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Mohamed A, Gao J, Chen YH, Abaza Y, Altman J, Jennings L, Vormittag-Nocito E, Sukhanova M, Lu X, Chen Q. CSF3R mutated myeloid neoplasms: Beyond chronic neutrophilic leukemia. Hum Pathol 2024; 149:66-74. [PMID: 38879086 DOI: 10.1016/j.humpath.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
CSF3R activating mutation is a genetic hallmark of chronic neutrophilic leukemia (CNL), and is also present in a subset of atypical chronic myeloid leukemia (aCML), but infrequent in other myeloid neoplasms. However, the occurrence of CSF3R mutations in various myeloid neoplasms is not well studied. Here we evaluate the spectrum of CSF3R mutations and the clinicopathologic features of CSF3R mutated myeloid neoplasms. We retrospectively identified CSF3R mutations in a variety of myeloid neoplasms: two CNL, three atypical chronic myeloid leukemia (aCML), nine acute myeloid leukemia (AML), one chronic myelomonocytic leukemia, and one myeloproliferative neoplasm. The prototypic T618I mutation was found in 50% of cases: CNL (2/2), aCML (2/3) and AML (4/9). We observed a new recurrent CSF3R mutation Q776* in 25% of cases, and a potential-germline mutation in a 20-year-old patient. Co-occurring mutations were often in epigenetic modifier and spliceosome. IDH/RUNX1 and tumor suppressor mutations were frequent in AML but absent in CNL/aCML. All CNL/aCML patients succumbed within 2-years of diagnosis. We demonstrate that CSF3R mutations are not restricted to CNL. CNL and aCML show similar clinicopathologic and molecular features, suggesting that CNL may be best classified as myelodysplastic/myeloproliferative neoplasm rather than myeloproliferative neoplasm.
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MESH Headings
- Humans
- Receptors, Colony-Stimulating Factor/genetics
- Male
- Mutation
- Middle Aged
- Female
- Aged
- Leukemia, Neutrophilic, Chronic/genetics
- Leukemia, Neutrophilic, Chronic/pathology
- Retrospective Studies
- Adult
- Young Adult
- Aged, 80 and over
- Myeloproliferative Disorders/genetics
- Myeloproliferative Disorders/pathology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- DNA Mutational Analysis
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/genetics
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/pathology
- Genetic Predisposition to Disease
- Biomarkers, Tumor/genetics
- Phenotype
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Affiliation(s)
- Ahmed Mohamed
- Department of Pathology, Northwestern University Feinberg School of Medicine, 251 E Huron Street, Chicago, IL, 60611, USA
| | - Juehua Gao
- Department of Pathology, Northwestern University Feinberg School of Medicine, 251 E Huron Street, Chicago, IL, 60611, USA.
| | - Yi-Hua Chen
- Department of Pathology, Northwestern University Feinberg School of Medicine, 251 E Huron Street, Chicago, IL, 60611, USA
| | - Yasmin Abaza
- Hematology Oncology Division, Department of Medicine, Northwestern University Feinberg School of Medicine, 251 E Huron Street, Chicago, IL, 60611, USA
| | - Jessica Altman
- Hematology Oncology Division, Department of Medicine, Northwestern University Feinberg School of Medicine, 251 E Huron Street, Chicago, IL, 60611, USA
| | - Lawrence Jennings
- Department of Pathology, Northwestern University Feinberg School of Medicine, 251 E Huron Street, Chicago, IL, 60611, USA
| | - Erica Vormittag-Nocito
- Department of Pathology, Northwestern University Feinberg School of Medicine, 251 E Huron Street, Chicago, IL, 60611, USA
| | - Madina Sukhanova
- Department of Pathology, Northwestern University Feinberg School of Medicine, 251 E Huron Street, Chicago, IL, 60611, USA
| | - Xinyan Lu
- Department of Pathology, Northwestern University Feinberg School of Medicine, 251 E Huron Street, Chicago, IL, 60611, USA
| | - Qing Chen
- Department of Pathology, Northwestern University Feinberg School of Medicine, 251 E Huron Street, Chicago, IL, 60611, USA
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2
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Cao X, Huber S, Ahari AJ, Traube FR, Seifert M, Oakes CC, Secheyko P, Vilov S, Scheller IF, Wagner N, Yépez VA, Blombery P, Haferlach T, Heinig M, Wachutka L, Hutter S, Gagneur J. Analysis of 3760 hematologic malignancies reveals rare transcriptomic aberrations of driver genes. Genome Med 2024; 16:70. [PMID: 38769532 PMCID: PMC11103968 DOI: 10.1186/s13073-024-01331-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/04/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Rare oncogenic driver events, particularly affecting the expression or splicing of driver genes, are suspected to substantially contribute to the large heterogeneity of hematologic malignancies. However, their identification remains challenging. METHODS To address this issue, we generated the largest dataset to date of matched whole genome sequencing and total RNA sequencing of hematologic malignancies from 3760 patients spanning 24 disease entities. Taking advantage of our dataset size, we focused on discovering rare regulatory aberrations. Therefore, we called expression and splicing outliers using an extension of the workflow DROP (Detection of RNA Outliers Pipeline) and AbSplice, a variant effect predictor that identifies genetic variants causing aberrant splicing. We next trained a machine learning model integrating these results to prioritize new candidate disease-specific driver genes. RESULTS We found a median of seven expression outlier genes, two splicing outlier genes, and two rare splice-affecting variants per sample. Each category showed significant enrichment for already well-characterized driver genes, with odds ratios exceeding three among genes called in more than five samples. On held-out data, our integrative modeling significantly outperformed modeling based solely on genomic data and revealed promising novel candidate driver genes. Remarkably, we found a truncated form of the low density lipoprotein receptor LRP1B transcript to be aberrantly overexpressed in about half of hairy cell leukemia variant (HCL-V) samples and, to a lesser extent, in closely related B-cell neoplasms. This observation, which was confirmed in an independent cohort, suggests LRP1B as a novel marker for a HCL-V subclass and a yet unreported functional role of LRP1B within these rare entities. CONCLUSIONS Altogether, our census of expression and splicing outliers for 24 hematologic malignancy entities and the companion computational workflow constitute unique resources to deepen our understanding of rare oncogenic events in hematologic cancers.
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Affiliation(s)
- Xueqi Cao
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Graduate School of Quantitative Biosciences (QBM), Munich, Germany
| | - Sandra Huber
- Munich Leukemia Laboratory (MLL), Munich, Germany
| | - Ata Jadid Ahari
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Franziska R Traube
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Marc Seifert
- Department of Haematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Christopher C Oakes
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Polina Secheyko
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Sergey Vilov
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | - Ines F Scheller
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | - Nils Wagner
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany
| | - Vicente A Yépez
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Piers Blombery
- Peter MacCallum Cancer Centre, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
- Torsten Haferlach Leukämiediagnostik Stiftung, Munich, Germany
| | | | - Matthias Heinig
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | - Leonhard Wachutka
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
| | | | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Graduate School of Quantitative Biosciences (QBM), Munich, Germany.
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
- Institute of Human Genetics, School of Medicine and Health, Technical University of Munich, Munich, Germany.
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3
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Zhang L, Deeb G, Deeb KK, Vale C, Peker Barclift D, Papadantonakis N. Measurable (Minimal) Residual Disease in Myelodysplastic Neoplasms (MDS): Current State and Perspectives. Cancers (Basel) 2024; 16:1503. [PMID: 38672585 PMCID: PMC11048433 DOI: 10.3390/cancers16081503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Myelodysplastic Neoplasms (MDS) have been traditionally studied through the assessment of blood counts, cytogenetics, and morphology. In recent years, the introduction of molecular assays has improved our ability to diagnose MDS. The role of Measurable (minimal) Residual Disease (MRD) in MDS is evolving, and molecular and flow cytometry techniques have been used in several studies. In this review, we will highlight the evolving concept of MRD in MDS, outline the various techniques utilized, and provide an overview of the studies reporting MRD and the correlation with outcomes.
