Noonan syndrome. Improved cancer risk estimates and refinement of surveillance recommendations will improve the care of individuals with RASopathies.
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Affiliation(s)
- Gina Ney
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, Maryland, USA
| | - Andrea Gross
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Alicia Livinski
- National Institutes of Health Library, National Institutes of Health, Bethesda, Maryland, USA
| | - Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, Maryland, USA
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14
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De Vos N, Hofmans M, Lammens T, De Wilde B, Van Roy N, De Moerloose B. Targeted therapy in juvenile myelomonocytic leukemia: Where are we now? Pediatr Blood Cancer 2022; 69:e29930. [PMID: 36094370 DOI: 10.1002/pbc.29930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/07/2022]
Abstract
Juvenile myelomonocytic leukemia (JMML) is a rare and aggressive clonal neoplasm of early childhood, classified as an overlap myeloproliferative/myelodysplastic neoplasm by the World Health Organization. In 90% of the patients with JMML, typical initiating mutations in the canonical Ras pathway genes NF1, PTPN11, NRAS, KRAS, and CBL can be identified. Hematopoietic stem cell transplantation (HSCT) currently is the established standard of care in most patients, although long-term survival is still only 50-60%. Given the limited therapeutic options and the important morbidity and mortality associated with HSCT, new therapeutic approaches are urgently needed. Hyperactivation of the Ras pathway as disease mechanism in JMML lends itself to the use of targeted therapy. Targeted therapy could play an important role in the future treatment of patients with JMML. This review presents a comprehensive overview of targeted therapies already developed and evaluated in vitro and in vivo in patients with JMML.
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Affiliation(s)
- Nele De Vos
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University, Ghent, Belgium
| | - Mattias Hofmans
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Tim Lammens
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Bram De Wilde
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Nadine Van Roy
- Cancer Research Institute Ghent, Ghent, Belgium.,Center for Medical Genetics Ghent, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Barbara De Moerloose
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
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15
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Wu M, Zhao Y, Dong X, Jin Y, Cheng S, Zhang N, Xu S, Gu S, Wu Y, Yang J, Yao L, Wang Y. Artificial intelligence-based preoperative prediction system for diagnosis and prognosis in epithelial ovarian cancer: A multicenter study. Front Oncol 2022; 12:975703. [PMID: 36212430 PMCID: PMC9532858 DOI: 10.3389/fonc.2022.975703] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Background Ovarian cancer (OC) is the most lethal gynecological malignancy, with limited early screening methods and poor prognosis. Artificial intelligence technology has made a great breakthrough in cancer diagnosis. Purpose We aim to develop a specific interpretable machine learning (ML) prediction model for the diagnosis and prognosis of epithelial ovarian cancer (EOC) based on a variety of biomarkers. Methods A total of 521 patients with EOC and 144 patients with benign gynecological diseases were enrolled including derivation datasets and an external validation cohort. The predicted information was acquired by 9 supervised ML methods, through 34 parameters. Behind predicted reasons for the best ML were improved by using the SHapley Additive exPlanations (SHAP) algorithm. In addition, the prognosis of EOC was analyzed by unsupervised clustering and Kaplan–Meier (KM) survival analysis. Results ML technology was superior to conventional logistic regression in predicting EOC diagnosis and XGBoost performed best in the external validation datasets. The AUC values of distinguishing EOC and benign disease patients, determining pathological type, grade and clinical stage were 0.958 (0.926-0.989), 0.792 (0.701-0.8834), 0.819 (0.687-0.950) and 0.68 (0.573-0.788) respectively. For negative CA-125 EOC patients, the AUC performance of XGBoost model was 0.835(0.763-0.907). We used unsupervised cluster analysis to identify EOC subgroups with significantly poor overall survival (p-value <0.0001) and recurrence-free survival (p-value <0.0001). Conclusions Based on the preoperative characteristics, we proved that ML algorithm can provide an acceptable diagnosis and prognosis prediction model for EOC patients. Meanwhile, SHAP analysis can improve the interpretability of ML models and contribute to precision medicine.
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Affiliation(s)
- Meixuan Wu
- Department of Obstetrics and Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yaqian Zhao
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Xuhui Dong
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yue Jin
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Shanshan Cheng
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Nan Zhang
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Shilin Xu
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Sijia Gu
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yongsong Wu
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jiani Yang
- Department of Obstetrics and Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Yu Wang, ; Liangqing Yao, ; Jiani Yang,
| | - Liangqing Yao
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- *Correspondence: Yu Wang, ; Liangqing Yao, ; Jiani Yang,
| | - Yu Wang
- Department of Obstetrics and Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Yu Wang, ; Liangqing Yao, ; Jiani Yang,
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16
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Imaizumi T, Meyer J, Wakamatsu M, Kitazawa H, Murakami N, Okuno Y, Yoshida T, Sajiki D, Hama A, Kojima S, Takahashi Y, Loh M, Stieglitz E, Muramatsu H. Clinical parameter-based prediction of DNA methylation classification generates a prediction model of prognosis in patients with juvenile myelomonocytic leukemia. Sci Rep 2022; 12:14753. [PMID: 36042365 PMCID: PMC9427938 DOI: 10.1038/s41598-022-18733-4] [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: 05/13/2022] [Accepted: 08/18/2022] [Indexed: 11/11/2022] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is a rare heterogeneous hematological malignancy of early childhood characterized by causative RAS pathway mutations. Classifying patients with JMML using global DNA methylation profiles is useful for risk stratification. We implemented machine learning algorithms (decision tree, support vector machine, and naïve Bayes) to produce a DNA methylation-based classification according to recent international consensus definitions using a well-characterized pooled cohort of patients with JMML (n = 128). DNA methylation was originally categorized into three subgroups: high methylation (HM), intermediate methylation (IM), and low methylation (LM), which is a trichotomized classification. We also dichotomized the subgroups as HM/IM and LM. The decision tree model showed high concordances with 450k-based methylation [82.3% (106/128) for the dichotomized and 83.6% (107/128) for the trichotomized subgroups, respectively]. With an independent cohort (n = 72), we confirmed that these models using both the dichotomized and trichotomized classifications were highly predictive of survival. Our study demonstrates that machine learning algorithms can generate clinical parameter-based models that predict the survival outcomes of patients with JMML and high accuracy. These models enabled us to rapidly and effectively identify candidates for augmented treatment following diagnosis.
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Affiliation(s)
- Takahiro Imaizumi
- Department of Advanced Medicine, Nagoya University Hospital, Nagoya, Japan
| | - Julia Meyer
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, USA
| | - Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan
| | - Hironobu Kitazawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan
| | - Norihiro Murakami
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Taro Yoshida
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan
| | - Daichi Sajiki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan
| | - Asahito Hama
- Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Nagoya First Hospital, Nagoya, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan
| | - Mignon Loh
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, USA
| | - Elliot Stieglitz
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, USA
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan.
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17
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Genomic and Epigenomic Landscape of Juvenile Myelomonocytic Leukemia. Cancers (Basel) 2022; 14:cancers14051335. [PMID: 35267643 PMCID: PMC8909150 DOI: 10.3390/cancers14051335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Juvenile myelomonocytic leukemia (JMML) is a rare pediatric myelodysplastic/myeloproliferative neoplasm characterized by the constitutive activation of the RAS pathway. In spite of the recent progresses in the molecular characterization of JMML, this disease is still a clinical challenge due to its heterogeneity, difficult diagnosis, poor prognosis, and the lack of curative treatment options other than hematopoietic stem cell transplantation (HSCT). In this review, we will provide a detailed overview of the genetic and epigenetic alterations occurring in JMML, and discuss their clinical relevance in terms of disease prognosis and risk of relapse after HSCT. We will also present the most recent advances on novel preclinical and clinical therapeutic approaches directed against JMML molecular targets. Finally, we will outline future research perspectives to further explore the oncogenic mechanism driving JMML leukemogenesis and progression, with special attention to the application of single-cell next-generation sequencing technologies. Abstract Juvenile myelomonocytic leukemia (JMML) is a rare myelodysplastic/myeloproliferative neoplasm of early childhood. Most of JMML patients experience an aggressive clinical course of the disease and require hematopoietic stem cell transplantation, which is currently the only curative treatment. JMML is characterized by RAS signaling hyperactivation, which is mainly driven by mutations in one of five genes of the RAS pathway, including PTPN11, KRAS, NRAS, NF1, and CBL. These driving mutations define different disease subtypes with specific clinico-biological features. Secondary mutations affecting other genes inside and outside the RAS pathway contribute to JMML pathogenesis and are associated with a poorer prognosis. In addition to these genetic alterations, JMML commonly presents aberrant epigenetic profiles that strongly correlate with the clinical outcome of the patients. This observation led to the recent publication of an international JMML stratification consensus, which defines three JMML clinical groups based on DNA methylation status. Although the characterization of the genomic and epigenomic landscapes in JMML has significantly contributed to better understand the molecular mechanisms driving the disease, our knowledge on JMML origin, cell identity, and intratumor and interpatient heterogeneity is still scarce. The application of new single-cell sequencing technologies will be critical to address these questions in the future.
