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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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Szuber N, Orazi A, Tefferi A. Chronic neutrophilic leukemia and atypical chronic myeloid leukemia: 2024 update on diagnosis, genetics, risk stratification, and management. Am J Hematol 2024; 99:1360-1387. [PMID: 38644693 DOI: 10.1002/ajh.27321] [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: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/23/2024]
Abstract
Chronic neutrophilic leukemia (CNL) is a rare BCR::ABL1-negative myeloproliferative neoplasm (MPN) defined by persistent mature neutrophilic leukocytosis and bone marrow granulocyte hyperplasia. Atypical chronic myeloid leukemia (aCML) (myelodysplastic "[MDS]/MPN with neutrophilia" per World Health Organization [WHO]) is a MDS/MPN overlap disorder featuring dysplastic neutrophilia and circulating myeloid precursors. Both manifest with frequent hepatosplenomegaly and less commonly, bleeding, with high rates of leukemic transformation and death. The 2022 revised WHO classification conserved CNL diagnostic criteria of leukocytosis ≥25 × 109/L, neutrophils ≥80% with <10% circulating precursors, absence of dysplasia, and presence of an activating CSF3R mutation. ICC criteria are harmonized with those of other myeloid entities, with a key distinction being lower leukocytosis threshold (≥13 × 109/L) for cases CSF3R-mutated. Criteria for aCML include leukocytosis ≥13 × 109/L, dysgranulopoiesis, circulating myeloid precursors ≥10%, and at least one cytopenia for MDS-thresholds (ICC). In both classifications ASXL1 and SETBP1 (ICC), or SETBP1 ± ETNK1 (WHO) mutations can be used to support the diagnosis. Both diseases show hypercellular bone marrow due to a granulocytic proliferation, aCML distinguished by dysplasia in granulocytes ± other lineages. Absence of monocytosis, rare/no basophilia, or eosinophilia, <20% blasts, and exclusion of other MPN, MDS/MPN, and tyrosine kinase fusions, are mandated. Cytogenetic abnormalities are identified in ~1/3 of CNL and ~15-40% of aCML patients. The molecular signature of CNL is a driver mutation in colony-stimulating factor 3 receptor-classically T618I, documented in >80% of cases. Atypical CML harbors a complex genomic backdrop with high rates of recurrent somatic mutations in ASXL1, SETBP1, TET2, SRSF2, EZH2, and less frequently in ETNK1. Leukemic transformation rates are ~10-25% and 30-40% for CNL and aCML, respectively. Overall survival is poor: 15-31 months in CNL and 12-20 months in aCML. The Mayo Clinic CNL risk model for survival stratifies patients according to platelets <160 × 109/L (2 points), leukocytes >60 × 109/L (1 point), and ASXL1 mutation (1 point); distinguishing low- (0-1 points) versus high-risk (2-4 points) categories. The Mayo Clinic aCML risk model attributes 1 point each for: age >67 years, hemoglobin <10 g/dL, and TET2 mutation, delineating low- (0-1 risk factor) and high-risk (≥2 risk factors) subgroups. Management is risk-driven and symptom-directed, with no current standard of care. Most commonly used agents include hydroxyurea, interferon, Janus kinase inhibitors, and hypomethylating agents, though none are disease-modifying. Hematopoietic stem cell transplant is the only potentially curative modality and should be considered in eligible patients. Recent genetic profiling has disclosed CBL, CEBPA, EZH2, NRAS, TET2, and U2AF1 to represent high-risk mutations in both entities. Actionable mutations (NRAS/KRAS, ETNK1) have also been identified, supporting novel agents targeting involved pathways. Preclinical and clinical studies evaluating new drugs (e.g., fedratinib, phase 2) and combinations are detailed.
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MESH Headings
- Humans
- Leukemia, Neutrophilic, Chronic/genetics
- Leukemia, Neutrophilic, Chronic/diagnosis
- Leukemia, Neutrophilic, Chronic/therapy
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/genetics
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/diagnosis
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/therapy
- Mutation
- Risk Assessment
- Receptors, Colony-Stimulating Factor/genetics
- Carrier Proteins
- Nuclear Proteins
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Affiliation(s)
- Natasha Szuber
- Department of Hematology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
| | - Attilio Orazi
- Department of Pathology, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Ayalew Tefferi
- Department of Internal Medicine, Division of Hematology, Mayo Clinic, Rochester, Minnesota, USA
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3
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Sadigh S, Kim AS. Molecular Pathology of Myeloid Neoplasms: Molecular Pattern Recognition. Clin Lab Med 2024; 44:339-353. [PMID: 38821648 DOI: 10.1016/j.cll.2023.08.007] [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] [Indexed: 06/02/2024]
Abstract
Despite the apparent complexity of the molecular genetic underpinnings of myeloid neoplasms, most myeloid mutational profiles can be understood within a simple framework. Somatic mutations accumulate in hematopoietic stem cells with aging and toxic insults, termed clonal hematopoiesis. These "old stem cells" mutations, predominantly in the epigenetic and RNA spliceosome pathways, act as "founding" driver mutations leading to a clonal myeloid neoplasm when sufficient in number and clone size. Subsequent mutations can create the genetic flavor of the myeloid neoplasm ("backseat" drivers) due to their enrichment in certain entities or act as progression events ("aggressive" drivers) during clonal evolution.