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Affiliation(s)
- Linsheng Zhang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - George Deeb
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kristin K. Deeb
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Colin Vale
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Deniz Peker Barclift
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nikolaos Papadantonakis
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
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4
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Gurbuxani S. SETBP1 sets the stage. Blood 2024; 143:1323-1324. [PMID: 38573606 DOI: 10.1182/blood.2023023757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
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5
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Winters AC, Pollyea DA. Molecular measurable residual disease: staring at red herrings. Haematologica 2024; 109:371-373. [PMID: 37584293 PMCID: PMC10828628 DOI: 10.3324/haematol.2023.283708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/17/2023] Open
Affiliation(s)
- Amanda C Winters
- University of Colorado Department of Pediatrics, Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO USA
| | - Daniel A Pollyea
- University of Colorado Division of Hematology, Department of Medicine, Aurora CO USA.
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6
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O'Brien G, Cecotka A, Manola KN, Pagoni MN, Polanska J, Badie C. Epigenetic signature of ionizing radiation in therapy-related AML patients. Heliyon 2024; 10:e23244. [PMID: 38163095 PMCID: PMC10757008 DOI: 10.1016/j.heliyon.2023.e23244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/26/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024] Open
Abstract
Therapy-related acute myeloid leukaemia (t-AML) is a late side effect of previous chemotherapy (ct-AML) and/or radiotherapy (rt-AML) or immunosuppressive treatment. t-AMLs, which account for ∼10-20 % of all AML cases, are extremely aggressive and have a poor prognosis compared to de novo AML. Our hypothesis is that exposure to radiation causes genome-wide epigenetic changes in rt-AML. An epigenome-wide association study was undertaken, measuring over 850K methylation sites across the genome from fifteen donors (five healthy, five de novo, and five t-AMLs). The study predominantly focussed on 94K sites that lie in CpG-rich gene promoter regions. Genome-wide hypomethylation was discovered in AML, primarily in intergenic regions. Additionally, genes specific to AML were identified with promoter hypermethylation. A two-step validation was conducted, both internally, using pyrosequencing to measure methylation levels in specific regions across fifteen primary samples, and externally, with an additional eight AML samples. We demonstrated that the MEST and GATA5 gene promoters, which were previously identified as tumour suppressors, were noticeably hypermethylated in rt-AML, as opposed to other subtypes of AML and control samples. These may indicate the epigenetic involvement in the development of rt-AML at the molecular level and could serve as potential targets for drug therapy in rt-AML.
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Affiliation(s)
- Gráinne O'Brien
- Cancer Mechanisms and Biomarkers Group, Radiation Effects Department Radiation, Chemical & Environmental Hazards, Harwell Campus, Chilton, Didcot, Oxfordshire OX11 ORQ, UK Health Security Agency (UKHSA), United Kingdom
| | - Agnieszka Cecotka
- Department of Data Science and Engineering, Silesian University of Technology, 44-121 Gliwice, Poland
| | - Kalliopi N. Manola
- Department of Biodiagnostic Sciences and Technologies, INRASTES, National Centre for Research' Demokritos', 15341 Agia Paraskevi, Greece
| | - Maria N. Pagoni
- Hematology-Lymphomas Department - BMT Unit, Evangelismos Hospital, 10676 Athens, Greece
| | - Joanna Polanska
- Department of Data Science and Engineering, Silesian University of Technology, 44-121 Gliwice, Poland
| | - Christophe Badie
- Cancer Mechanisms and Biomarkers Group, Radiation Effects Department Radiation, Chemical & Environmental Hazards, Harwell Campus, Chilton, Didcot, Oxfordshire OX11 ORQ, UK Health Security Agency (UKHSA), United Kingdom
- Environmental Research Group Within the School of Public Health, Faculty of Medicine at Imperial College of Science, Technology and Medicine, London W12 0BZ, United Kingdom
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7
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Han L, Wu J, Lyu X, Yu J, Han X, Zhao H, Bian Z, Li W, Fan W, He C, Wang W, Zhang M, Li Y, Liu C, Sun H, Cao H, Sang L, Zhang J, Jiang Z, Peng J. Genetic mutation signature for relapse prediction in normal karyotype acute myeloid leukemia. Exp Hematol 2023; 128:67-76. [PMID: 37739208 DOI: 10.1016/j.exphem.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/28/2023] [Accepted: 09/08/2023] [Indexed: 09/24/2023]
Abstract
Risk stratification for normal karyotype acute myeloid leukemia (NK-AML) remains unsatisfactory, which is reflected by the high incidence of leukemia relapse. This study aimed to evaluate the role of gene mutations and clinical characterization in predicting the relapse of patients with NK-AML. A prognostic system for NK-AML was constructed. A panel of gene mutations was explored using next-generation sequencing. A nomogram algorithm was used to build a genomic mutation signature (GMS) nomogram (GMSN) model that combines GMS, measurable residual disease, and clinical factors to predict relapse in 347 patients with NK-AML from four centers. Patients in the GMS-high group had a higher 5-year incidence of relapse than those in the GMS-low group (p < 0.001). The 5-year incidence of relapse was also higher in patients in the GMSN-high group than in those in the GMSN-intermediate and -low groups (p < 0.001). The 5-year disease-free survival and overall survival rates were lower in patients in the GMSN-high group than in those in the GMSN-intermediate and -low groups (p < 0.001) as confirmed by training and validation cohorts. This study illustrates the potential of GMSN as a predictor of NK-AML relapse.
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Affiliation(s)
- Lijie Han
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Jiaying Wu
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaodong Lyu
- Central Lab, the Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Jifeng Yu
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaolin Han
- Department of Hematology, the First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Hongmian Zhao
- Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, China
| | - Zhilei Bian
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Li
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenjuan Fan
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chen He
- Laboratory of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Weimin Wang
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mengmeng Zhang
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yafei Li
- Laboratory of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chao Liu
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hui Sun
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haixia Cao
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Li'na Sang
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Zhang
- Department of Oncology, the Second Affiliated Hospital of Guizhou Medical University, Kaili, China
| | - Zhongxing Jiang
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Jie Peng
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Department of Oncology, the Second Affiliated Hospital of Guizhou Medical University, Kaili, China.
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8
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Stacey SN, Zink F, Halldorsson GH, Stefansdottir L, Gudjonsson SA, Einarsson G, Hjörleifsson G, Eiriksdottir T, Helgadottir A, Björnsdottir G, Thorgeirsson TE, Olafsdottir TA, Jonsdottir I, Gretarsdottir S, Tragante V, Magnusson MK, Jonsson H, Gudmundsson J, Olafsson S, Holm H, Gudbjartsson DF, Sulem P, Helgason A, Thorsteinsdottir U, Tryggvadottir L, Rafnar T, Melsted P, Ulfarsson MÖ, Vidarsson B, Thorleifsson G, Stefansson K. Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis. Nat Genet 2023; 55:2149-2159. [PMID: 37932435 PMCID: PMC10703693 DOI: 10.1038/s41588-023-01555-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/28/2023] [Indexed: 11/08/2023]
Abstract
Clonal hematopoiesis (CH) arises when a substantial proportion of mature blood cells is derived from a single hematopoietic stem cell lineage. Using whole-genome sequencing of 45,510 Icelandic and 130,709 UK Biobank participants combined with a mutational barcode method, we identified 16,306 people with CH. Prevalence approaches 50% in elderly participants. Smoking demonstrates a dosage-dependent impact on risk of CH. CH associates with several smoking-related diseases. Contrary to published claims, we find no evidence that CH is associated with cardiovascular disease. We provide evidence that CH is driven by genes that are commonly mutated in myeloid neoplasia and implicate several new driver genes. The presence and nature of a driver mutation alters the risk profile for hematological disorders. Nevertheless, most CH cases have no known driver mutations. A CH genome-wide association study identified 25 loci, including 19 not implicated previously in CH. Splicing, protein and expression quantitative trait loci were identified for CD164 and TCL1A.