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18
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Oliveira AF, Tansini A, Toledo T, Balceiro R, Lee MLM, Villela N, Ikeuty P, Metze K, Lopes LF, Lorand-Metze I. Immunophenotypic changes in juvenile myelomonocytic leukaemia after treatment with hypomethylating agent: Do they help to evaluate dept of response? Br J Haematol 2022; 197:339-348. [PMID: 35187646 DOI: 10.1111/bjh.18089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/27/2022] [Accepted: 01/30/2022] [Indexed: 11/29/2022]
Abstract
5-Azacitidine has been used before stem cell transplantation in juvenile myelomonocytic leukaemia (JMML) patients. Recently, we have described immunophenotypic features in JMML at diagnosis. Here, our aim was to examine the changes in the immunophenotypic features during azacitidine treatment, correlating it with clinical response. Patients treated with 5-azacitidine were evaluated at diagnosis and after three and six cycles of medication. Among 32 patients entering the study, 28 patients were examined after three cycles and 25 patients after six. Patients showed a reduction in CD34/CD117+ cells: median 3.35% at diagnosis, 2.8% after three cycles and 1.63% after six. B-cell progenitors were decreased at diagnosis and decreased after treatment. Monocytes decreased: 11.91% to 6.4% and 4.18% respectively. Complete response was associated with increase in classical monocytes. T lymphocytes, reduced at diagnosis, increased in patients responding to 5-azacitidine. Immunophenotypic aberrancies including expression of CD7 in myeloid progenitors remained after treatment. This feature was associated with a worse response to treatment, as well as presence of NF1. Immunophenotyping was feasible in all patients. Clinical response was associated with a decrease of myeloid progenitors and monocytes and a rise in T lymphocytes although phenotypic aberrancies persisted. The largest effect was observed after three cycles.
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Affiliation(s)
- Anita Frisanco Oliveira
- Barretos Children´s Cancer Hospital, Barretos, Brazil.,Brazilian Co-operative Group of Pediatric Myelodysplastic Syndrome (GCB-SMD-PED), Myeloproliferative Diseases Committee, Barretos, Brazil
| | - Aline Tansini
- Barretos Children´s Cancer Hospital, Barretos, Brazil.,Brazilian Co-operative Group of Pediatric Myelodysplastic Syndrome (GCB-SMD-PED), Morfology and Flow Cytometry Committee, Barretos, Brazil
| | - Thais Toledo
- Barretos Children´s Cancer Hospital, Barretos, Brazil.,Brazilian Co-operative Group of Pediatric Myelodysplastic Syndrome (GCB-SMD-PED), Morfology and Flow Cytometry Committee, Barretos, Brazil
| | | | - Maria Lucia Martino Lee
- Brazilian Co-operative Group of Pediatric Myelodysplastic Syndrome (GCB-SMD-PED), Myeloproliferative Diseases Committee, Barretos, Brazil
| | - Neysimelia Villela
- Barretos Children´s Cancer Hospital, Hematopoietic Stem Cell Transplantation, Barretos, Brazil.,Brazilian Co-operative Group of Pediatric Myelodysplastic Syndrome (GCB-SMD-PED), HSCT Committee, Barretos, Brazil
| | - Patricia Ikeuty
- Brazilian Co-operative Group of Pediatric Myelodysplastic Syndrome (GCB-SMD-PED), HSCT Committee, Barretos, Brazil
| | - Konradin Metze
- Department of Pathology, Faculty Medical Sciences, State University of Campinas, Campinas, Brazil
| | - Luiz Fernando Lopes
- Barretos Children´s Cancer Hospital, Barretos, Brazil.,Brazilian Co-operative Group of Pediatric Myelodysplastic Syndrome (GCB-SMD-PED), Barretos, Brazil
| | - Irene Lorand-Metze
- Brazilian Co-operative Group of Pediatric Myelodysplastic Syndrome (GCB-SMD-PED), Morfology and Flow Cytometry Committee, Barretos, Brazil.,Department of Internal Medicine, Faculty Medical Sciences, State University of Campinas, Campinas, Brazil
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19
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Behnert A, Meyer J, Parsa JY, Hechmer A, Loh ML, Olshen A, de Smith AJ, Stieglitz E. Exploring the genetic and epigenetic origins of juvenile myelomonocytic leukemia using newborn screening samples. Leukemia 2022; 36:279-282. [PMID: 34183765 PMCID: PMC8720242 DOI: 10.1038/s41375-021-01331-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 01/09/2023]
Affiliation(s)
- Astrid Behnert
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA, USA
| | - Julia Meyer
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA, USA
| | | | - Aaron Hechmer
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Adam Olshen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
| | - Elliot Stieglitz
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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20
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Simple and robust methylation test for risk stratification of patients with juvenile myelomonocytic leukemia. Blood Adv 2021; 5:5507-5518. [PMID: 34580726 PMCID: PMC8714717 DOI: 10.1182/bloodadvances.2021005080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/23/2021] [Indexed: 11/20/2022] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is a rare myelodysplastic/myeloproliferative neoplasm that develops during infancy and early childhood. The array-based international consensus definition of DNA methylation has recently classified patients with JMML into the following 3 groups: high (HM), intermediate (IM), and low methylation (LM). To develop a simple and robust methylation clinical test, 137 patients with JMML were analyzed using the Digital Restriction Enzyme Analysis of Methylation (DREAM), which is a next-generation sequencing-based methylation analysis. Unsupervised consensus clustering of the discovery cohort (n = 99) using DREAM data identified HM (HM_DREAM; n = 35) and LM subgroups (LM_DREAM; n = 64). Of the 98 cases that could be compared with the international consensus classification, 90 HM (n = 30) and LM (n = 60) cases had 100% concordance with DREAM clustering results. Of the remaining 8 cases comprising the IM group, 4 were classified as belonging to the HM_DREAM group and 4 to the LM_DREAM group. A machine-learning classifier was successfully constructed using a support vector machine (SVM), which divided the validation cohort (n = 38) into HM (HM_SVM, n = 18) and LM (LM_SVM; n = 20) groups. Patients with the HM_SVM profile had a significantly poorer 5-year overall survival rate than those with the LM_SVM profile. In conclusion, we developed a robust methylation test using DREAM for patients with JMML. This simple and straightforward test can be easily incorporated into diagnosis to generate a methylation classification for patients so they can receive risk-adapted treatment in the context of future clinical trials.
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21
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Kim HS, Lee JW, Kang D, Yu H, Kim Y, Kang H, Lee JM, Ahn A, Cho B, Kim S, Chung NG, Kim Y, Kim M. Characteristics of RAS pathway mutations in juvenile myelomonocytic leukaemia: a single-institution study from Korea. Br J Haematol 2021; 195:748-756. [PMID: 34590720 DOI: 10.1111/bjh.17861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/13/2021] [Indexed: 11/27/2022]
Abstract
Juvenile myelomonocytic leukaemia (JMML), a rare clonal haematopoietic disorder of childhood, is characterised as a myelodysplastic/myeloproliferative neoplasm. Despite ground-breaking genetic discoveries, JMML remains difficult to diagnose given its diverse clinical features and disease course. A total of 24 patients with JMML were diagnosed and treated at a single institution, and their genetic profiles and association with clinical and laboratory characteristics were analysed. In all, 22 of the patients received allogeneic haematopoietic stem cell transplantation after myeloablative conditioning, mostly from a haploidentical family donor. RAS pathway mutations were identified in 88% of patients: PTPN11 [nine (38%)], NRAS [nine (38%)], KRAS [two (8%)], NF1 [five (21%)] and CBL [one (4%)]. Secondary mutations were found in 25% of patients: SETBP1, JAK3, ASXL1, GATA2, KIT, KDM6A, and BCOR. Six patients showed cytogenetic abnormalities, including three with monosomy 7. The estimated 5-year event-free survival (EFS) and overall survival (± standard error) of the entire cohort were 58·9 (10·9)% and 73·5 (10·8)% respectively. NRAS (+) patients had a higher 5-year EFS than NRAS (-) patients [72·9 (16·5)% vs. 52·5 (13·1)%, P = 0·127]. NRAS (+) patients had a better 5-year EFS than PTPN11 (+) patients [41·7 (17·3)%, P = 0·071]. Our study revealed the genetic characteristics of Korean JMML patients with RAS pathway and secondary mutations.