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Affiliation(s)
- Sam Sadigh
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
| | - Annette S Kim
- Division of Diagnostic Genetics and Genomics, Department of Pathology, University of Michigan/Michigan Medicine, 2800 Plymouth Road, NCRC 36-1221-79, Ann Arbor, MI 48109, USA.
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4
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Zheng J, Gu M, Xiao S, Li C, Mi H, Xu X. Novel SETBP1 D874V adjacent to the degron causes canonical schinzel-giedion syndrome: a case report and review of the literature. BMC Pediatr 2024; 24:309. [PMID: 38711130 DOI: 10.1186/s12887-024-04779-y] [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: 11/01/2023] [Accepted: 04/22/2024] [Indexed: 05/08/2024] Open
Abstract
Schinzel-Giedion syndrome (SGS) is a severe multisystem disorder characterized by distinctive facial features, profound intellectual disability, refractory epilepsy, cortical visual impairment, hearing loss, and various congenital anomalies. SGS is attributed to gain-of-function (GoF) variants in the SETBP1 gene, with reported variants causing canonical SGS located within a 12 bp hotspot region encoding SETBP1 residues aa868-871 (degron). Here, we describe a case of typical SGS caused by a novel heterozygous missense variant, D874V, adjacent to the degron. The female patient was diagnosed in the neonatal period and presented with characteristic facial phenotype (midface retraction, prominent forehead, and low-set ears), bilateral symmetrical talipes equinovarus, overlapping toes, and severe bilateral hydronephrosis accompanied by congenital heart disease, consistent with canonical SGS. This is the first report of a typical SGS caused by a, SETBP1 non-degron missense variant. This case expands the genetic spectrum of SGS and provides new insights into genotype-phenotype correlations.
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Affiliation(s)
- Jing Zheng
- Department of Pediatrics, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan Province, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Meiqun Gu
- Department of Pediatrics, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan Province, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Shasha Xiao
- Department of Pediatrics, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan Province, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Chongzhen Li
- Department of Pediatrics, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan Province, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Hongying Mi
- Department of Pediatrics, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan Province, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Xiaoyan Xu
- Department of Pediatrics, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan Province, China.
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China.
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Crespiatico I, Zaghi M, Mastini C, D'Aliberti D, Mauri M, Mercado CM, Fontana D, Spinelli S, Crippa V, Inzoli E, Manghisi B, Civettini I, Ramazzotti D, Sangiorgio V, Gengotti M, Brambilla V, Aroldi A, Banfi F, Barone C, Orsenigo R, Riera L, Riminucci M, Corsi A, Breccia M, Morotti A, Cilloni D, Roccaro A, Sacco A, Stagno F, Serafini M, Mottadelli F, Cazzaniga G, Pagni F, Chiarle R, Azzoni E, Sessa A, Gambacorti-Passerini C, Elli EM, Mologni L, Piazza R. First-hit SETBP1 mutations cause a myeloproliferative disorder with bone marrow fibrosis. Blood 2024; 143:1399-1413. [PMID: 38194688 DOI: 10.1182/blood.2023021349] [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: 06/20/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024] Open
Abstract
ABSTRACT SETBP1 mutations are found in various clonal myeloid disorders. However, it is unclear whether they can initiate leukemia, because SETBP1 mutations typically appear as later events during oncogenesis. To answer this question, we generated a mouse model expressing mutated SETBP1 in hematopoietic tissue: this model showed profound alterations in the differentiation program of hematopoietic progenitors and developed a myeloid neoplasm with megakaryocytic dysplasia, splenomegaly, and bone marrow fibrosis, prompting us to investigate SETBP1 mutations in a cohort of 36 triple-negative primary myelofibrosis (TN-PMF) cases. We identified 2 distinct subgroups, one carrying SETBP1 mutations and the other completely devoid of somatic variants. Clinically, a striking difference in disease aggressiveness was noted, with patients with SETBP1 mutation showing a much worse clinical course. In contrast to myelodysplastic/myeloproliferative neoplasms, in which SETBP1 mutations are mostly found as a late clonal event, single-cell clonal hierarchy reconstruction in 3 patients with TN-PMF from our cohort revealed SETBP1 to be a very early event, suggesting that the phenotype of the different SETBP1+ disorders may be shaped by the opposite hierarchy of the same clonal SETBP1 variants.