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Affiliation(s)
| | | | - Gisli H Halldorsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | - Thorunn A Olafsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Immunology, Landspitali University Hospital, Reykjavik, Iceland
| | | | | | - Magnus K Magnusson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Agnar Helgason
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Pall Melsted
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Magnus Ö Ulfarsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Brynjar Vidarsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Hematology, Landspitali University Hospital, Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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9
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Hallermayr A, Keßler T, Steinke-Lange V, Heitzer E, Holinski-Feder E, Speicher M. The utility of liquid biopsy in clinical genetic diagnosis of cancer and monogenic mosaic disorders. MED GENET-BERLIN 2023; 35:275-284. [PMID: 38835734 PMCID: PMC11006364 DOI: 10.1515/medgen-2023-2066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Liquid biopsy for minimally invasive diagnosis and monitoring of cancer patients is progressing toward routine clinical practice. With the implementation of highly sensitive next-generation sequencing (NGS) based assays for the analysis of cfDNA, however, consideration of the utility of liquid biopsy for clinical genetic testing is critical. While the focus of liquid biopsy for cancer diagnosis is the detection of circulating tumor DNA (ctDNA) as a fraction of total cell-free DNA (cfDNA), cfDNA analysis reveals both somatic mosaic tumor and germline variants and clonal hematopoiesis. Here we outline advantages and limitations of mosaic and germline variant detection as well as the impact of clonal hematopoiesis on liquid biopsy in cancer diagnosis. We also evaluate the potential of cfDNA analysis for the molecular diagnosis of monogenic mosaic disorders.
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Affiliation(s)
| | - Thomas Keßler
- MGZ - Medizinisch Genetisches Zentrum München Germany
| | | | - Ellen Heitzer
- Medical University of Graz Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria) Graz Austria
| | | | - Michael Speicher
- Medical University of Graz Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria), Neue Stiftingtalstraße 2 Graz Austria
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10
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Zhang M, Lang X, Chen X, Lv Y. Prospective Identification of Prognostic Hot-Spot Mutant Gene Signatures for Leukemia: A Computational Study Based on Integrative Analysis of TCGA and cBioPortal Data. Mol Biotechnol 2023; 65:1898-1912. [PMID: 36879146 DOI: 10.1007/s12033-023-00704-3] [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: 09/15/2022] [Accepted: 02/14/2023] [Indexed: 03/08/2023]
Abstract
The advantage of an increasing amount of bioinformatics data on leukemias intrigued us to explore the hot-spot mutation profiles and investigate the implications of those hot-spot mutations in patient survival. We retrieved somatic mutations and their distribution in protein domains through data analysis of The Cancer Genome Atlas and cBioPortal databases. After determining differentially expressed mutant genes related to leukemia, we further conducted principal component analysis and single-factor Cox regression analyses. Moreover, survival analysis was performed for the obtained candidate genes, followed by a multi-factor Cox proportional hazard model method for the impacts of the candidate genes on the survival and prognosis of patients with leukemia. At last, the signaling pathways involved in leukemia were investigated by gene set enrichment analysis. There were 223 somatic missense mutation hot-spots identified with pertinence to leukemia, which were distributed in 41 genes. Differential expression in leukemia was witnessed in 39 genes. We found a close correlation between seven genes and the prognosis of leukemia patients, among which, three genes could significantly influence the survival rate. In addition, among these three genes, CD74 and P2RY8 were highlighted due to close pertinence with survival conditions of leukemia patients. Finally, data suggested that B cell receptor, Hedgehog, and TGF-beta signaling pathways were enriched in low-hazard patients. In conclusion, these data underline the involvement of hot-spot mutations of CD74 and P2RY8 genes in survival status of leukemia patients, highlighting their as novel therapeutic targets or prognostic indicators for leukemia patients. Summary of Graphical Abstract: We identified 223 leukemia-associated somatic missense mutation hotspots concentrated in 41 different genes from 2297 leukemia patients in the TCGA database. Differential analysis of leukemic and normal samples from the TCGA and GTEx databases revealed that 39 of these 41 genes showed significant differential expression in leukemia. These 39 genes were subjected to PCA analysis, univariate Cox analysis, survival analysis, multivariate Cox regression analysis, GSEA pathway enrichment analysis, and then the association with leukemia survival prognosis and related pathways were investigated.
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Affiliation(s)
- Min Zhang
- Department of Hematology, The First People's Hospital of Yongkang, Affiliated to Hangzhou Medical College, No. 599, Jinshan West Road, Yongkang, Jinhua City, Zhejiang Province, 321300, People's Republic of China.
| | - Xianghua Lang
- Department of Hematology, The First People's Hospital of Yongkang, Affiliated to Hangzhou Medical College, No. 599, Jinshan West Road, Yongkang, Jinhua City, Zhejiang Province, 321300, People's Republic of China
| | - Xinyi Chen
- Department of Hematology, The First People's Hospital of Yongkang, Affiliated to Hangzhou Medical College, No. 599, Jinshan West Road, Yongkang, Jinhua City, Zhejiang Province, 321300, People's Republic of China
| | - Yuke Lv
- Department of Hematology, The First People's Hospital of Yongkang, Affiliated to Hangzhou Medical College, No. 599, Jinshan West Road, Yongkang, Jinhua City, Zhejiang Province, 321300, People's Republic of China
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11
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Nadal N, Auger N, Bidet A, Nguyen-Khac F. Cytogenetics in the management of clonal chromosomal abnormalities of undetermined significance and persistent polyclonal B-cell lymphocytosis: Guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH). Curr Res Transl Med 2023; 71:103426. [PMID: 38016423 DOI: 10.1016/j.retram.2023.103426] [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: 07/04/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/30/2023]
Abstract
Acquired clonal chromosomal abnormalities (CAs) are usually considered to be disease-related. However, when a CA of this type is the only abnormality present (and especially in small clones), the clinical significance is unclear. Here, we review the literature on recurrent CAs whose significance is regularly subject to debate. Our objective was to help with their interpretation and develop guidelines for sex chromosome loss, trisomy 15, trisomy 8, deletion 20q and other isolated non-myelodysplastic neoplasm (MDS)-defining CAs. We suggest that non-MDS-defining CAs correspond to clonal hematopoiesis of indeterminate potential (CHIP) in the absence of cytopenia and clonal cytopenia of undetermined significance (CCUS) in the presence of cytopenia. Lastly, we review the literature on persistent polyclonal binucleated B-cell lymphocytosis; although usually benign, this condition may correspond to a premalignant state.