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Affiliation(s)
- Hoon Seok Kim
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jae Wook Lee
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dain Kang
- Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Haein Yu
- Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yeojae Kim
- Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyunhye Kang
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jong-Mi Lee
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ari Ahn
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Bin Cho
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seongkoo Kim
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Nack-Gyun Chung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
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22
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Nf1 and Sh2b3 mutations cooperate in vivo in a mouse model of juvenile myelomonocytic leukemia. Blood Adv 2021; 5:3587-3591. [PMID: 34464969 DOI: 10.1182/bloodadvances.2020003754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/09/2021] [Indexed: 11/20/2022] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is initiated in early childhood by somatic mutations that activate Ras signaling. Although some patients have only a single identifiable oncogenic mutation, others have 1 or more additional alterations. Such secondary mutations, as a group, are associated with an increased risk of relapse after hematopoietic stem cell transplantation or transformation to acute myeloid leukemia. These clinical observations suggest a cooperative effect between initiating and secondary mutations. However, the roles of specific genes in the prognosis or clinical presentation of JMML have not been described. In this study, we investigate the impact of secondary SH2B3 mutations in JMML. We find that patients with SH2B3 mutations have adverse outcomes, as well as higher white blood cell counts and hemoglobin F levels in the peripheral blood. We further demonstrate this interaction in genetically engineered mice. Deletion of Sh2b3 cooperates with conditional Nf1 deletion in a dose-dependent fashion. These studies illustrate that haploinsufficiency for Sh2b3 contributes to the severity of myeloproliferative disease and provide an experimental system for testing treatments for a high-risk cohort of JMML patients.
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23
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Juvenile myelomonocytic leukemia in the molecular era: a clinician's guide to diagnosis, risk-stratification, and treatment. Blood Adv 2021; 5:4783-4793. [PMID: 34525182 PMCID: PMC8759142 DOI: 10.1182/bloodadvances.2021005117] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/03/2021] [Indexed: 12/03/2022] Open
Abstract
Juvenile myelomonocytic leukemia is an overlapping myeloproliferative and myelodysplastic disorder of early childhood . It is associated with a spectrum of diverse outcomes ranging from spontaneous resolution in rare patients to transformation to acute myeloid leukemia in others that is generally fatal. This unpredictable clinical course, along with initially descriptive diagnostic criteria, led to decades of productive international research. Next-generation sequencing now permits more accurate molecular diagnoses in nearly all patients. However, curative treatment is still reliant on allogeneic hematopoietic cell transplantation for most patients, and additional advances will be required to improve risk stratification algorithms that distinguish those that can be observed expectantly from others who require swift hematopoietic cell transplantation.
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24
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Induced Pluripotent Stem Cells to Model Juvenile Myelomonocytic Leukemia: New Perspectives for Preclinical Research. Cells 2021; 10:cells10092335. [PMID: 34571984 PMCID: PMC8465353 DOI: 10.3390/cells10092335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is a malignant myeloproliferative disorder arising in infants and young children. The origin of this neoplasm is attributed to an early deregulation of the Ras signaling pathway in multipotent hematopoietic stem/progenitor cells. Since JMML is notoriously refractory to conventional cytostatic therapy, allogeneic hematopoietic stem cell transplantation remains the mainstay of curative therapy for most cases. However, alternative therapeutic approaches with small epigenetic molecules have recently entered the stage and show surprising efficacy at least in specific subsets of patients. Hence, the establishment of preclinical models to test novel agents is a priority. Induced pluripotent stem cells (IPSCs) offer an opportunity to imitate JMML ex vivo, after attempts to generate immortalized cell lines from primary JMML material have largely failed in the past. Several research groups have previously generated patient-derived JMML IPSCs and successfully differentiated these into myeloid cells with extensive phenotypic similarities to primary JMML cells. With infinite self-renewal and the capability to differentiate into multiple cell types, JMML IPSCs are a promising resource to advance the development of treatment modalities targeting specific vulnerabilities. This review discusses current reprogramming techniques for JMML stem/progenitor cells, related clinical applications, and the challenges involved.
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25
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Donor Killer Immunoglobulin Receptor Gene Content and Ligand Matching and Outcomes of Pediatric Patients with Juvenile Myelomonocytic Leukemia Following Unrelated Donor Transplantation. Transplant Cell Ther 2021; 27:926.e1-926.e10. [PMID: 34407489 DOI: 10.1016/j.jtct.2021.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 11/21/2022]
Abstract
Natural killer (NK) cell determinants predict relapse-free survival after allogeneic hematopoietic cell transplantation (HCT) for acute myelogenous leukemia, and previous studies have shown a beneficial graft-versus-leukemia effect in patients with juvenile myelomonocytic leukemia (JMML). However, whether NK cell determinants predict protection against relapse for JMML patients undergoing HCT is unknown. Therefore, we investigated NK cell-related donor and recipient immunogenetics as determinants of HCT outcomes in patients with JMML. Patients with JMML (age 0 to <19 years) who underwent a first allogeneic HCT from an unrelated donor between 2000 and 2017 and had available donor samples from the Center for International Blood and Marrow Transplant Research Repository were included. Donor killer immunoglobulin receptor (KIR) typing was performed on pre-HCT samples. The primary endpoint was disease-free survival (DFS); secondary endpoints included relapse, grade II-IV acute graft versus-host-disease (aGVHD), chronic GVHD (cGVHD), GVHD-free relapse-free survival, transplantation-related mortality, and overall survival (OS). Donor KIR models tested included KIR genotype (AA versus Bx), B content (0-1 versus ≥2), centromeric and telomeric region score (AA versus AB versus BB), B content score (best, better, or neutral), composite score (2 versus 3 versus 4), activating KIR content, and the presence of KIR2DS4. Ligand-ligand and KIR-ligand mismatch effects on outcomes were analyzed in HLA-mismatched donors (≤7/8; n = 74) only. Univariate analyses were performed for primary and secondary outcomes of interest, with a P value <.05 considered significant. One hundred sixty-five patients (113 males), with a median follow-up of 85 months (range, 6 to 216 months) met the study criteria. Of these, 111 underwent an unrelated donor HCT and 54 underwent a UCB HCT. Almost all (n = 161; 98%) received a myeloablative conditioning regimen. After exclusion of recipients of reduced-intensity/nonmyeloablative conditioning regimens and ex vivo T cell-depleted grafts (n = 8), there were 42 AA donors and 115 Bx donors, respectively. Three-year DFS, OS, relapse, and GRFS for the entire cohort were 58% (95% confidence interval [CI], 50% to 66%), 67% (95% CI, 59% to 74%), 26% (95% CI, 19% to 33%), and 27% (95% CI, 19% to 35%), respectively. The cumulative incidence of grade II-IV aGVHD at 100 days was 36% (95% CI, 27% to 44%), and that of cGVHD at 1 year was 23% (95% CI, 17% to 30%). There were no differences between AA donors and Bx donors for any recipient survival outcomes. The risk of grade II-IV aGVHD was lower in patients with donors with a B content score of ≥2 (hazard ratio [HR], 0.46; 95% CI, 0.26 to 0.83; P = .01), an activating KIR content score of >3 (HR, 0.52; 95% CI, 0.29 to 0.95; P = .032), centromeric A/B score (HR, 0.57; 95% CI, 033 to 0.98; P = .041), and telomeric A/B score (HR, 0.58; 95% CI, 0.34 to 1.00; P = .048). To our knowledge, this is the first study analyzing the association of NK cell determinants and outcomes in JMML HCT recipients. This study identifies potential benefits of donor KIR-B genotypes in reducing aGVHD. Our findings warrant further study of the role of NK cells in enhancing the graft-versus-leukemia effect via recognition of JMML blasts.
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26
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Nathany S, Chatterjee G, Ghai S, Moulik NR, Shetty D, Subramanian PG, Tembhare P, Gujral S, Dhamne C, Banavali S, Narula G, Patkar N. Mutational landscape of Juvenile Myelomonocytic Leukemia (JMML)-A real-world context. Int J Lab Hematol 2021; 43:1531-1538. [PMID: 34387930 DOI: 10.1111/ijlh.13680] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/22/2021] [Accepted: 07/31/2021] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Juvenile myelomonocytic leukemia (JMML) is a rare childhood neoplasm (<5% cases), which has been categorized under myelodysplastic/myeloproliferative neoplasms (MDS/MPN) in the recent classification by the World Health Organization. METHODS We developed a 51-gene (151.5kB) low-cost targeted myeloid panel based on single-molecule molecular inversion probes to comprehensively evaluate the genomic profile of Juvenile myelomonocytic leukemia (JMML). RESULTS A total of 50 children with clinical and pathological features of JMML were sequenced at high coverage. Among the 50 patients, 44(88%) harbored mutations in one of the RAS/MAPK-pathway genes, most frequently in NRAS (32%), followed by PTPN11 (28%) and NF1 (22%). One-fifth of children had more than one mutation, with 5 cases harboring two RAS pathway mutations. Monosomy 7 was detected in 32% (16) patients, and five of these did not harbor any RAS pathway mutations. Children with monosomy 7 showed shorter overall survival compared with their wild-type counterparts (P = .02). CONCLUSION Our study highlights that comprehensive genomic profiling identifies at least one mutation in almost 90% of JMML patients. Performing genomic analysis at baseline might help in triaging children with JMML for allogenic stem cell transplant in resource-constrained settings.