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Affiliation(s)
- Ilaria Crespiatico
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Mattia Zaghi
- Neuroepigenetics Unit, Division of Neuroscience, Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele Scientific Institute, Milan, Italy
| | - Cristina Mastini
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Deborah D'Aliberti
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Mario Mauri
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Carl Mirko Mercado
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Diletta Fontana
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Silvia Spinelli
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Valentina Crippa
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Elena Inzoli
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Beatrice Manghisi
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Ivan Civettini
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Valentina Sangiorgio
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Michele Gengotti
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | | | - Andrea Aroldi
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Federica Banfi
- Neuroepigenetics Unit, Division of Neuroscience, Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele Scientific Institute, Milan, Italy
| | - Cristiana Barone
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Roberto Orsenigo
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Vall d'Hebron Research Institute, Vall d'Hebron Hospital Barcelona UAB, Barcelona, Spain
| | - Ludovica Riera
- Department of Pathology, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Mara Riminucci
- Department of Molecular Medicine, Azienda Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | - Alessandro Corsi
- Department of Molecular Medicine, Azienda Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | - Massimo Breccia
- Department of Translational and Precision Medicine, Azienda Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | - Alessandro Morotti
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Turin, Italy
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Turin, Italy
| | - Aldo Roccaro
- Clinical Trial Center, Translational Research and Phase I Unit, Azienda Socio Sanitaria Territoriale Spedali Civili di Brescia, Brescia, Italy
| | - Antonio Sacco
- Clinical Trial Center, Translational Research and Phase I Unit, Azienda Socio Sanitaria Territoriale Spedali Civili di Brescia, Brescia, Italy
| | - Fabio Stagno
- Division of Hematology, Azienda Ospedaliero Universitaria Policlinico G. Rodolico-S. Marco, Catania, Italy
| | - Marta Serafini
- Centro Tettamanti, Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Federica Mottadelli
- Centro Tettamanti, Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Giovanni Cazzaniga
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
- Centro Tettamanti, Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Fabio Pagni
- Department of Pathology, University of Milan-Bicocca, Monza, Italy
| | - Roberto Chiarle
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Italy
- Department of Pathology, Children's Hospital and Harvard Medical School, Boston, MA
- European Institute of Oncology Istituto di Ricovero e Cura a Carattere Scientifico, Division of Haematopathology, Milan, Italy
| | - Emanuele Azzoni
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Alessandro Sessa
- Neuroepigenetics Unit, Division of Neuroscience, Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele Scientific Institute, Milan, Italy
| | - Carlo Gambacorti-Passerini
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Elena Maria Elli
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
| | - Luca Mologni
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
- Hematology Division and Bone Marrow Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo dei Tintori, Monza, Italy
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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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7
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Miolo G, Colavito D, Della Puppa L, Corona G. Delayed Bone Age in a Child with a Novel Loss-of-Function Variant in SETBP1 Gene Sheds Light on the Potential Role of SETBP1 Protein in Skeletal Development. Mol Syndromol 2024; 15:167-174. [PMID: 38585550 PMCID: PMC10996347 DOI: 10.1159/000535057] [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: 04/03/2023] [Accepted: 11/06/2023] [Indexed: 04/09/2024] Open
Abstract
Introduction SETBP1 gene variants that decrease or eliminate protein activity have been associated with phenotypes characterized by speech apraxia and intellectual disabilities. This condition, distinctly separated from Schinzel-Giedion syndrome, is referred to as autosomal dominant mental retardation 29 (ADR29). Case Presentation In this report, we present the case of a 6-year-old male patient exhibiting fine and global motor skill impairments along with expressive language delay. The patient carried a novel germline, heterozygous, de novo nonsense variant in the SETBP1 gene, specifically the c.532C>T variant, which prematurely terminates protein translation at amino acid 178, p.(Gln178*), and removes more than 10% of the reference protein isoform consisting of 1,596 amino acids. According to the American College of Medical Genetics and Genomics (ACMG) guidelines, this variant has been classified as pathogenic. Conclusion Given the limited number of ADR29 cases reported to date, it is critical to focus attention on the phenotypic features of each new individual and seek out previously undocumented defects. The clinical findings found in our patient align with current knowledge on the correlation between the genotypes characterized by loss-of-function variants in SETBP1 gene and a particular neurological phenotype. Furthermore, the presence of a severely delayed bone age in this patient, which we report for the first time, could indicate a possible indirect but significant contribution of the SETBP1 protein in bone development and maturation processes. This finding highlights the need for further investigation into the potential effects of SETBP1 gene variants on bone health and the possible involvement of the SETBP1 protein in skeletal growth and development.
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Affiliation(s)
- Gianmaria Miolo
- Medical Oncology and Cancer Prevention Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
- Department of Medical Laboratory, Genetics Section, Pordenone Hospital, Pordenone, Italy
| | | | - Lara Della Puppa
- Oncogenetics and Functional Oncogenomics Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Giuseppe Corona
- Immunopathology and Cancer Biomarkers Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
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8
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Liu L, Song X, Dong W, Li Z, Guo D. Case report: Safety and efficacy of synergistic treatment using selinexor and azacitidine in patients with atypical chronic myeloid leukemia with resistance to decitabine. Front Oncol 2024; 14:1353818. [PMID: 38384813 PMCID: PMC10879427 DOI: 10.3389/fonc.2024.1353818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
Background Atypical chronic myeloid leukemia (aCML) is a BCR::ABL1 negative myelodysplastic/myeloproliferative neoplasm with poor overall survival. Some patients can be treated by allogeneic hematopoietic stem cell transplantation (allo-HSCT) from suitable donors. The effectiveness of decitabine or azacitidine (AZA) has recently been reported; however, their combined efficacy with selinexor has not yet been reported. Case description In this study, we report the case of a patient with aCML who was successfully treated with selinexor combined with AZA. A 67-year-old man with a history of gastric mucosa-associated lymphoid tissue (MALT) lymphoma was admitted to the hospital with fatigue and emaciation. He was diagnosed with aCML and no longer responded to decitabine treatment after undergoing seven cycles. The patient was subsequently administered hydroxyurea (HU), selinexor, and AZA. After four courses of combination therapy, his blood cell counts improved; he no longer required transfusions and was able to discontinue HU. The patient continued receiving selinexor and AZA without severe complications. This case is the first to show that combinatorial selinexor and AZA therapy can effectively treat aCML. Conclusion Our case sheds light on the importance of selinexor and AZA combined therapy in the exploration of new treatment strategies for aCML. Moreover, this treatment approach offers the possibility of bridging with allo-HSCT.