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Affiliation(s)
- N Nadal
- Service de génétique chromosomique et moléculaire, CHU Dijon, Dijon, France.
| | - N Auger
- Génétique des tumeurs, Gustave Roussy, Villejuif, France
| | - A Bidet
- Laboratoire d'hématologie, CHU Bordeaux, Bordeaux, France
| | - F Nguyen-Khac
- Drug Resistance in Hematological Malignancies, Centre de Recherche des Cordeliers, UMRS 1138, INSERM, Sorbonne Université, Université Paris Cité, Paris, France; Service d'Hématologie Biologique, Hôpital Pitié-Salpêtrière, AP-HP, Paris, France
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12
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Shin DY. TP53 Mutation in Acute Myeloid Leukemia: An Old Foe Revisited. Cancers (Basel) 2023; 15:4816. [PMID: 37835510 PMCID: PMC10571655 DOI: 10.3390/cancers15194816] [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: 08/02/2023] [Revised: 09/20/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
INTRODUCTION TP53 is the most commonly mutated gene in human cancers and was the first tumor suppressor gene to be discovered in the history of medical science. Mutations in the TP53 gene occur at various genetic locations and exhibit significant heterogeneity among patients. Mutations occurring primarily within the DNA-binding domain of TP53 result in the loss of the p53 protein's DNA-binding capability. However, a complex phenotypic landscape often combines gain-of-function, dominant negative, or altered specificity features. This complexity poses a significant challenge in developing an effective treatment strategy, which eradicates TP53-mutated cancer clones. This review summarizes the current understanding of TP53 mutations in AML and their implications. TP53 mutation in AML: In patients with acute myeloid leukemia (AML), six hotspot mutations (R175H, G245S, R248Q/W, R249S, R273H/S, and R282W) within the DNA-binding domain are common. TP53 mutations are frequently associated with a complex karyotype and subgroups of therapy-related or secondary AML. The presence of TP53 mutation is considered as a poor prognostic factor. TP53-mutated AML is even classified as a distinct subgroup of AML by itself, as TP53-mutated AML exhibits a significantly distinct landscape in terms of co-mutation and gene expression profiles compared with wildtype (WT)-TP53 AML. CLINICAL IMPLICATIONS To better predict the prognosis in cancer patients with different TP53 mutations, several predictive scoring systems have been proposed based on screening experiments, to assess the aggressiveness of TP53-mutated cancer cells. Among those scoring systems, a relative fitness score (RFS) could be applied to AML patients with TP53 mutations in terms of overall survival (OS) and event-free survival (EFS). The current standard treatment, which includes cytotoxic chemotherapy and allogeneic hematopoietic stem cell transplantation, is largely ineffective for patients with TP53-mutated AML. Consequently, most patients with TP53-mutated AML succumb to leukemia within several months, despite active anticancer treatment. Decitabine, a hypomethylating agent, is known to be relatively effective in patients with AML. Numerous trials are ongoing to investigate the effects of novel drugs combined with hypomethylating agents, TP53-targeting agents or immunologic agents. CONCLUSIONS Developing an effective treatment strategy for TP53-mutated AML through innovative and multidisciplinary research is an urgent task. Directly targeting mutated TP53 holds promise as an approach to combating TP53-mutated AML, and recent developments in immunologic agents for AML offer hope in this field.
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Affiliation(s)
- Dong-Yeop Shin
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea; ; Tel.: +82-2-2072-7209; Fax: +82-2-762-9662
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
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13
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Klapp V, Álvarez-Abril B, Leuzzi G, Kroemer G, Ciccia A, Galluzzi L. The DNA Damage Response and Inflammation in Cancer. Cancer Discov 2023; 13:1521-1545. [PMID: 37026695 DOI: 10.1158/2159-8290.cd-22-1220] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/27/2023] [Accepted: 02/23/2023] [Indexed: 04/08/2023]
Abstract
Genomic stability in normal cells is crucial to avoid oncogenesis. Accordingly, multiple components of the DNA damage response (DDR) operate as bona fide tumor suppressor proteins by preserving genomic stability, eliciting the demise of cells with unrepairable DNA lesions, and engaging cell-extrinsic oncosuppression via immunosurveillance. That said, DDR sig-naling can also favor tumor progression and resistance to therapy. Indeed, DDR signaling in cancer cells has been consistently linked to the inhibition of tumor-targeting immune responses. Here, we discuss the complex interactions between the DDR and inflammation in the context of oncogenesis, tumor progression, and response to therapy. SIGNIFICANCE Accumulating preclinical and clinical evidence indicates that DDR is intimately connected to the emission of immunomodulatory signals by normal and malignant cells, as part of a cell-extrinsic program to preserve organismal homeostasis. DDR-driven inflammation, however, can have diametrically opposed effects on tumor-targeting immunity. Understanding the links between the DDR and inflammation in normal and malignant cells may unlock novel immunotherapeutic paradigms to treat cancer.
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Affiliation(s)
- Vanessa Klapp
- Department of Radiation Oncology, Weill Cornell Medical College, New York, New York
- Tumor Stroma Interactions, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Beatriz Álvarez-Abril
- Department of Radiation Oncology, Weill Cornell Medical College, New York, New York
- Department of Hematology and Oncology, Hospital Universitario Morales Meseguer, Murcia, Spain
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York
- Herbert Irving Comprehensive Cancer Center, New York, New York
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, New York
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le Cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York
- Herbert Irving Comprehensive Cancer Center, New York, New York
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, New York
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, New York
- Sandra and Edward Meyer Cancer Center, New York, New York
- Caryl and Israel Englander Institute for Precision Medicine, New York, New York
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14
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Fu R, Dong H, Zhang D, Zhou H, Zhang X, Huang Y, Liu X, Xue F, Liu W, Chen Y, Sun T, Ju M, Dai X, Yang R, Zhang L. Clinical features and current treatment status of essential thrombocythemia in older adults: a multicenter real-world study in China. Ann Hematol 2023:10.1007/s00277-023-05317-z. [PMID: 37354213 DOI: 10.1007/s00277-023-05317-z] [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: 01/26/2023] [Accepted: 06/11/2023] [Indexed: 06/26/2023]
Abstract
Approximately half of patients diagnosed with essential thrombocythemia (ET) are older adults (aged ≥ 60 years), but to date, little is known about the clinical and molecular characteristics of older patients diagnosed according to the 2016 World Health Organization criteria. We retrospectively collected clinical and molecular data from 282 older (≥ 60 years) and 621 younger ET patients (18-59 years) in China from March 1, 2012 to November 1, 2021 and summarized the clinical characteristics and treatment of these older ET patients. Compared to younger patients, older patients had a higher incidence of the JAK2V617F mutation (P = 0.001), a lower incidence of CALR mutations (P = 0.033) and a higher rate of epigenetic mutations (P < 0.001), TP53 mutations (P = 0.005), and RNA splicing mutations (P < 0.001). Older patients had not only a higher incidence of thrombosis but also a higher incidence of bleeding events. Furthermore, older patients had a significantly higher mortality rate after disease progression (P = 0.050) or after thrombotic events (P = 0.013). Risk factors for thrombosis or prognosis were significantly different between older patients and the entire ET cohort. In older patients, non-driver mutations contributed significantly to thrombotic complications and a poor prognosis, while the JAK2V617F mutation was a risk factor for overall survival but not for thrombotic events. The application of interferon in older ET patients was not inferior to that of hydroxyurea in terms of efficacy and safety. Older patients presented unique characteristics different from those of younger patients, which could provide new information for formulating more appropriate treatment and follow-up strategies.