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Affiliation(s)
- Shrinidhi Nathany
- Department of Hematopathology, Advanced Centre for Treatment and Research in Cancer, Tata Memorial Centre, Mumbai, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Gaurav Chatterjee
- Department of Hematopathology, Advanced Centre for Treatment and Research in Cancer, Tata Memorial Centre, Mumbai, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Shruti Ghai
- Department of Hematopathology, Advanced Centre for Treatment and Research in Cancer, Tata Memorial Centre, Mumbai, India
| | - Nirmalya Roy Moulik
- Homi Bhabha National Institute (HBNI), Mumbai, India.,Pediatric Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Dhanalaxmi Shetty
- Homi Bhabha National Institute (HBNI), Mumbai, India.,Department of Cancer Cytogenetics, Advanced Centre for treatment and research in cancer, Tata Memorial Centre, Mumbai, India
| | - P G Subramanian
- Department of Hematopathology, Advanced Centre for Treatment and Research in Cancer, Tata Memorial Centre, Mumbai, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Prashant Tembhare
- Department of Hematopathology, Advanced Centre for Treatment and Research in Cancer, Tata Memorial Centre, Mumbai, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Sumeet Gujral
- Department of Hematopathology, Advanced Centre for Treatment and Research in Cancer, Tata Memorial Centre, Mumbai, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Chetan Dhamne
- Homi Bhabha National Institute (HBNI), Mumbai, India.,Pediatric Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Sripad Banavali
- Homi Bhabha National Institute (HBNI), Mumbai, India.,Pediatric Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Gaurav Narula
- Homi Bhabha National Institute (HBNI), Mumbai, India.,Pediatric Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Nikhil Patkar
- Department of Hematopathology, Advanced Centre for Treatment and Research in Cancer, Tata Memorial Centre, Mumbai, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
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27
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Response to upfront azacitidine in juvenile myelomonocytic leukemia in the AZA-JMML-001 trial. Blood Adv 2021; 5:2901-2908. [PMID: 34297046 DOI: 10.1182/bloodadvances.2020004144] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/25/2021] [Indexed: 11/20/2022] Open
Abstract
Allogeneic hematopoietic stem cell transplantation (HSCT) is the only curative therapy for most children with juvenile myelomonocytic leukemia (JMML). Novel therapies controlling the disorder prior to HSCT are needed. We conducted a phase 2, multicenter, open-label study to evaluate the safety and antileukemic activity of azacitidine monotherapy prior to HSCT in newly diagnosed JMML patients. Eighteen patients enrolled from September 2015 to November 2017 were treated with azacitidine (75 mg/m2) administered IV once daily on days 1 to 7 of a 28-day cycle. The primary end point was the number of patients with clinical complete remission (cCR) or clinical partial remission (cPR) after 3 cycles of therapy. Pharmacokinetics, genome-wide DNA-methylation levels, and variant allele frequencies of leukemia-specific index mutations were also analyzed. Sixteen patients completed 3 cycles and 5 patients completed 6 cycles. After 3 cycles, 11 patients (61%) were in cPR and 7 (39%) had progressive disease. Six of 16 patients (38%) who needed platelet transfusions were transfusion-free after 3 cycles. All 7 patients with intermediate- or low-methylation signatures in genome-wide DNA-methylation studies achieved cPR. Seventeen patients received HSCT; 14 (82%) were leukemia-free at a median follow-up of 23.8 months (range, 7.0-39.3 months) after HSCT. Azacitidine was well tolerated and plasma concentration--time profiles were similar to observed profiles in adults. In conclusion, azacitidine monotherapy is a suitable option for children with newly diagnosed JMML. Although long-term safety and efficacy remain to be fully elucidated in this population, these data demonstrate that azacitidine provides valuable clinical benefit to JMML patients prior to HSCT. This trial was registered at www.clinicaltrials.gov as #NCT02447666.
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28
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Mayerhofer C, Niemeyer CM, Flotho C. Current Treatment of Juvenile Myelomonocytic Leukemia. J Clin Med 2021; 10:3084. [PMID: 34300250 PMCID: PMC8305558 DOI: 10.3390/jcm10143084] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 02/06/2023] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is a rare pediatric leukemia characterized by mutations in five canonical RAS pathway genes. The diagnosis is made by typical clinical and hematological findings associated with a compatible mutation. Although this is sufficient for clinical decision-making in most JMML cases, more in-depth analysis can include DNA methylation class and panel sequencing analysis for secondary mutations. NRAS-initiated JMML is heterogeneous and adequate management ranges from watchful waiting to allogeneic hematopoietic stem cell transplantation (HSCT). Upfront azacitidine in KRAS patients can achieve long-term remissions without HSCT; if HSCT is required, a less toxic preparative regimen is recommended. Germline CBL patients often experience spontaneous resolution of the leukemia or exhibit stable mixed chimerism after HSCT. JMML driven by PTPN11 or NF1 is often rapidly progressive, requires swift HSCT and may benefit from pretransplant therapy with azacitidine. Because graft-versus-leukemia alloimmunity is central to cure high risk patients, the immunosuppressive regimen should be discontinued early after HSCT.
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Affiliation(s)
- Christina Mayerhofer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (C.M.); (C.M.N.)
| | - Charlotte M. Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (C.M.); (C.M.N.)
- German Cancer Consortium (DKTK), 79106 Freiburg, Germany
| | - Christian Flotho
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (C.M.); (C.M.N.)
- German Cancer Consortium (DKTK), 79106 Freiburg, Germany
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29
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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: 4] [Impact Index Per Article: 1.3] [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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30
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Genome-wide DNA methylation analysis pre- and post-lenalidomide treatment in patients with myelodysplastic syndrome with isolated deletion (5q). Ann Hematol 2021; 100:1463-1471. [PMID: 33903952 PMCID: PMC8116243 DOI: 10.1007/s00277-021-04492-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/08/2021] [Indexed: 11/28/2022]
Abstract
Myelodysplastic syndrome (MDS) with isolated deletion of chromosome 5q (MDS del5q) is a distinct subtype of MDS with quite favorable prognosis and excellent response to treatment with lenalidomide. Still, a relevant percentage of patients do not respond to lenalidomide and even experience progression to acute myeloid leukemia (AML). In this study, we aimed to investigate whether global DNA methylation patterns could predict response to lenalidomide. Genome-wide DNA methylation analysis using Illumina 450k methylation arrays was performed on n=51 patients with MDS del5q who were uniformly treated with lenalidomide in a prospective multicenter trial of the German MDS study group. To study potential direct effects of lenalidomide on DNA methylation, 17 paired samples pre- and post-treatment were analyzed. Our results revealed no relevant effect of lenalidomide on methylation status. Furthermore, methylation patterns prior to therapy could not predict lenalidomide response. However, methylation clustering identified a group of patients with a trend towards inferior overall survival. These patients showed hypermethylation of several interesting target genes, including genes of relevant signaling pathways, potentially indicating the evaluation of novel therapeutic targets.
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31
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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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32
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Greenmyer JR, Kohorst M. Pediatric Neoplasms Presenting with Monocytosis. Curr Hematol Malig Rep 2021; 16:235-246. [PMID: 33630234 DOI: 10.1007/s11899-021-00611-x] [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] [Accepted: 02/01/2021] [Indexed: 11/24/2022]
Abstract
PURPOSE OF REVIEW Juvenile myelomonocytic leukemia (JMML) is a rare but severe pediatric neoplasm with hematopoietic stem cell transplant as its only established curative option. The development of targeted therapeutics for JMML is being guided by an understanding of the pathobiology of this condition. Here, we review JMML with an emphasis on genetics in order to (i) demonstrate the relationship between JMML genotype and clinical phenotype and (ii) explore potential genetic targets of novel JMML therapies. RECENT FINDINGS DNA hypermethylation studies have demonstrated consistently that methylation is related to disease severity. Increasing understanding of methylation in JMML may open the door to novel therapies, such as DNA methyltransferase inhibitors. The PI3K/AKT/MTOR, JAK/STAT, and RAF/MEK/ERK pathways are being investigated as therapeutic targets for JMML. Future therapy for JMML will be driven by an increased understanding of pathobiology. Targeted therapeutic approaches hold potential for improving outcomes in patients with JMML.