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Affiliation(s)
- Lu Liu
- Department of Hematology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Xiaofeng Song
- Department of Hand and Foot Surgery, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Wenhao Dong
- Department of Hematology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Zhao Li
- Department of Hematology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Dongmei Guo
- Department of Hematology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
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9
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Elli EM, Mauri M, D'Aliberti D, Crespiatico I, Fontana D, Redaelli S, Pelucchi S, Spinelli S, Manghisi B, Cavalca F, Aroldi A, Ripamonti A, Ferrari S, Palamini S, Mottadelli F, Massimino L, Ramazzotti D, Cazzaniga G, Piperno A, Gambacorti-Passerini C, Piazza R. Idiopathic erythrocytosis: a germline disease? Clin Exp Med 2024; 24:11. [PMID: 38244120 PMCID: PMC10799805 DOI: 10.1007/s10238-023-01283-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/08/2023] [Indexed: 01/22/2024]
Abstract
Polycythemia Vera (PV) is typically caused by V617F or exon 12 JAK2 mutations. Little is known about Polycythemia cases where no JAK2 variants can be detected, and no other causes identified. This condition is defined as idiopathic erythrocytosis (IE). We evaluated clinical-laboratory parameters of a cohort of 56 IE patients and we determined their molecular profile at diagnosis with paired blood/buccal-DNA exome-sequencing coupled with a high-depth targeted OncoPanel to identify a possible underling germline or somatic cause. We demonstrated that most of our cohort (40/56: 71.4%) showed no evidence of clonal hematopoiesis, suggesting that IE is, in large part, a germline disorder. We identified 20 low mutation burden somatic variants (Variant allelic fraction, VAF, < 10%) in only 14 (25%) patients, principally involving DNMT3A and TET2. Only 2 patients presented high mutation burden somatic variants, involving DNMT3A, TET2, ASXL1 and WT1. We identified recurrent germline variants in 42 (75%) patients occurring mainly in JAK/STAT, Hypoxia and Iron metabolism pathways, among them: JAK3-V722I and HIF1A-P582S; a high fraction of patients (48.2%) resulted also mutated in homeostatic iron regulatory gene HFE-H63D or C282Y. By generating cellular models, we showed that JAK3-V722I causes activation of the JAK-STAT5 axis and upregulation of EPAS1/HIF2A, while HIF1A-P582S causes suppression of hepcidin mRNA synthesis, suggesting a major role for these variants in the onset of IE.
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Affiliation(s)
- E M Elli
- Division of Hematology and Bone Marrow Transplant Unit, Fondazione IRCCS, San Gerardo dei Tintori, Monza, Italy
| | - M Mauri
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - D D'Aliberti
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - I Crespiatico
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - D Fontana
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - S Redaelli
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - S Pelucchi
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - S Spinelli
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - B Manghisi
- Division of Hematology and Bone Marrow Transplant Unit, Fondazione IRCCS, San Gerardo dei Tintori, Monza, Italy
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - F Cavalca
- Division of Hematology and Bone Marrow Transplant Unit, Fondazione IRCCS, San Gerardo dei Tintori, Monza, Italy
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - A Aroldi
- Division of Hematology and Bone Marrow Transplant Unit, Fondazione IRCCS, San Gerardo dei Tintori, Monza, Italy
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - A Ripamonti
- Division of Hematology and Bone Marrow Transplant Unit, Fondazione IRCCS, San Gerardo dei Tintori, Monza, Italy
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - S Ferrari
- Division of Hematology and Bone Marrow Transplant Unit, Fondazione IRCCS, San Gerardo dei Tintori, Monza, Italy
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - S Palamini
- Tettamanti Research Center, IRCCS, San Gerardo dei Tintori, Monza, Italy
| | - F Mottadelli
- Monza and Brianza Foundation for the Child and his Mother (MBBM), IRCCS, San Gerardo dei Tintori, Monza, Italy
| | - L Massimino
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - D Ramazzotti
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - G Cazzaniga
- Tettamanti Research Center, IRCCS, San Gerardo dei Tintori, Monza, Italy
| | - A Piperno
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - C Gambacorti-Passerini
- Division of Hematology and Bone Marrow Transplant Unit, Fondazione IRCCS, San Gerardo dei Tintori, Monza, Italy
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - R Piazza
- Division of Hematology and Bone Marrow Transplant Unit, Fondazione IRCCS, San Gerardo dei Tintori, Monza, Italy.
- Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy.