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Affiliation(s)
- Rongfeng Fu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Huan Dong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Donglei Zhang
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Hu Zhou
- Department of Hematology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Hemostasis and Thrombosis Diagnostic Engineering Research Center of Henan Province, Zhengzhou, 450008, Henan, China
| | - Xian Zhang
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Yueting Huang
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen, 361000, Fujian, China
| | - Xiaofan Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Feng Xue
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Wei Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Yunfei Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Ting Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Mankai Ju
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Xinyue Dai
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Renchi Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
| | - Lei Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
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15
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Slade MJ, Ghasemi R, O'Laughlin M, Burton T, Fulton RS, Abel HJ, Duncavage EJ, Ley TJ, Jacoby MA, Spencer DH. Persistent Molecular Disease in Adult Patients With AML Evaluated With Whole-Exome and Targeted Error-Corrected DNA Sequencing. JCO Precis Oncol 2023; 7:e2200559. [PMID: 37079859 PMCID: PMC10530963 DOI: 10.1200/po.22.00559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/03/2023] [Accepted: 03/01/2023] [Indexed: 04/22/2023] Open
Abstract
PURPOSE Persistent molecular disease (PMD) after induction chemotherapy predicts relapse in AML. In this study, we used whole-exome sequencing (WES) and targeted error-corrected sequencing to assess the frequency and mutational patterns of PMD in 30 patients with AML. MATERIALS AND METHODS The study cohort included 30 patients with adult AML younger than 65 years who were uniformly treated with standard induction chemotherapy. Tumor/normal WES was performed for all patients at presentation. PMD analysis was evaluated in bone marrow samples obtained during clinicopathologic remission using repeat WES and analysis of patient-specific mutations and error-corrected sequencing of 40 recurrently mutated AML genes (MyeloSeq). RESULTS WES for patient-specific mutations detected PMD in 63% of patients (19/30) using a minimum variant allele fraction (VAF) of 2.5%. In comparison, MyeloSeq identified persistent mutations above 0.1% VAF in 77% of patients (23/30). PMD was usually present at relatively high levels (>2.5% VAFs), such that WES and MyeloSeq agreed for 73% of patients despite differences in detection limits. Mutations in DNMT3A, ASXL1, and TET2 (ie, DTA mutations) were persistent in 16 of 17 patients, but WES also detected non-DTA mutations in 14 of these patients, which for some patients distinguished residual AML cells from clonal hematopoiesis. Surprisingly, MyeloSeq detected additional variants not identified at presentation in 73% of patients that were consistent with new clonal cell populations after chemotherapy. CONCLUSION PMD and clonal hematopoiesis are both common in patients with AML in first remission. These findings demonstrate the importance of baseline testing for accurate interpretation of mutation-based tumor monitoring assays for patients with AML and highlight the need for clinical trials to determine whether these complex mutation patterns correlate with clinical outcomes in AML.
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Affiliation(s)
- Michael J. Slade
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Reza Ghasemi
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Michelle O'Laughlin
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Tasha Burton
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Haley J. Abel
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Eric J. Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Timothy J. Ley
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Meagan A. Jacoby
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - David H. Spencer
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
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16
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Xiao J, Xie J, Zhou B, Liu Y, Lu J, Jiang A, Yao H, Qiu Q, Ding Z, Xue S, Tang X, Qiu H, Chen S, Shen H, Wu D, Xu Y. RUNX1 together with DAT mutations predicted poor outcome in acute myeloid leukemia. Leuk Lymphoma 2023:1-11. [PMID: 36964663 DOI: 10.1080/10428194.2023.2190433] [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: 03/26/2023]
Abstract
We retrospectively explored the prognostic impact of DAT mutations at diagnosis in 122 RUNX1mut AML patients. RUNX1 missense mutation was dominant in the RUNT domain, and frameshift mutation was dominant in the TAD domain. DAT mutations occurred in 38.5% of RUNX1mut AML. After propensity score matching, DATpos patients had worse two-year relapse-free survival (RFS) than DATneg patients (p = .041). Moreover, RUNX1high (VAF ≥ 37.6%) patients showed poorer two-year overall survival (OS) and RFS than RUNX1low (VAF < 37.6%) patients (OS, p = .033; RFS, p = .027), especially in the RUNX1highDATpos group. Additionally, multivariate analysis confirmed that DAT mutations at diagnosis were an independent adverse factor for RFS. There were no significant differences in two-year OS and RFS between DATpos and DATneg patients or between RUNX1high and RUNX1low patients who undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT). Collectively, DAT mutations at diagnosis were adverse factors for RFS, and allo-HSCT could likely improve the poor outcomes of these patients.
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Affiliation(s)
- Jinyan Xiao
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Jundan Xie
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Biqi Zhou
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Yujie Liu
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Jing Lu
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Airui Jiang
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Hong Yao
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Qiaocheng Qiu
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Zixuan Ding
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Shengli Xue
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Xiaowen Tang
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Huiying Qiu
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Suning Chen
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Hongjie Shen
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Depei Wu
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Yang Xu
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
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17
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Paired Comparison of Routine Molecular Screening of Patient Samples with Advanced Non-Small Cell Lung Cancer in Circulating Cell-Free DNA Using Three Targeted Assays. Cancers (Basel) 2023; 15:cancers15051574. [PMID: 36900363 PMCID: PMC10001056 DOI: 10.3390/cancers15051574] [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: 12/30/2022] [Revised: 01/29/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
INTRODUCTION Progressive advanced non-small cell lung cancer (NSCLC) accounts for about 80-85% of all lung cancers. Approximately 10-50% of patients with NSCLC harbor targetable activating mutations, such as in-frame deletions in Exon 19 (Ex19del) of EGFR. Currently, for patients with advanced NSCLC, testing for sensitizing mutations in EGFR is mandatory prior to the administration of tyrosine kinase inhibitors. PATIENTS AND METHODS Plasma was collected from patients with NSCLC. We carried out targeted NGS using the Plasma-SeqSensei™ SOLID CANCER IVD kit on cfDNA (circulating free DNA). Clinical concordance for plasma detection of known oncogenic drivers was reported. In a subset of cases, validation was carried out using an orthogonal OncoBEAMTM EGFR V2 assay, as well as with our custom validated NGS assay. Somatic alterations were filtered, removing somatic mutations attributable to clonal hematopoiesis for our custom validated NGS assay. RESULTS In the plasma samples, driver targetable mutations were studied, with a mutant allele frequency (MAF) ranging from 0.00% (negative detection) to 82.25%, using the targeted next-generation sequencing Plasma-SeqSensei™ SOLID CANCER IVD Kit. In comparison with the OncoBEAMTM EGFR V2 kit, the EGFR concordance is 89.16% (based on the common genomic regions). The sensitivity and specificity rates based on the genomic regions (EGFR exons 18, 19, 20, and 21) were 84.62% and 94.67%. Furthermore, the observed clinical genomic discordances were present in 25% of the samples: 5% in those linked to the lower of coverage of the OncoBEAMTM EGFR V2 kit, 7% in those induced by the sensitivity limit on the EGFR with the Plasma-SeqSensei™ SOLID CANCER IVD Kit, and 13% in the samples linked to the larger KRAS, PIK3CA, BRAF coverage of the Plasma-SeqSensei™ SOLID CANCER IVD kit. Most of these somatic alterations were cross validated in our orthogonal custom validated NGS assay, used in the routine management of patients. The concordance is 82.19% in the common genomic regions (EGFR exons 18, 19, 20, 21; KRAS exons 2, 3, 4; BRAF exons 11, 15; and PIK3CA exons 10, 21). The sensitivity and specificity rates were 89.38% and 76.12%, respectively. The 32% of genomic discordances were composed of 5% caused by the limit of coverage of the Plasma-SeqSensei™ SOLID CANCER IVD kit, 11% induced by the sensitivity limit of our custom validated NGS assay, and 16% linked to the additional oncodriver analysis, which is only covered by our custom validated NGS assay. CONCLUSIONS The Plasma-SeqSensei™ SOLID CANCER IVD kit resulted in de novo detection of targetable oncogenic drivers and resistance alterations, with a high sensitivity and accuracy for low and high cfDNA inputs. Thus, this assay is a sensitive, robust, and accurate test.