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Affiliation(s)
| | - Mira Kohorst
- Pediatric Hematology and Oncology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
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33
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Hofmans M, Lammens T, Depreter B, Wu Y, Erlacher M, Caye A, Cavé H, Flotho C, de Haas V, Niemeyer CM, Stary J, Van Nieuwerburgh F, Deforce D, Van Loocke W, Van Vlierberghe P, Philippé J, De Moerloose B. Long non-coding RNAs as novel therapeutic targets in juvenile myelomonocytic leukemia. Sci Rep 2021; 11:2801. [PMID: 33531590 PMCID: PMC7854679 DOI: 10.1038/s41598-021-82509-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/20/2021] [Indexed: 12/15/2022] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) treatment primarily relies on hematopoietic stem cell transplantation and results in long-term overall survival of 50-60%, demonstrating a need to develop novel treatments. Dysregulation of the non-coding RNA transcriptome has been demonstrated before in this rare and unique disorder of early childhood. In this study, we investigated the therapeutic potential of targeting overexpressed long non-coding RNAs (lncRNAs) in JMML. Total RNA sequencing of bone marrow and peripheral blood mononuclear cell preparations from 19 untreated JMML patients and three healthy children revealed 185 differentially expressed lncRNA genes (131 up- and 54 downregulated). LNA GapmeRs were designed for 10 overexpressed and validated lncRNAs. Molecular knockdown (≥ 70% compared to mock control) after 24 h of incubation was observed with two or more independent GapmeRs in 6 of them. For three lncRNAs (lnc-THADA-4, lnc-ACOT9-1 and NRIR) knockdown resulted in a significant decrease of cell viability after 72 h of incubation in primary cultures of JMML mononuclear cells, respectively. Importantly, the extent of cellular damage correlated with the expression level of the lncRNA of interest. In conclusion, we demonstrated in primary JMML cell cultures that knockdown of overexpressed lncRNAs such as lnc-THADA-4, lnc-ACOT9-1 and NRIR may be a feasible therapeutic strategy.
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Affiliation(s)
- Mattias Hofmans
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium. .,Department of Diagnostic Sciences, Ghent University Hospital, Corneel Heymanslaan 10, Ghent, 9000, Belgium.
| | - Tim Lammens
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Barbara Depreter
- Department of Laboratory Medicine Hematology, University Hospital Brussels, Brussels, Belgium
| | - Ying Wu
- Faculty of Biology, University of Freiburg, Freiburg, Germany.,Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miriam Erlacher
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium, Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany
| | - Aurélie Caye
- Department of Genetics, University Hospital of Robert Debré (APHP) and INSERM U1131, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Hélène Cavé
- Department of Genetics, University Hospital of Robert Debré (APHP) and INSERM U1131, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Christian Flotho
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium, Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany
| | - Valerie de Haas
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Dutch Childhood Oncology Group, The Hague, The Netherlands
| | - Charlotte M Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium, Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany
| | - Jan Stary
- Department of Pediatric Hematology/Oncology, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Filip Van Nieuwerburgh
- Laboratory for Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- Laboratory for Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Wouter Van Loocke
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jan Philippé
- Department of Diagnostic Sciences, Ghent University Hospital, Corneel Heymanslaan 10, Ghent, 9000, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Barbara De Moerloose
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
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34
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Klco JM, Mullighan CG. Advances in germline predisposition to acute leukaemias and myeloid neoplasms. Nat Rev Cancer 2021; 21:122-137. [PMID: 33328584 PMCID: PMC8404376 DOI: 10.1038/s41568-020-00315-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/28/2020] [Indexed: 12/17/2022]
Abstract
Although much work has focused on the elucidation of somatic alterations that drive the development of acute leukaemias and other haematopoietic diseases, it has become increasingly recognized that germline mutations are common in many of these neoplasms. In this Review, we highlight the different genetic pathways impacted by germline mutations that can ultimately lead to the development of familial and sporadic haematological malignancies, including acute lymphoblastic leukaemia, acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS). Many of the genes disrupted by somatic mutations in these diseases (for example, TP53, RUNX1, IKZF1 and ETV6) are the same as those that harbour germline mutations in children and adolescents who develop these malignancies. Moreover, the presumption that familial leukaemias only present in childhood is no longer true, in large part due to the numerous studies demonstrating germline DDX41 mutations in adults with MDS and AML. Lastly, we highlight how different cooperating events can influence the ultimate phenotype in these different familial leukaemia syndromes.
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Affiliation(s)
- Jeffery M Klco
- Department of Pathology and the Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Charles G Mullighan
- Department of Pathology and the Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.
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35
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Dal Molin A, Hofmans M, Gaffo E, Buratin A, Cavé H, Flotho C, de Haas V, Niemeyer CM, Stary J, Van Vlierberghe P, Philippé J, De Moerloose B, Te Kronnie G, Bresolin S, Lammens T, Bortoluzzi S. CircRNAs Dysregulated in Juvenile Myelomonocytic Leukemia: CircMCTP1 Stands Out. Front Cell Dev Biol 2021; 8:613540. [PMID: 33490078 PMCID: PMC7815690 DOI: 10.3389/fcell.2020.613540] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022] Open
Abstract
Juvenile myelomonocytic leukemia (JMML), a rare myelodysplastic/myeloproliferative neoplasm of early childhood, is characterized by clonal growth of RAS signaling addicted stem cells. JMML subtypes are defined by specific RAS pathway mutations and display distinct gene, microRNA (miRNA) and long non-coding RNA expression profiles. Here we zoom in on circular RNAs (circRNAs), molecules that, when abnormally expressed, may participate in malignant deviation of cellular processes. CirComPara software was used to annotate and quantify circRNAs in RNA-seq data of a “discovery cohort” comprising 19 JMML patients and 3 healthy donors (HD). In an independent set of 12 JMML patients and 6 HD, expression of 27 circRNAs was analyzed by qRT-PCR. CircRNA-miRNA-gene networks were reconstructed using circRNA function prediction and gene expression data. We identified 119 circRNAs dysregulated in JMML and 59 genes showing an imbalance of the circular and linear products. Our data indicated also circRNA expression differences among molecular subgroups of JMML. Validation of a set of deregulated circRNAs in an independent cohort of JMML patients confirmed the down-regulation of circOXNAD1 and circATM, and a marked up-regulation of circLYN, circAFF2, and circMCTP1. A new finding in JMML links up-regulated circMCTP1 with known tumor suppressor miRNAs. This and other predicted interactions with miRNAs connect dysregulated circRNAs to regulatory networks. In conclusion, this study provides insight into the circRNAome of JMML and paves the path to elucidate new molecular disease mechanisms putting forward circMCTP1 up-regulation as a robust example.
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Affiliation(s)
- Anna Dal Molin
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Mattias Hofmans
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University Hospital, Ghent, Belgium
| | - Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Alessia Buratin
- Department of Molecular Medicine, University of Padova, Padua, Italy.,Department of Biology, University of Padova, Padua, Italy
| | - Hélène Cavé
- Department of Genetics, University Hospital of Robert Debré, Paris, France.,INSERM U1131, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Christian Flotho
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University of Freiburg, Freiburg, Germany
| | - Valerie de Haas
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Dutch Childhood Oncology Group, The Hague, Netherlands
| | - Charlotte M Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University of Freiburg, Freiburg, Germany
| | - Jan Stary
- Department of Pediatric Hematology/Oncology, Charles University and University Hospital Motol, Prague, Czechia
| | - Pieter Van Vlierberghe
- Cancer Research Institute Ghent, Ghent, Belgium.,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Jan Philippé
- Department of Diagnostic Sciences, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Barbara De Moerloose
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | | | - Silvia Bresolin
- Onco-Hematology, Stem Cell Transplant and Gene Therapy Laboratory, IRP-Istituto di Ricerca Pediatrica, Padua, Italy.,Department of Maternal and Child Health, Padua University, Padua, Italy
| | - Tim Lammens
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Stefania Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padua, Italy.,Interdepartmental Research Center for Innovative Biotechnologies, University of Padova, Padua, Italy
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36
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Hecht A, Meyer JA, Behnert A, Wong E, Chehab F, Olshen A, Hechmer A, Aftandilian C, Bhat R, Choi SW, Chonat S, Farrar JE, Fluchel M, Frangoul H, Han JH, Kolb EA, Kuo DJ, MacMillan ML, Maese L, Maloney KW, Narendran A, Oshrine B, Schultz KR, Sulis ML, Van Mater D, Tasian SK, Hofmann WK, Loh ML, Stieglitz E. Molecular and phenotypic diversity of CBL-mutated juvenile myelomonocytic leukemia. Haematologica 2020; 107:178-186. [PMID: 33375775 PMCID: PMC8719097 DOI: 10.3324/haematol.2020.270595] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Indexed: 11/22/2022] Open
Abstract
Mutations in the CBL gene were first identified in adults with various myeloid malignancies. Some patients with juvenile myelomonocytic leukemia (JMML) were also noted to harbor mutations in CBL, but were found to have generally less aggressive disease courses compared to patients with other forms of Ras pathway-mutant JMML. Importantly, and in contrast to most reports in adults, the majority of CBL mutations in JMML patients are germline with acquired uniparental disomy occurring in affected marrow cells. Here, we systematically studied a large cohort of 33 JMML patients with CBL mutations and found that this disease is highly diverse in presentation and overall outcome. Moreover, we discovered somatically acquired CBL mutations in 15% of pediatric patients who presented with more aggressive disease. Neither clinical features nor methylation profiling were able to distinguish patients with somatic CBL mutations from those with germline CBL mutations, highlighting the need for germline testing. Overall, we demonstrate that disease courses are quite heterogeneous even among patients with germline CBL mutations. Prospective clinical trials are warranted to find ideal treatment strategies for this diverse cohort of patients.