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10
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Whitlock JH, Wilk EJ, Howton TC, Clark AD, Lasseigne BN. The landscape of SETBP1 gene expression and transcription factor activity across human tissues. PLoS One 2024; 19:e0296328. [PMID: 38165902 PMCID: PMC10760659 DOI: 10.1371/journal.pone.0296328] [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: 10/26/2023] [Accepted: 12/11/2023] [Indexed: 01/04/2024] Open
Abstract
The SET binding protein 1 (SETBP1) gene encodes a transcription factor (TF) involved in various cellular processes. Variants in SETBP1 can result in three different diseases determined by the introduction (germline vs. somatic) and location of the variant. Germline variants cause the ultra-rare pediatric Schinzel Giedion Syndrome (SGS) and SETBP1 haploinsufficiency disorder (SETBP1-HD), characterized by severe multisystemic abnormalities with neurodegeneration or a less severe brain phenotype accompanied by hypotonia and strabismus, respectively. Somatic variants in SETBP1 are associated with hematological malignancies and cancer development in other tissues in adults. To better understand the tissue-specific mechanisms involving SETBP1, we analyzed publicly available RNA-sequencing (RNA-seq) data from the Genotype-Tissue Expression (GTEx) project. We found SETBP1 and its known target genes were widely expressed across 31 adult human tissues. K-means clustering identified three distinct expression patterns of SETBP1 targets across tissues. Functional enrichment analysis (FEA) of each cluster revealed gene sets related to transcriptional regulation, DNA binding, and mitochondrial function. TF activity analysis of SETBP1 and its target TFs revealed tissue-specific TF activity, underscoring the role of tissue context-driven regulation and suggesting its impact in SETBP1-associated disease. In addition to uncovering tissue-specific molecular signatures of SETBP1 expression and TF activity, we provide a Shiny web application to facilitate exploring TF activity across human tissues for 758 TFs. This study provides insight into the landscape of SETBP1 expression and TF activity across 31 non-diseased human tissues and reveals tissue-specific expression and activity of SETBP1 and its targets. In conjunction with the web application we constructed, our framework enables researchers to generate hypotheses related to the role tissue backgrounds play with respect to gene expression and TF activity in different disease contexts.
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Affiliation(s)
- Jordan H. Whitlock
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Elizabeth J. Wilk
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Amanda D. Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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11
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Klein SK, Huls GA, Visser O, Kluin-Nelemans HC, Dinmohamed AG. Characteristics, primary treatment, and survival of MDS/MPN with neutrophilia: a population-based study. Blood Adv 2023; 7:7554-7563. [PMID: 37934881 PMCID: PMC10761362 DOI: 10.1182/bloodadvances.2023011181] [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: 07/10/2023] [Revised: 10/02/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
Myelodysplastic and myeloproliferative neoplasms (MDS/MPN) with neutrophilia, until recently called atypical chronic myeloid leukemia (aCML), being part of the MDS/MPN is a very rare disease with poor prognosis. Although emerging data reveal its cytogenetic and molecular profile, integrated survival and treatment data remain scarce. We analyzed a cohort of 347 adult patients diagnosed with MDS/MPN with neutrophilia, registered in the Netherlands Cancer Registry between 2001 and 2019. Our demographic baseline data align with other cohorts. We observed cytogenetic aberrations exclusively in patients aged >65 years, with trisomy 8 being the most common abnormality. We identified 16 distinct molecular mutations, with some patients (16/101) harboring up to 3 different mutations; ASXL1 being the most frequent one (22%). In a multivariable Cox regression analysis, only age, hemoglobin level and allogeneic hematopoietic stem cell transplant (alloHSCT) were associated with overall survival (aged >65 years; hazard ratio [HR] 1.85; P = .001 and alloHSCT HR, 0.51; P = .039). Because no other treatment modality seemed to affect survival and might cause toxicity, we propose that all patients eligible for alloHSCT should, whenever possible, receive an allogeneic transplant. It is imperative that we strive to improve outcomes for patients who are not eligible for alloHSCT. Tackling this challenge requires international collaborative efforts to conduct prospective intervention studies.
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MESH Headings
- Adult
- Humans
- Aged
- Myelodysplastic Syndromes/diagnosis
- Myelodysplastic Syndromes/therapy
- Myelodysplastic Syndromes/genetics
- Prospective Studies
- Myelodysplastic-Myeloproliferative Diseases/genetics
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/diagnosis
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/genetics
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/therapy
- Chromosome Aberrations
- Leukocytosis
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Affiliation(s)
- Saskia K. Klein
- Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gerwin A. Huls
- Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Otto Visser
- Department of Registration, Netherlands Comprehensive Cancer Organization, Utrecht, The Netherlands
| | - Hanneke C. Kluin-Nelemans
- Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Avinash G. Dinmohamed
- Department of Research and Development, Netherlands Comprehensive Cancer Organization, Utrecht, The Netherlands
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Hematology, Amsterdam UMC, Cancer Center Amsterdam, Amsterdam, The Netherlands
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12
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Szabelska-Beresewicz A, Zyprych-Walczak J, Siatkowski I, Okoniewski M. Ambiguous genes due to aligners and their impact on RNA-seq data analysis. Sci Rep 2023; 13:21770. [PMID: 38066001 PMCID: PMC10709571 DOI: 10.1038/s41598-023-41085-6] [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: 05/02/2023] [Accepted: 08/22/2023] [Indexed: 12/18/2023] Open
Abstract
The main scope of the study is ambiguous genes, i.e. genes whose expression is difficult to estimate from the data produced by next-generation sequencing technologies. We focused on the RNA sequencing (RNA-Seq) type of experiment performed on the Illumina platform. It is crucial to identify such genes and understand the cause of their difficulty, as these genes may be involved in some diseases. By giving misleading results, they could contribute to a misunderstanding of the cause of certain diseases, which could lead to inappropriate treatment. We thought that the ambiguous genes would be difficult to map because of their complex structure. So we looked at RNA-seq analysis using different mappers to find genes that would have different measurements from the aligners. We were able to identify such genes using a generalized linear model with two factors: mappers and groups introduced by the experiment. A large proportion of ambiguous genes are pseudogenes. High sequence similarity of pseudogenes to functional genes may indicate problems in alignment procedures. In addition, predictive analysis verified the performance of difficult genes in classification. The effectiveness of classifying samples into specific groups was compared, including the expression of difficult and not difficult genes as covariates. In almost all cases considered, ambiguous genes have less predictive power.