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18
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The Secondary Myelodysplastic Neoplasms (MDS) Jigsaw. Cancers (Basel) 2023; 15:cancers15051483. [PMID: 36900275 PMCID: PMC10000488 DOI: 10.3390/cancers15051483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/08/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
There is a great deal of controversy in the hematologic community regarding the classification of secondary myelodysplastic neoplasms (MDSs). Current classifications are based on the presence of genetic predisposition and MDS post-cytotoxic therapy (MDS-pCT) etiologies. However, since these risk factors are not exclusive for secondary MDSs and there are multiple overlapping scenarios, a comprehensive and definitive classification is yet to come. In addition, a sporadic MDS might arise after a primary tumor fulfills the diagnostic criteria of MDS-pCT without a causative cytotoxicity. In this review, we describe the triggering pieces of a secondary MDS jigsaw: previous cytotoxic therapy, germline predisposition and clonal hematopoiesis. Epidemiological and translational efforts are needed to put these pieces together and ascertain the real weight of each of these pieces in each MDS patient. Future classifications must contribute to understanding the role of secondary MDS jigsaw pieces in different concomitant or independent clinical scenarios associated with the primary tumor.
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19
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Chi KN, Barnicle A, Sibilla C, Lai Z, Corcoran C, Barrett JC, Adelman CA, Qiu P, Easter A, Dearden S, Oxnard GR, Agarwal N, Azad A, de Bono J, Mateo J, Olmos D, Thiery-Vuillemin A, Harrington EA. Detection of BRCA1, BRCA2, and ATM Alterations in Matched Tumor Tissue and Circulating Tumor DNA in Patients with Prostate Cancer Screened in PROfound. Clin Cancer Res 2023; 29:81-91. [PMID: 36043882 PMCID: PMC9811161 DOI: 10.1158/1078-0432.ccr-22-0931] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/01/2022] [Accepted: 08/15/2022] [Indexed: 02/06/2023]
Abstract
PURPOSE Not all patients with metastatic castration-resistant prostate cancer (mCRPC) have sufficient tumor tissue available for multigene molecular testing. Furthermore, samples may fail because of difficulties within the testing procedure. Optimization of screening techniques may reduce failure rates; however, a need remains for additional testing methods to detect cancers with alterations in homologous recombination repair genes. We evaluated the utility of plasma-derived circulating tumor DNA (ctDNA) in identifying deleterious BRCA1, BRCA2 (BRCA), and ATM alterations in screened patients with mCRPC from the phase III PROfound study. PATIENTS AND METHODS Tumor tissue samples were sequenced prospectively at Foundation Medicine, Inc. (FMI) using an investigational next-generation sequencing (NGS) assay based on FoundationOne®CDx to inform trial eligibility. Matched ctDNA samples were retrospectively sequenced at FMI, using an investigational assay based on FoundationOne®Liquid CDx. RESULTS 81% (503/619) of ctDNA samples yielded an NGS result, of which 491 had a tumor tissue result. BRCA and ATM status in tissue compared with ctDNA showed 81% positive percentage agreement and 92% negative percentage agreement, using tissue as reference. At variant-subtype level, using tissue as reference, concordance was high for nonsense (93%), splice (87%), and frameshift (86%) alterations but lower for large rearrangements (63%) and homozygous deletions (27%), with low ctDNA fraction being a limiting factor. CONCLUSIONS We demonstrate that ctDNA can greatly complement tissue testing in identifying patients with mCRPC and BRCA or ATM alterations who are potentially suitable for receiving targeted PARP inhibitor treatments, particularly patients with no or insufficient tissue for genomic analyses.
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Affiliation(s)
- Kim N. Chi
- BC Cancer Agency, Vancouver, Canada
- Corresponding Author: Kim N. Chi, University of British Columbia Chief Medical Officer, BC Cancer, 686 West Broadway, Vancouver, British Columbia, V5Z 1G1 Canada. Phone: 604-877-6000; Fax: 604-877-0585; E-mail:
| | - Alan Barnicle
- Translational Medicine, AstraZeneca, Cambridge, United Kingdom
| | - Caroline Sibilla
- Precision Medicine and Biosamples, AstraZeneca, Cambridge, United Kingdom
| | - Zhongwu Lai
- Translational Medicine, AstraZeneca, Waltham, Massachusetts
| | - Claire Corcoran
- Precision Medicine and Biosamples, AstraZeneca, Cambridge, United Kingdom
| | | | | | - Ping Qiu
- Merck & Co., Inc., Rahway, New Jersey
| | - Ashley Easter
- Oncology Business Unit, AstraZeneca, Cambridge, United Kingdom
| | - Simon Dearden
- Precision Medicine and Biosamples, AstraZeneca, Cambridge, United Kingdom
| | | | - Neeraj Agarwal
- Huntsman Cancer Institute, University of Utah (NCI-CCC), Salt Lake City, Utah
| | - Arun Azad
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Johann de Bono
- The Institute of Cancer Research and The Royal Marsden, London, United Kingdom
| | - Joaquin Mateo
- Vall d'Hebron Institute of Oncology and Vall d'Hebron University Hospital, Barcelona, Spain
| | - David Olmos
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
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20
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Aukema SM, Glaser S, van den Hout MFCM, Dahlum S, Blok MJ, Hillmer M, Kolarova J, Sciot R, Schott DA, Siebert R, Stumpel CTRM. Molecular characterization of an embryonal rhabdomyosarcoma occurring in a patient with Kabuki syndrome: report and literature review in the light of tumor predisposition syndromes. Fam Cancer 2023; 22:103-118. [PMID: 35856126 PMCID: PMC9829644 DOI: 10.1007/s10689-022-00306-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/05/2022] [Indexed: 01/13/2023]
Abstract
Kabuki syndrome is a well-recognized syndrome characterized by facial dysmorphism and developmental delay/intellectual disability and in the majority of patients a germline variant in KMT2D is found. As somatic KMT2D variants can be found in 5-10% of tumors a tumor predisposition in Kabuki syndrome is discussed. So far less than 20 patients with Kabuki syndrome and a concomitant malignancy have been published. Here we report on a female patient with Kabuki syndrome and a c.2558_2559delCT germline variant in KMT2D who developed an embryonal rhabdomyosarcoma (ERMS) at 10 years. On tumor tissue we performed DNA-methylation profiling and exome sequencing (ES). Copy number analyses revealed aneuploidies typical for ERMS including (partial) gains of chromosomes 2, 3, 7, 8, 12, 15, and 20 and 3 focal deletions of chromosome 11p. DNA methylation profiling mapped the case to ERMS by a DNA methylation-based sarcoma classifier. Sequencing suggested gain of the wild-type KMT2D allele in the trisomy 12. Including our patient literature review identified 18 patients with Kabuki syndrome and a malignancy. Overall, the landscape of malignancies in patients with Kabuki syndrome was reminiscent of that of the pediatric population in general. Histopathological and molecular data were only infrequently reported and no report included next generation sequencing and/or DNA-methylation profiling. Although we found no strong arguments pointing towards KS as a tumor predisposition syndrome, based on the small numbers any relation cannot be fully excluded. Further planned studies including profiling of additional tumors and long term follow-up of KS-patients into adulthood could provide further insights.
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Affiliation(s)
- Sietse M Aukema
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands.
| | - Selina Glaser
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Mari F C M van den Hout
- Department of Pathology, Research Institute GROW, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sonja Dahlum
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Morten Hillmer
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Julia Kolarova
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Raf Sciot
- Department of Pathology, University Hospital, University of Leuven, 3000, Louvain, Belgium
| | - Dina A Schott
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands
- Department of Pediatrics, Zuyderland Medical Center, Heerlen, The Netherlands
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Constance T R M Stumpel
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands.
- Department of Clinical Genetics and GROW-School for Oncology & Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands.