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Affiliation(s)
- Anna Hecht
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA; Department of Hematology/Oncology, University Hospital Mannheim, Heidelberg University
| | - Julia A Meyer
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco
| | - Astrid Behnert
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco
| | - Eric Wong
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco
| | - Farid Chehab
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Adam Olshen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA; Department of Epidemiology and Biostatistics, University of California
| | - Aaron Hechmer
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco
| | | | - Rukhmi Bhat
- Northwestern University Feinberg School of Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | - Sung Won Choi
- Blood and Marrow Transplantation Program, University of Michigan, Ann Arbor, MI
| | - Satheesh Chonat
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA; Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Jason E Farrar
- Arkansas Children's Research Institute, Little Rock, AR; Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Mark Fluchel
- University of Utah, Department of Pediatrics, Division of Pediatric Hematology-Oncology, Salt Lake City, UT
| | - Haydar Frangoul
- The Children's Hospital at TriStar Centennial and Sarah Cannon Research Institute, Nashville, TN
| | - Jennifer H Han
- Division of Pediatric Hematology-Oncology, University of California, San Diego/ Rady Children's Hospital San Diego
| | - Edward A Kolb
- Nemours Center for Cancer and Blood Disorders/Alfred I. DuPont Hospital for Children, Wilmington, DE
| | - Dennis J Kuo
- Division of Pediatric Hematology-Oncology, University of California, San Diego/ Rady Children's Hospital San Diego
| | - Margaret L MacMillan
- Blood and Marrow Transplant Program, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN
| | - Luke Maese
- Department of Pediatrics and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | | | - Aru Narendran
- Pediatric Hematology and Oncology, Alberta Children's Hospital, Calgary, Alberta
| | | | - Kirk R Schultz
- British Columbia Children's Hospital and Research Institute, Vancouver, British Columbia
| | - Maria L Sulis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center. 1275 York Avenue. 10065 New York, NY
| | - David Van Mater
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Sarah K Tasian
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia; Department of Pediatrics and Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Wolf-Karsten Hofmann
- Department of Hematology/Oncology, University Hospital Mannheim, Heidelberg University
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco
| | - Elliot Stieglitz
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco.
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37
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Quek CWN, Foong YW, Tan SK, Soh SY, Tan PL, Koh MJA. Leukemia cutis in a child with juvenile myelomonocytic leukemia presenting with Sweet syndrome-like lesions and a history of multiple juvenile xanthogranulomas. JAAD Case Rep 2020; 6:1138-1140. [PMID: 33134454 PMCID: PMC7591327 DOI: 10.1016/j.jdcr.2020.08.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Chrystie Wan Ning Quek
- National University of Singapore Yong Loo Lin School of Medicine, Singapore
- Correspondence to: Chrystie Wan Ning Quek, IBDP, National University of Singapore Yong Loo Lin School of Medicine, 12 Science Drive 2, Singapore 117549.
| | - Yee Wah Foong
- Dermatology Service, KK Women's and Children's Hospital, Singapore
| | | | - Shui Yen Soh
- Haematology/Oncology Service, KK Women's and Children's Hospital, Singapore
| | - Poh Lin Tan
- Paediatrics Service, National University Hospital, Singapore
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38
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Schönung M, Meyer J, Nöllke P, Olshen AB, Hartmann M, Murakami N, Wakamatsu M, Okuno Y, Plass C, Loh ML, Niemeyer CM, Muramatsu H, Flotho C, Stieglitz E, Lipka DB. International Consensus Definition of DNA Methylation Subgroups in Juvenile Myelomonocytic Leukemia. Clin Cancer Res 2020; 27:158-168. [PMID: 33139265 DOI: 10.1158/1078-0432.ccr-20-3184] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/01/2020] [Accepted: 10/21/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Known clinical and genetic markers have limitations in predicting disease course and outcome in juvenile myelomonocytic leukemia (JMML). DNA methylation patterns in JMML have correlated with outcome across multiple studies, suggesting it as a biomarker to improve patient stratification. However, standardized approaches to classify JMML on the basis of DNA methylation patterns are lacking. We, therefore, sought to define an international consensus for DNA methylation subgroups in JMML and develop classification methods for clinical implementation. EXPERIMENTAL DESIGN Published DNA methylation data from 255 patients with JMML were used to develop and internally validate a classifier model. Accuracy across platforms (EPIC-arrays and MethylSeq) was tested using a technical validation cohort (32 patients). The suitability of both methods for single-patient classification was demonstrated using an independent cohort (47 patients). RESULTS Analysis of pooled, published data established three DNA methylation subgroups as a de facto standard. Unfavorable prognostic parameters (PTPN11 mutation, elevated fetal hemoglobin, and older age) were significantly enriched in the high methylation (HM) subgroup. A classifier was then developed that predicted subgroups with 98% accuracy across different technological platforms. Applying the classifier to an independent validation cohort confirmed an association of HM with secondary mutations, high relapse incidence, and inferior overall survival (OS), while the low methylation subgroup was associated with a favorable disease course. Multivariable analysis established DNA methylation subgroups as the only significant factor predicting OS. CONCLUSIONS This study provides an international consensus definition for DNA methylation subgroups in JMML. We developed and validated methods which will facilitate the design of risk-stratified clinical trials in JMML.
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Affiliation(s)
- Maximilian Schönung
- Section Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Julia Meyer
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, California
| | - Peter Nöllke
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Adam B Olshen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Mark Hartmann
- Section Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Norihiro Murakami
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Christoph Plass
- Division Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Charlotte M Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), partner site Freiburg, Germany
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Christian Flotho
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), partner site Freiburg, Germany
| | - Elliot Stieglitz
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Daniel B Lipka
- Section Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany. .,Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
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39
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Sill M, Plass C, Pfister SM, Lipka DB. Molecular tumor classification using DNA methylome analysis. Hum Mol Genet 2020; 29:R205-R213. [PMID: 32657331 DOI: 10.1093/hmg/ddaa147] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 12/18/2022] Open
Abstract
Tumor classifiers based on molecular patterns promise to define and reliably classify tumor entities. The high tissue- and cell type-specificity of DNA methylation, as well as its high stability, makes DNA methylation an ideal choice for the development of tumor classifiers. Herein, we review existing tumor classifiers using DNA methylome analysis and will provide an overview on their emerging impact on cancer classification, the detection of novel cancer subentities and patient stratification with a focus on brain tumors, sarcomas and hematopoietic malignancies. Furthermore, we provide an outlook on the enormous potential of DNA methylome analysis to complement classical histopathological and genetic diagnostics, including the emerging field of epigenomic analysis in liquid biopsies.
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Affiliation(s)
- Martin Sill
- Hopp Children's Cancer Center at the National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology (B062), German Cancer Research Center and German Cancer Consortium, 69120 Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center at the National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology (B062), German Cancer Research Center and German Cancer Consortium, 69120 Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Daniel B Lipka
- Division of Translational Medical Oncology, Section Translational Cancer Epigenomics, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
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40
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Neven Q, Boulanger C, Bruwier A, de Ville de Goyet M, Meyts I, Moens L, Van Damme A, Brichard B. Clinical Spectrum of Ras-Associated Autoimmune Leukoproliferative Disorder (RALD). J Clin Immunol 2020; 41:51-58. [PMID: 33011939 DOI: 10.1007/s10875-020-00883-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/26/2020] [Indexed: 12/30/2022]
Abstract
Ras-associated autoimmune leukoproliferative disorder (RALD) is a clinical entity initially identified in patients evaluated for an autoimmune lymphoproliferative syndrome (ALPS)-like phenotype. It remains a matter of debate whether RALD is a chronic and benign lymphoproliferative disorder or a pre-malignant condition. We report the case of a 7-year-old girl diagnosed with RALD due to somatic KRAS mutation who progressed to a juvenile myelomonocytic leukemia phenotype and finally evolved into acute myeloid leukemia. The case report prompted a literature review by a search for all RALD cases published in PubMed and Embase. We identified 27 patients with RALD. The male-to-female ratio was 1:1 and median age at disease onset was 2 years (range 3 months-36 years). Sixteen patients (59%) harbored somatic mutations in KRAS and 11 patients (41%) somatic mutations in NRAS. The most common features were splenomegaly (26/27 patients), autoimmune cytopenia (15/16 patients), monocytosis (18/24 patients), pericarditis (6 patients), and skin involvement (4 patients). Two patients went on to develop a hematopoietic malignancy. In summary, the current case documents an additional warning about the long-term risk of malignancy in RALD.