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Affiliation(s)
- Alicja Szabelska-Beresewicz
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637, Poznan, Poland
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637, Poznan, Poland.
| | - Idzi Siatkowski
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637, Poznan, Poland
| | - Michał Okoniewski
- Scientific IT Services, ETH Zurich, Weinbergstrasse 11, 8092, Zurich, Switzerland
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13
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Breccia M. Atypical CML: diagnosis and treatment. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2023; 2023:476-482. [PMID: 38066919 PMCID: PMC10727105 DOI: 10.1182/hematology.2023000448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Atypical chronic myeloid leukemia (aCML) is included in the group of myelodysplastic/myeloproliferative neoplasms by the International Consensus Classification and has been renamed as MDS/MPN with neutrophilia by the fifth edition of World Health Organization classification. It is always characterized by morphologic identification of granulocytic dysplasia with >10% circulating immature myeloid cells, 2 distinguished features that differentiate this disease among the others. Somatic mutations may help to diagnose but are not specifically pathognomonic of the disease, with the most detected including ASXL1, SETBP1, NRAS, KRAS, SRSF2, and TET2 and with low-frequency CBL, CSF3R, JAK2, and ETNK1. The genomic landscape of aCML has been recently unravelling, revealing that SETBP1 and ETNK1 are usually not ancestral but secondary events associated with disease progression. Unfortunately, until now, no consensus on risk stratification and treatment has been developed: Mayo Clinic prognostic score identified as adverse events age >67 years, hemoglobin level <10 g/dL, and TET2 mutations. Although some possible genetic markers have been identified, allogeneic transplant remains the only curative strategy.
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MESH Headings
- Humans
- Aged
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/diagnosis
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/genetics
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/therapy
- Myelodysplastic-Myeloproliferative Diseases/diagnosis
- Mutation
- Prognosis
- Disease Progression
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Affiliation(s)
- Massimo Breccia
- Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
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14
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Whitlock JH, Soelter TM, Howton TC, Wilk EJ, Oza VH, Lasseigne BN. Cell-type-specific gene expression and regulation in the cerebral cortex and kidney of atypical Setbp1 S858R Schinzel Giedion Syndrome mice. J Cell Mol Med 2023; 27:3565-3577. [PMID: 37872881 PMCID: PMC10660642 DOI: 10.1111/jcmm.18001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/27/2023] [Accepted: 10/05/2023] [Indexed: 10/25/2023] Open
Abstract
Schinzel Giedion Syndrome (SGS) is an ultra-rare autosomal dominant Mendelian disease presenting with abnormalities spanning multiple organ systems. The most notable phenotypes involve severe developmental delay, progressive brain atrophy, and drug-resistant seizures. SGS is caused by spontaneous variants in SETBP1, which encodes for the epigenetic hub SETBP1 transcription factor (TF). SETBP1 variants causing classical SGS cluster at the degron, disrupting SETBP1 protein degradation and resulting in toxic accumulation, while those located outside cause milder atypical SGS. Due to the multisystem phenotype, we evaluated gene expression and regulatory programs altered in atypical SGS by snRNA-seq of the cerebral cortex and kidney of Setbp1S858R heterozygous mice (corresponds to the human likely pathogenic SETBP1S867R variant) compared to matched wild-type mice by constructing cell-type-specific regulatory networks. Setbp1 was differentially expressed in excitatory neurons, but known SETBP1 targets were differentially expressed and regulated in many cell types. Our findings suggest molecular drivers underlying neurodevelopmental phenotypes in classical SGS also drive atypical SGS, persist after birth, and are present in the kidney. Our results indicate SETBP1's role as an epigenetic hub leads to cell-type-specific differences in TF activity, gene targeting, and regulatory rewiring. This research provides a framework for investigating cell-type-specific variant impact on gene expression and regulation.
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Affiliation(s)
- Jordan H. Whitlock
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Tabea M. Soelter
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Elizabeth J. Wilk
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Vishal H. Oza
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
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15
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Whitlock JH, Wilk EJ, Howton TC, Clark AD, Lasseigne BN. The landscape of SETBP1 gene expression and transcription factor activity across human tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.551337. [PMID: 37873221 PMCID: PMC10592643 DOI: 10.1101/2023.08.08.551337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background The SET binding protein 1 (SETBP1) gene encodes a transcription factor (TF) involved in various cellular processes. Distinct SETBP1 variants have been linked to three different diseases. Germline variants cause the ultra-rare pediatric Schinzel Giedion Syndrome (SGS) and SETBP1 haploinsufficiency disorder (SETBP1-HD), characterized by severe multisystemic abnormalities with neurodegeneration or a less severe brain phenotype accompanied by hypotonia and strabismus, respectively. Somatic variants in SETBP1 are associated with hematological malignancies and cancer development in other tissues in adults. Results To better understand the tissue-specific mechanisms involving SETBP1, we analyzed publicly available RNA-sequencing data from the Genotype-Tissue Expression (GTEx) project. We found SETBP1, and its known target genes were widely expressed across 31 adult human tissues. K-means clustering identified three distinct expression patterns of SETBP1 targets across tissues. Functional enrichment analysis (FEA) of each cluster revealed gene sets related to transcription regulation, DNA binding, and mitochondrial function. TF activity analysis of SETBP1 and its target TFs revealed tissue-specific TF activity, underscoring the role of tissue context-driven regulation and suggesting its impact in SETBP1-associated disease. In addition to uncovering tissue-specific molecular signatures of SETBP1 expression and TF activity, we provide a Shiny web application to facilitate exploring TF activity across human tissues for 758 TFs. Conclusions This study provides insight into the landscape of SETBP1 expression and TF activity across 31 non-diseased human tissues and reveals tissue-specific expression and activity of SETBP1 and its targets. In conjunction with the web application we constructed, our framework enables researchers to generate hypotheses related to the role tissue backgrounds play with respect to gene expression and TF activity in different disease contexts.