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21
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Huber S, Haferlach T, Meggendorfer M, Hutter S, Hoermann G, Summerer I, Fuhrmann I, Baer C, Kern W, Haferlach C. Mutations in spliceosome genes in myelodysplastic neoplasms and their association to ring sideroblasts. Leukemia 2023; 37:500-502. [PMID: 36463343 PMCID: PMC9898028 DOI: 10.1038/s41375-022-01783-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/07/2022]
Affiliation(s)
- Sandra Huber
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Torsten Haferlach
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Manja Meggendorfer
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Stephan Hutter
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Gregor Hoermann
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Isolde Summerer
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Irene Fuhrmann
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Constance Baer
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Wolfgang Kern
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
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22
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Xu JJ, Chalk AM, Wall M, Langdon WY, Smeets MF, Walkley CR. Srsf2 P95H/+ co-operates with loss of TET2 to promote myeloid bias and initiate a chronic myelomonocytic leukemia-like disease in mice. Leukemia 2022; 36:2883-2893. [PMID: 36271153 DOI: 10.1038/s41375-022-01727-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022]
Abstract
Recurrent mutations in RNA splicing proteins and epigenetic regulators contribute to the development of myelodysplastic syndrome (MDS) and related myeloid neoplasms. In chronic myelomonocytic leukemia (CMML), SRSF2 mutations occur in ~50% of patients and TET2 mutations in ~60%. Clonal analysis indicates that either mutation can arise as the founder lesion. Based on human cancer genetics we crossed an inducible Srsf2P95H/+ mutant model with Tet2fl/fl mice to mutate both concomitantly in hematopoietic stem cells. At 20-24 weeks post mutation induction, we observed subtle differences in the Srsf2/Tet2 mutants compared to either single mutant. Under conditions of native hematopoiesis with aging, we see a distinct myeloid bias and monocytosis in the Srsf2/Tet2 mutants. A subset of the compound Srsf2/Tet2 mutants display an increased granulocytic and distinctive monocytic proliferation (myelomonocytic hyperplasia), with increased immature promonocytes and monoblasts and binucleate promonocytes. Exome analysis of progressed disease demonstrated mutations in genes and pathways similar to those reported in human CMML. Upon transplantation, recipients developed leukocytosis, monocytosis, and splenomegaly. We reproduce Srsf2/Tet2 co-operativity in vivo, yielding a disease with core characteristics of CMML, unlike single Srsf2 or Tet2 mutation. This model represents a significant step toward building high fidelity and genetically tractable models of CMML.
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Affiliation(s)
- Jane Jialu Xu
- St Vincent's Institute, Fitzroy, VIC, 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC, 3065, Australia
- Columbia Stem Cell Initiative, Columbia University Irving Medical Centre, New York City, NY, 10032, USA
| | - Alistair M Chalk
- St Vincent's Institute, Fitzroy, VIC, 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Meaghan Wall
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia
| | - Wallace Y Langdon
- School of Biomedical Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Monique F Smeets
- St Vincent's Institute, Fitzroy, VIC, 3065, Australia.
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC, 3065, Australia.
| | - Carl R Walkley
- St Vincent's Institute, Fitzroy, VIC, 3065, Australia.
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC, 3065, Australia.
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23
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Huber S, Haferlach T, Meggendorfer M, Hutter S, Hoermann G, Baer C, Kern W, Haferlach C. SF3B1 mutated MDS: Blast count, genetic co-abnormalities and their impact on classification and prognosis. Leukemia 2022; 36:2894-2902. [PMID: 36261576 PMCID: PMC9712089 DOI: 10.1038/s41375-022-01728-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022]
Abstract
Recently, MDS with mutated SF3B1 and blast count <5% was proposed as distinct entity with favorable prognosis by the international working group for the prognosis of MDS (IWG-PM), the 5th edition of the WHO classification and the International Consensus Classification. To further characterize this entity with respect to the genomic landscape, AML transformation rate and clinical outcome, we analyzed 734 MDS patients by whole genome sequencing. SF3B1 mutations were identified in 31% (n = 231), most frequently accompanied by TET2 mutations (29%). 144/231 (62%) SF3B1mut samples fulfilled entity criteria proposed by IWG-PM (SF3B1ent). These cases were associated with longer survival, lower AML transformation rate, normal karyotypes and harbored less accompanying mutations compared to SF3B1mut samples not falling into the proposed SF3B1 entity (SF3B1nent). Of SF3B1mut cases 7% (15/231; SF3B1ent: 3/144 [2%]; SF3B1nent: 12/87 [14%]) progressed to AML compared to 15% SF3B1 wild-type patients (75/503). Of these 15 SF3B1mut cases, 10 (67%) showed RUNX1 mutations at MDS or AML stage. Multivariate analysis revealed that del(5q) and RUNX1 mutations were independent negative prognostic factors for overall survival, while blast count >5% was not. In conclusion, SF3B1mut MDS has a favorable prognosis independent of blast count if karyotype and RUNX1 mutations are considered.
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Affiliation(s)
- Sandra Huber
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Stephan Hutter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Gregor Hoermann
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Constance Baer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
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24
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Renosi F, Callanan M, Lefebvre C. Genetics and Epigenetics in Neoplasms with Plasmacytoid Dendritic Cells. Cancers (Basel) 2022; 14:cancers14174132. [PMID: 36077669 PMCID: PMC9454802 DOI: 10.3390/cancers14174132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Differential diagnosis between Blastic pDC Neoplasm (BPDCN) and Acute Myeloid Leukemia with pDC expansion (pDC-AML) is particularly challenging, and genomic features can help in diagnosis. This review aims at clarifying recent data on genomics features because the past five years have generated a large amount of original data regarding pDC neoplasms. The genetic landscape of BPDCN is now well-defined, with important updates concerning MYC/MYC rearrangements, but also epigenetic defects and novel concepts in oncogenic and immune pathways. Concerning pDC-AML, they now appear to exhibit an original mutation landscape, especially with RUNX1 mutations, which is of interest for diagnostic criteria and for therapeutic purposes. We highlight here these two different profiles, which contribute to differential diagnosis between BPDCN and pDC-AML. This point is particularly important for the study of different therapeutic strategies between BPDCN and AML. Abstract Plasmacytoid Dendritic Cells (pDC) are type I interferon (IFN)-producing cells that play a key role in immune responses. Two major types of neoplastic counterparts for pDC are now discriminated: Blastic pDC Neoplasm (BPDCN) and Mature pDC Proliferation (MPDCP), associated with myeloid neoplasm. Two types of MPDCP are now better described: Chronic MyeloMonocytic Leukemia with pDC expansion (pDC-CMML) and Acute Myeloid Leukemia with pDC expansion (pDC-AML). Differential diagnosis between pDC-AML and BPDCN is particularly challenging, and genomic features can help for diagnosis. Here, we systematically review the cytogenetic, molecular, and transcriptional characteristics of BPDCN and pDC-AML. BPDCN are characterized by frequent complex karyotypes with recurrent MYB/MYC rearrangements as well as recurrent deletions involving ETV6, IKZF1, RB1, and TP53 loci. Epigenetic and splicing pathways are also particularly mutated, while original processes are dysregulated, such as NF-kB, TCF4, BCL2, and IFN pathways; neutrophil-specific receptors; and cholinergic signaling. In contrast, cytogenetic abnormalities are limited in pDC-AML and are quite similar to other AML. Interestingly, RUNX1 is the most frequently mutated gene (70% of cases). These typical genomic features are of potential interest for diagnosis, and also from a prognostic or therapeutic perspective.