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Affiliation(s)
- Quentin Neven
- Department of Pediatric Hematology and Oncology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Avenue Hippocrate 10, 1200, Brussels, Belgium.
| | - Cécile Boulanger
- Department of Pediatric Hematology and Oncology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Avenue Hippocrate 10, 1200, Brussels, Belgium
| | - Annelyse Bruwier
- Department of Pediatrics, Grand Hôpital de Charleroi, Charleroi, Belgium
| | - Maëlle de Ville de Goyet
- Department of Pediatric Hematology and Oncology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Avenue Hippocrate 10, 1200, Brussels, Belgium
| | - Isabelle Meyts
- Laboratory for Inborn Errors of Immunity, Department of Immunology, Microbiology and Transplantation, University Hospitals Leuven, Leuven, Belgium
- Department of Pediatrics, ERN-RITA Core Center, University Hospitals Leuven, Leuven, Belgium
| | - Leen Moens
- Laboratory for Inborn Errors of Immunity, Department of Immunology, Microbiology and Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - An Van Damme
- Department of Pediatric Hematology and Oncology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Avenue Hippocrate 10, 1200, Brussels, Belgium
| | - Bénédicte Brichard
- Department of Pediatric Hematology and Oncology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Avenue Hippocrate 10, 1200, Brussels, Belgium
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41
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Wajid M A, Gupta AK, Das G, Sahoo D, Meena JP, Seth R. Outcomes of juvenile myelomonocytic leukemia patients after sequential therapy with cytarabine and 6-mercaptopurine. Pediatr Hematol Oncol 2020; 37:573-581. [PMID: 32459546 DOI: 10.1080/08880018.2020.1767244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Juvenile myelomonocytic leukemia(JMML) is a pediatric myeloproliferative disorder. Allogeneic hematopoietic stem cell transplant (HSCT) is the only curative treatment for JMML. Pre-transplant therapy is a matter of controversy, and there are no firm recommendations. Whether chemotherapy is effective in achieving durable remission is questionable. Patients diagnosed as JMML at our center from January-2014 to December-2019 were retrospectively analyzed. All patients treated with at least one cycle of sequential therapy with subcutaneous cytarabine and oral 6-mercaptopurine were further assessed. The total number of patients diagnosed during the study period was 33. Patients were divided into two groups: patients who did not get any chemotherapy (n = 13) and ones who received at least one cycle of chemotherapy(n = 20). Age, total leukocyte count (TLC), monocyte percent, platelet count and spleen size were comparable between the two groups. There was no difference in the overall survival between the two groups, but 6 out of 20 patients showed a response to chemotherapy (2 complete remission, 4 partial remission). Two patients out of 20 underwent hematopoietic stem cell transplant (HSCT). The patients who achieved complete remission received 12 cycles of chemotherapy and have been in follow up for 28 months and 50 months respectively. Our results showed that sequential therapy with 6-mercaptopurine and cytarabine may be offered to patients in whom HSCT is not feasible or as a bridge therapy in those awaiting HSCT. The advantages of this approach include low cost, out-patient management and decreased requirement of blood components. In a subset of patients it may achieve remission.
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Affiliation(s)
- Abdul Wajid M
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi
| | - Aditya Kumar Gupta
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi
| | - Gargi Das
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi
| | - Debasish Sahoo
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi
| | - Jagdish Prasad Meena
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi
| | - Rachna Seth
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi
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42
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Ney GM, McKay L, Koschmann C, Mody R, Li Q. The Emerging Role of Ras Pathway Signaling in Pediatric Cancer. Cancer Res 2020; 80:5155-5163. [PMID: 32907837 PMCID: PMC10081825 DOI: 10.1158/0008-5472.can-20-0916] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/04/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022]
Abstract
As genomic sequencing has become more widely available, the high prevalence of Ras pathway mutations in pediatric diseases has begun to emerge. Germline Ras-activating mutations have been known to contribute to cancer predisposition in a group of disorders known as the RASopathies, and now large pediatric sequencing studies have identified frequent somatic Ras pathway alterations across a diverse group of pediatric malignancies. These include glial brain tumors, relapsed high-risk neuroblastoma, embryonal rhabdomyosarcoma, acute myeloid leukemia, and relapsed acute lymphoblastic leukemia, and their prognostic impact is becoming increasingly better understood. Clinically, there has been success in targeting the Ras pathway in pediatric diseases, including the use of MEK inhibitors in plexiform neurofibromas associated with neurofibromatosis type 1 and the use of Ras pathway inhibitors in low-grade gliomas. Given the importance of this pathway in pediatric cancer, it is imperative that future studies strive to better understand the functional significance of these mutations, including their role in tumor growth and treatment resistance and how they can be better targeted to improve outcomes.
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Affiliation(s)
- Gina M Ney
- Department of Pediatrics, University of Michigan, Ann Arbor, MI.
| | - Laura McKay
- Department of Pediatrics, University of Michigan, Ann Arbor, MI
| | - Carl Koschmann
- Department of Pediatrics, University of Michigan, Ann Arbor, MI
| | - Rajen Mody
- Department of Pediatrics, University of Michigan, Ann Arbor, MI
| | - Qing Li
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI. .,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI
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43
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Weichenhan D, Lipka DB, Lutsik P, Goyal A, Plass C. Epigenomic technologies for precision oncology. Semin Cancer Biol 2020; 84:60-68. [PMID: 32822861 DOI: 10.1016/j.semcancer.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 12/15/2022]
Abstract
Epigenetic patterns in a cell control the expression of genes and consequently determine the phenotype of a cell. Cancer cells possess altered epigenomes which include aberrant patterns of DNA methylation, histone tail modifications, nucleosome positioning and of the three-dimensional chromatin organization within a nucleus. These altered epigenetic patterns are potential useful biomarkers to detect cancer cells and to classify tumor types. In addition, the cancer epigenome dictates the response of a cancer cell to therapeutic intervention and, therefore its knowledge, will allow to predict response to different therapeutic approaches. Here we review the current state-of-the-art technologies that have been developed to decipher epigenetic patterns on the genomic level and discuss how these methods are potentially useful for precision oncology.
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Affiliation(s)
- Dieter Weichenhan
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Daniel B Lipka
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, National Center for Tumor Diseases Heidelberg & German Cancer Research Center, Im Neuenheimer Feld 581, D-69120, Heidelberg, Germany; Faculty of Medicine, Medical Center, Otto-von-Guericke-University, Leipziger Straße 44, D-39120, Magdeburg, Germany.
| | - Pavlo Lutsik
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Ashish Goyal
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Christoph Plass
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
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44
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Hwang SH, Yeom H, Han BI, Ham BJ, Lee YM, Han MR, Lee M. Predicting Carcinogenic Mechanisms of Non-Genotoxic Carcinogens via Combined Analysis of Global DNA Methylation and In Vitro Cell Transformation. Int J Mol Sci 2020; 21:ijms21155387. [PMID: 32751172 PMCID: PMC7432388 DOI: 10.3390/ijms21155387] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/17/2020] [Accepted: 07/27/2020] [Indexed: 12/13/2022] Open
Abstract
An in vitro cell transformation assay (CTA) is useful for the detection of non-genotoxic carcinogens (NGTXCs); however, it does not provide information on their modes of action. In this study, to pursue a mechanism-based approach in the risk assessment of NGTXCs, we aimed to develop an integrated strategy comprising an in vitro Bhas 42 CTA and global DNA methylation analysis. For this purpose, 10 NGTXCs, which were also predicted to be negative through Derek/Sarah structure-activity relationship analysis, were first tested for transforming activity in Bhas 42 cells. Methylation profiles using reduced representation bisulfite sequencing were generated for seven NGTXCs that were positive in CTAs. In general, the differentially methylated regions (DMRs) within promoter regions showed slightly more bias toward hypermethylation than the DMRs across the whole genome. We also identified 13 genes associated with overlapping DMRs within the promoter regions in four NGTXCs, of which seven were hypermethylated and six were hypomethylated. Using ingenuity pathway analysis, the genes with DMRs at the CpG sites were found to be enriched in cancer-related categories, including "cell-to-cell signaling and interaction" as well as "cell death and survival". Moreover, the networks related to "cell death and survival", which were considered to be associated with carcinogenesis, were identified in six NGTXCs. These results suggest that epigenetic changes supporting cell transformation processes occur during non-genotoxic carcinogenesis. Taken together, our combined system can become an attractive component for an integrated approach for the testing and assessment of NGTXCs.
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Affiliation(s)
- Sung-Hee Hwang
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea; (S.-H.H.); (H.Y.)
| | - Hojin Yeom
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea; (S.-H.H.); (H.Y.)
| | - Byeal-I Han
- Institute for New Drug Development, Incheon National University, Incheon 22012, Korea;
| | - Byung-Joo Ham
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul 02841, Korea;
| | - Yong-Moon Lee
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheoungju-si, Chungcheongbuk-do 28160, Korea;
| | - Mi-Ryung Han
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea; (S.-H.H.); (H.Y.)