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Affiliation(s)
- Jordan H. Whitlock
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, AL, U.S.A
| | - Elizabeth J. Wilk
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, AL, U.S.A
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, AL, U.S.A
| | - Amanda D. Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, AL, U.S.A
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, AL, U.S.A
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16
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Tanaka A, Nishimura K, Saika W, Kon A, Koike Y, Tatsumi H, Takeda J, Nomura M, Zang W, Nakayama M, Matsuda M, Yamazaki H, Fukumoto M, Ito H, Hayashi Y, Kitamura T, Kawamoto H, Takaori-Kondo A, Koseki H, Ogawa S, Inoue D. SETBP1 is dispensable for normal and malignant hematopoiesis. Leukemia 2023; 37:1802-1811. [PMID: 37464069 DOI: 10.1038/s41375-023-01970-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
SETBP1 is a potential epigenetic regulator whose hotspot mutations preventing proteasomal degradation are recurrently detected in myeloid malignancies with poor prognosis. It is believed that the mutant SETBP1 exerts amplified effects of wild-type SETBP1 rather than neomorphic functions. This indicates that dysregulated quantitative control of SETBP1 would result in the transformation of hematopoietic cells. However, little is known about the roles of endogenous SETBP1 in malignant and normal hematopoiesis. Thus, we integrated the analyses of primary AML and healthy samples, cancer cell lines, and a newly generated murine model, Vav1-iCre;Setbp1fl/fl. Despite the expression in long-term hematopoietic stem cells, SETBP1 depletion in normal hematopoiesis minimally alters self-renewal, differentiation, or reconstitution in vivo. Indeed, its loss does not profoundly alter transcription or chromatin accessibilities. Furthermore, although AML with high SETBP1 mRNA is associated with genetic and clinical characteristics for dismal outcomes, SETBP1 is dispensable for the development or maintenance of AML. Contrary to the evidence that SETBP1 mutations are restricted to myeloid malignancies, dependency on SETBP1 mRNA expression is not observed in AML. These unexpected results shed light on the unrecognized idea that a physiologically nonessential gene can act as an oncogene when the machinery of protein degradation is damaged.
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Affiliation(s)
- Atsushi Tanaka
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koutarou Nishimura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Wataru Saika
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Department of Hematology, Shiga University of Medical Science, Shiga, Japan
| | - Ayana Kon
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yui Koike
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Hiromi Tatsumi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - June Takeda
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masaki Nomura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Facility for iPS Cell Therapy, CiRA Foundation, Kyoto, Japan
| | - Weijia Zang
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manabu Nakayama
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, Chiba, Japan
| | - Masashi Matsuda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Hiromi Yamazaki
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Miki Fukumoto
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Hiromi Ito
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Yasutaka Hayashi
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Toshio Kitamura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Daichi Inoue
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan.
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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17
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Kohyanagi N, Ohama T. The impact of SETBP1 mutations in neurological diseases and cancer. Genes Cells 2023; 28:629-641. [PMID: 37489294 DOI: 10.1111/gtc.13057] [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: 05/30/2023] [Accepted: 07/05/2023] [Indexed: 07/26/2023]
Abstract
SE translocation (SET) is a cancer-promoting factor whose expression is upregulated in many cancers. High SET expression positively correlates with a poor cancer prognosis. SETBP1 (SET-binding protein 1/SEB/MRD29), identified as SET-binding protein, is the causative gene of Schinzel-Giedion syndrome, which is characterized by severe intellectual disability and a distorted facial appearance. Mutations in these genetic regions are also observed in some blood cancers, such as myelodysplastic syndromes, and are associated with a poor prognosis. However, the physiological role of SETBP1 and the molecular mechanisms by which the mutations lead to disease progression have not yet been fully elucidated. In this review, we will describe the current epidemiological data on SETBP1 mutations and shed light on the current knowledge about the SET-dependent and -independent functions of SETBP1.
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Affiliation(s)
- Naoki Kohyanagi
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Takashi Ohama
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
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18
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Strasser B, Grünberger M, Steindl R, Heibl S, Thaler J, Haushofer A. Differential diagnoses and the mutational landscape of myelodysplastic/myeloproliferative neoplasm with neutrophilia: A case report. Mol Clin Oncol 2023; 19:62. [PMID: 37456801 PMCID: PMC10345896 DOI: 10.3892/mco.2023.2658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Myelodysplastic/myeloproliferative neoplasm with neutrophilia (MDS/MPN-N; previously referred to as atypical chronic myeloid leukemia) is a type of myelodysplastic syndrome/myeloproliferative neoplasm. A molecular genetic precondition for diagnosis is BCR::ABL negativity; further diagnostic criteria include clinicopathological assessments, such as peripheral blood leukocyte counts, the number of neutrophils and their precursors, and the presence of dysgranulopoiesis. The present case report highlights the importance of differential diagnoses with a stringent diagnostic workup according to the 5th Edition of the World Health Organization Classification of Hematolymphoid Tumors. A systematic review of the literature from 2013 to 2022 covering the mutational landscape of MDS/MPN-N was also performed to highlight recent improvements in the molecular genetic diagnostics of this disease.