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Affiliation(s)
- Florian Renosi
- INSERM, EFS BFC, UMR1098 RIGHT, University of Bourgogne Franche-Comté, F-25000 Besancon, France
- Laboratoire d’Hématologie et d’Immunologie Régional, Etablissement Français du Sang Bourgogne Franche-Comté, F-25000 Besancon, France
- Correspondence:
| | - Mary Callanan
- INSERM 1231 and 1209, University of Bourgogne-Franche Comté, F-21000 Dijon, France
- Service d’Oncologie Génétique, CHU Dijon Bourgogne, F-21000 Dijon, France
| | - Christine Lefebvre
- INSERM 1209 and CNRS UMR 5309, Université Grenoble-Alpes, F-38000 Grenoble, France
- Laboratoire de Génétique des hémopathies, Institut de Biologie et de Pathologie, CHU Grenoble Alpes, F-38000 Grenoble, France
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25
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Molecular Pathways in Clonal Hematopoiesis: From the Acquisition of Somatic Mutations to Transformation into Hematologic Neoplasm. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081135. [PMID: 36013314 PMCID: PMC9410004 DOI: 10.3390/life12081135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022]
Abstract
Hematopoietic stem cell aging, through the acquisition of somatic mutations, gives rise to clonal hematopoiesis (CH). While a high prevalence of CH has been described in otherwise healthy older adults, CH confers an increased risk of both hematologic and non-hematologic diseases. Classification of CH into clonal hematopoiesis of indeterminate potential (CHIP) and clonal cytopenia of undetermined significance (CCUS) further describes this neoplastic myeloid precursor state and stratifies individuals at risk of developing clinically significant complications. The sequential acquisition of driver mutations, such as DNMT3A, TET2, and ASXL1, provide a selective advantage and lead to clonal expansion. Inflammation, microbiome signatures, and external selective pressures also contribute to clonal evolution. Despite significant progress in recent years, the precise molecular mechanisms driving CH transformation to hematologic neoplasms are not well defined. Further understanding of these complex mechanisms may improve risk stratification and introduce therapeutic interventions in CH. Here we discuss the genetic drivers underpinning CH, mechanisms for clonal evolution, and transformation to hematologic neoplasm.
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26
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Fei F, Natkunam Y, Zehnder JL, Stehr H, Gratzinger D. Diagnostic Impact of Next-Generation Sequencing Panels for Lymphoproliferative Neoplasms on Small-Volume Biopsies. Am J Clin Pathol 2022; 158:345-361. [PMID: 35552630 DOI: 10.1093/ajcp/aqac045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES We investigated the feasibility and utility of next-generation sequencing (NGS)-based targeted somatic mutation panels and IG/TR gene rearrangement assays in the diagnosis of lymphoproliferative disorders (LPDs) in small-volume biopsies. MATERIALS We performed a retrospective, single-institution review of all NGS assays requested over a 3-year period by hematopathologists for diagnostic purposes on small-volume biopsies. RESULTS We identified 59 small-volume biopsies. The TR assay was most commonly requested (42 [71%]), followed by the somatic mutation panel (32 [54%]) and IG assay (26 [44%]). NGS studies were associated with a change in the diagnostic line in about half of cases (28 [47%]) and in a change in the likelihood of a diagnosis in a further 16 cases (27%); there was no diagnostic impact of NGS testing in 15 cases (25%). CONCLUSIONS Implementation of NGS panel somatic mutation or IG/TR gene rearrangement assays on small-volume biopsies contributes to the diagnosis of LPDs in the majority of select cases for diagnostic purposes. The molecular diagnosis is considered in the context of the clinical, histologic, and immunophenotypic findings and does not by itself lead to a definitive diagnosis in small-volume biopsies.
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Affiliation(s)
- Fei Fei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yasodha Natkunam
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dita Gratzinger
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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27
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Watt SM, Hua P, Roberts I. Increasing Complexity of Molecular Landscapes in Human Hematopoietic Stem and Progenitor Cells during Development and Aging. Int J Mol Sci 2022; 23:ijms23073675. [PMID: 35409034 PMCID: PMC8999121 DOI: 10.3390/ijms23073675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
The past five decades have seen significant progress in our understanding of human hematopoiesis. This has in part been due to the unprecedented development of advanced technologies, which have allowed the identification and characterization of rare subsets of human hematopoietic stem and progenitor cells and their lineage trajectories from embryonic through to adult life. Additionally, surrogate in vitro and in vivo models, although not fully recapitulating human hematopoiesis, have spurred on these scientific advances. These approaches have heightened our knowledge of hematological disorders and diseases and have led to their improved diagnosis and therapies. Here, we review human hematopoiesis at each end of the age spectrum, during embryonic and fetal development and on aging, providing exemplars of recent progress in deciphering the increasingly complex cellular and molecular hematopoietic landscapes in health and disease. This review concludes by highlighting links between chronic inflammation and metabolic and epigenetic changes associated with aging and in the development of clonal hematopoiesis.
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Affiliation(s)
- Suzanne M. Watt
- Stem Cell Research, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9BQ, UK
- Myeloma Research Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, North Terrace, Adelaide 5005, Australia
- Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide 5001, Australia
- Correspondence: or ; Tel.: +61-403-393-755
| | - Peng Hua
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China;
| | - Irene Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, and NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK;
- Department of Paediatrics and NIHR Oxford Biomedical Research Centre Haematology Theme, University of Oxford, Oxford OX3 9DU, UK
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28
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Visconte V, Maciejewski JP. Clonal dynamics of hematopoietic stem cell compartment in aplastic anemia. Semin Hematol 2022; 59:47-53. [DOI: 10.1053/j.seminhematol.2021.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 11/11/2022]
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29
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Camacho V, Kuznetsova V, Welner RS. Inflammatory Cytokines Shape an Altered Immune Response During Myeloid Malignancies. Front Immunol 2021; 12:772408. [PMID: 34804065 PMCID: PMC8595317 DOI: 10.3389/fimmu.2021.772408] [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: 09/08/2021] [Accepted: 10/19/2021] [Indexed: 12/14/2022] Open
Abstract
The immune microenvironment is a critical driver and regulator of leukemic progression and hematological disease. Recent investigations have demonstrated that multiple immune components play a central role in regulating hematopoiesis, and dysfunction at the immune cell level significantly contributes to neoplastic disease. Immune cells are acutely sensitive to remodeling by leukemic inflammatory cytokine exposure. Importantly, immune cells are the principal cytokine producers in the hematopoietic system, representing an untapped frontier for clinical interventions. Due to a proinflammatory cytokine environment, dysregulation of immune cell states is a hallmark of hematological disease and neoplasia. Malignant immune adaptations have profound effects on leukemic blast proliferation, disease propagation, and drug-resistance. Conversely, targeting the immune landscape to restore hematopoietic function and limit leukemic expansion may have significant therapeutic value. Despite the fundamental role of the immune microenvironment during the initiation, progression, and treatment response of hematological disease, a detailed examination of how leukemic cytokines alter immune cells to permit, promote, or inhibit leukemia growth is lacking. Here we outline an immune-based model of leukemic transformation and highlight how the profound effect of immune alterations on the trajectory of malignancy. The focus of this review is to summarize current knowledge about the impacts of pro- and anti-inflammatory cytokines on immune cells subsets, their modes of action, and immunotherapeutic approaches with the potential to improve clinical outcomes for patients suffering from hematological myeloid malignancies.
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Affiliation(s)
- Virginia Camacho
- Department of Medicine, Division of Hematology/Oncology, O'Neal Comprehensive Cancer Center at the University of Alabama at Birmingham, Birmingham, AL, United States
| | - Valeriya Kuznetsova
- Department of Medicine, Division of Hematology/Oncology, O'Neal Comprehensive Cancer Center at the University of Alabama at Birmingham, Birmingham, AL, United States
| | - Robert S Welner
- Department of Medicine, Division of Hematology/Oncology, O'Neal Comprehensive Cancer Center at the University of Alabama at Birmingham, Birmingham, AL, United States
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