- Institute for New Drug Development, Incheon National University, Incheon 22012, Korea;
- INU Human Genome Center, Incheon National University, Incheon 22012, Korea
- Correspondence: (M.-R.H.); (M.L.); Tel.: +82-32-835-8247 (M.L.)
| | - Michael Lee
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea; (S.-H.H.); (H.Y.)
- Institute for New Drug Development, Incheon National University, Incheon 22012, Korea;
- INU Human Genome Center, Incheon National University, Incheon 22012, Korea
- Correspondence: (M.-R.H.); (M.L.); Tel.: +82-32-835-8247 (M.L.)
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Wakamatsu M, Okuno Y, Murakami N, Miwata S, Kitazawa H, Narita K, Kataoka S, Ichikawa D, Hamada M, Taniguchi R, Suzuki K, Kawashima N, Nishikawa E, Narita A, Nishio N, Kojima S, Muramatsu H, Takahashi Y. Detection of subclonal SETBP1 and JAK3 mutations in juvenile myelomonocytic leukemia using droplet digital PCR. Leukemia 2020; 35:259-263. [PMID: 32307441 DOI: 10.1038/s41375-020-0817-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/21/2020] [Accepted: 03/26/2020] [Indexed: 01/03/2023]
Affiliation(s)
- Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Norihiro Murakami
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shunsuke Miwata
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hironobu Kitazawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kotaro Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinsuke Kataoka
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Daisuke Ichikawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Motoharu Hamada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Rieko Taniguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kyogo Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nozomu Kawashima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Eri Nishikawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuhiro Nishio
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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46
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After 95 years, it's time to eRASe JMML. Blood Rev 2020; 43:100652. [PMID: 31980238 DOI: 10.1016/j.blre.2020.100652] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 12/07/2019] [Accepted: 12/23/2019] [Indexed: 12/16/2022]
Abstract
Juvenile myelomonocytic leukaemia (JMML) is a rare clonal disorder of early childhood. Constitutive activation of the RAS pathway is the initial event in JMML. Around 90% of patients diagnosed with JMML carry a mutation in the PTPN11, NRAS, KRAS, NF1 or CBL genes. It has been demonstrated that after this first genetic event, an additional somatic mutation or epigenetic modification is involved in disease progression. The available genetic and clinical data have enabled researchers to establish relationships between JMML and several clinical conditions, including Noonan syndrome, Ras-associated lymphoproliferative disease, and Moyamoya disease. Despite scientific progress and the development of more effective treatments, JMML is still a deadly disease: the 5-year survival rate is ~50%. Here, we report on recent research having led to a better understanding of the genetic and molecular mechanisms involved in JMML.
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47
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Meynier S, Rieux-Laucat F. FAS and RAS related Apoptosis defects: From autoimmunity to leukemia. Immunol Rev 2019; 287:50-61. [PMID: 30565243 DOI: 10.1111/imr.12720] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 09/09/2018] [Indexed: 02/07/2023]
Abstract
The human adaptive immune system recognizes almost all the pathogens that we encounter and all the tumor antigens that may arise during our lifetime. Primary immunodeficiencies affecting lymphocyte development or function therefore lead to severe infections and tumor susceptibility. Furthermore, the fact that autoimmunity is a frequent feature of primary immunodeficiencies reveals a third function of the adaptive immune system: its self-regulation. Indeed, the generation of a broad repertoire of antigen receptors (via a unique strategy of random somatic rearrangements of gene segments in T cell and B cell receptor loci) inevitably creates receptors with specificity for self-antigens and thus leads to the presence of autoreactive lymphocytes. There are many different mechanisms for controlling the emergence or action of autoreactive lymphocytes, including clonal deletion in the primary lymphoid organs, receptor editing, anergy, suppression of effector lymphocytes by regulatory lymphocytes, and programmed cell death. Here, we review the genetic defects affecting lymphocyte apoptosis and that are associated with lymphoproliferation and autoimmunity, together with the role of somatic mutations and their potential involvement in more common autoimmune diseases.
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Affiliation(s)
- Sonia Meynier
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, Paris, France.,Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Frédéric Rieux-Laucat
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, Paris, France.,Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, Paris, France
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Abstract
Abstract
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. This can be achieved by leveraging omics information for accurate molecular characterization of tumors. Tumor tissue biopsies are currently the main source of information for molecular profiling. However, biopsies are invasive and limited in resolving spatiotemporal heterogeneity in tumor tissues. Alternative non-invasive liquid biopsies can exploit patient’s body fluids to access multiple layers of tumor-specific biological information (genomes, epigenomes, transcriptomes, proteomes, metabolomes, circulating tumor cells, and exosomes). Analysis and integration of these large and diverse datasets using statistical and machine learning approaches can yield important insights into tumor biology and lead to discovery of new diagnostic, predictive, and prognostic biomarkers. Translation of these new diagnostic tools into standard clinical practice could transform oncology, as demonstrated by a number of liquid biopsy assays already entering clinical use. In this review, we highlight successes and challenges facing the rapidly evolving field of cancer biomarker research.
Lay Summary
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. The discovery of biomarkers for precision oncology has been accelerated by high-throughput experimental and computational methods, which can inform fine-grained characterization of tumors for clinical decision-making. Moreover, advances in the liquid biopsy field allow non-invasive sampling of patient’s body fluids with the aim of analyzing circulating biomarkers, obviating the need for invasive tumor tissue biopsies. In this review, we highlight successes and challenges facing the rapidly evolving field of liquid biopsy cancer biomarker research.
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49
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Genetic and epigenetic factors interacting with clonal hematopoiesis resulting in chronic myelomonocytic leukemia. Curr Opin Hematol 2019; 27:2-10. [PMID: 31688455 DOI: 10.1097/moh.0000000000000553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW Since 2016, the WHO has recognized the significant phenotypic heterogeneity of chronic myelomonocytic leukemia (CMML) as a myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN) overlap disease. Although sharing many somatic mutations with MDS and MPN, the purpose of this review is to put recent biological findings of CMML in the context of evolutionary theory, highlighting it as a distinct evolutionary trajectory occurring in the context of clonal hematopoiesis. RECENT FINDINGS Clonal hematopoiesis of indeterminate potential (CHIP), with a mutational spectrum and prevalence correlated with age, has been defined. Enriched in DNMT3A, TET2, and ASXL1 mutations, clonal evolution can progress into various evolutionary trajectories including CMML. Impact of founder mutations (primarily TET2) on increased hematopoietic stem cell fitness has been well characterized. Epistatic interactions between mutations and epigenetic events have been explored, both in CMML and its pediatric counterpart juvenile myelomonocytic leukemia, including CMML transformation to acute myeloid leukemia. Together, these findings have contributed significantly toward CMML evolutionary dynamics. SUMMARY Despite relatively few 'driver' mutations in CMML, evolutionary development of chronic leukemia remains incompletely understood. Recent studies have shed light on the importance of studying epigenetic consequences of mutations and epistasis between key mutations to better understand clonal architecture and evolutionary dynamics.
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Hofmans M, Schröder R, Lammens T, Flotho C, Niemeyer C, Van Roy N, Decaluwe W, Philippé J, De Moerloose B. Noonan syndrome-associated myeloproliferative disorder with somatically acquired monosomy 7: impact on clinical decision making. Br J Haematol 2019; 187:E83-E86. [PMID: 31617209 DOI: 10.1111/bjh.16191] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Mattias Hofmans
- Division of Paediatric Haematology-Oncology and Stem Cell Transplantation, Department of Paediatrics, Ghent University Hospital, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Rieke Schröder
- Division of Paediatric Haematology and Oncology, Department of Paediatrics and Adolescent Medicine, Medical Centre, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tim Lammens
- Division of Paediatric Haematology-Oncology and Stem Cell Transplantation, Department of Paediatrics, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Christian Flotho
- Division of Paediatric Haematology and Oncology, Department of Paediatrics and Adolescent Medicine, Medical Centre, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium, Partner Site Freiburg, German Cancer Research Centre, Heidelberg, Germany
| | - Charlotte Niemeyer
- Division of Paediatric Haematology and Oncology, Department of Paediatrics and Adolescent Medicine, Medical Centre, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium, Partner Site Freiburg, German Cancer Research Centre, Heidelberg, Germany
| | - Nadine Van Roy
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.,Centre for Medical Genetics, Ghent University, Ghent, Belgium
| | - Wim Decaluwe
- Department of Paediatrics, Neonatal Intensive Care, AZ Sint-Jan Bruges, Bruges, Belgium
| | - Jan Philippé
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Barbara De Moerloose
- Division of Paediatric Haematology-Oncology and Stem Cell Transplantation, Department of Paediatrics, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
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