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Affiliation(s)
- Bernhard Strasser
- Institute of Laboratory Medicine, Hospital Wels-Grieskirchen, A-4600 Wels, Austria
| | - Monika Grünberger
- Institute of Laboratory Medicine, Hospital Wels-Grieskirchen, A-4600 Wels, Austria
| | - Rita Steindl
- Department of Molecular Biology, Hospital Wels-Grieskirchen, A-4600 Wels, Austria
| | - Sonja Heibl
- Department of Internal Medicine IV, Hospital Wels-Grieskirchen, A-4600 Wels, Austria
| | - Josef Thaler
- Department of Internal Medicine IV, Hospital Wels-Grieskirchen, A-4600 Wels, Austria
| | - Alexander Haushofer
- Institute of Laboratory Medicine, Hospital Wels-Grieskirchen, A-4600 Wels, Austria
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19
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Luo M, Miao YR, Ke YJ, Guo AY, Zhang Q. A comprehensive landscape of transcription profiles and data resources for human leukemia. Blood Adv 2023; 7:3435-3449. [PMID: 36595475 PMCID: PMC10362280 DOI: 10.1182/bloodadvances.2022008410] [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: 06/27/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 01/04/2023] Open
Abstract
As a heterogeneous group of hematologic malignancies, leukemia has been widely studied at the transcriptome level. However, a comprehensive transcriptomic landscape and resources for different leukemia subtypes are lacking. Thus, in this study, we integrated the RNA sequencing data sets of >3000 samples from 14 leukemia subtypes and 53 related cell lines via a unified analysis pipeline. We depicted the corresponding transcriptomic landscape and developed a user-friendly data portal LeukemiaDB. LeukemiaDB was designed with 5 main modules: protein-coding gene, long noncoding RNA (lncRNA), circular RNA, alternative splicing, and fusion gene modules. In LeukemiaDB, users can search and browse the expression level, regulatory modules, and molecular information across leukemia subtypes or cell lines. In addition, a comprehensive analysis of data in LeukemiaDB demonstrates that (1) different leukemia subtypes or cell lines have similar expression distribution of the protein-coding gene and lncRNA; (2) some alternative splicing events are shared among nearly all leukemia subtypes, for example, MYL6 in A3SS, MYB in A5SS, HMBS in retained intron, GTPBP10 in mutually exclusive exons, and POLL in skipped exon; (3) some leukemia-specific protein-coding genes, for example, ABCA6, ARHGAP44, WNT3, and BLACE, and fusion genes, for example, BCR-ABL1 and KMT2A-AFF1 are involved in leukemogenesis; (4) some highly correlated regulatory modules were also identified in different leukemia subtypes, for example, the HOXA9 module in acute myeloid leukemia and the NOTCH1 module in T-cell acute lymphoblastic leukemia. In summary, the developed LeukemiaDB provides valuable insights into oncogenesis and progression of leukemia and, to the best of our knowledge, is the most comprehensive transcriptome resource of human leukemia available to the research community.
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Affiliation(s)
- Mei Luo
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Ya-Ru Miao
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Ya-Juan Ke
- Dian Diagnostics Group Co, Ltd, Hangzhou, China
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Hangzhou, China
| | - An-Yuan Guo
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qiong Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
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20
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Jain T, Ware AD, Dalton WB, Pasca S, Tsai HL, Gocke CD, Gondek LP, Xian RR, Borowitz MJ, Levis MJ. Co-occurring mutations in ASXL1, SRSF2, and SETBP1 define a subset of myelodysplastic/ myeloproliferative neoplasm with neutrophilia. Leuk Res 2023; 131:107345. [PMID: 37354804 DOI: 10.1016/j.leukres.2023.107345] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/12/2023] [Accepted: 06/19/2023] [Indexed: 06/26/2023]
Abstract
Identification of genomic signatures with consistent clinicopathological features in myelodysplastic/myeloproliferative neoplasm (MDS/MPN) is critical for improved diagnosis, elucidation of biology, inclusion in clinical trials, and development of therapies. We describe clinical and pathological features with co-existence of mutations in ASXL1 (missense or nonsense), SRSF2, and SKI homologous region of SETBP1, in 18 patients. Median age was 68 years with a male predominance (83%). Leukocytosis and neutrophilia were common at presentation. Marrow features included hypercellularity, granulocytic hyperplasia with megakaryocytic atypia, while the majority had myeloid hyperplasia and/or erythroid hypoplasia, myeloid dysplasia, and aberrant CD7 expression on blasts. Mutations in growth signaling pathways (RAS or JAK2) were noted at diagnosis or acquired during the disease course in 83% of patients. Two patients progressed upon acquisition of FLT3-TKD (acute myeloid leukemia) or KIT (aggressive systemic mastocytosis) mutations. The prognosis is poor with only two long-term survivors, thus far, who underwent blood or marrow transplantation. We propose that the presence of co-occurring ASXL1, SRSF2, and SETBP1 mutations can be diagnostic of a subtype of MDS/MPN with neutrophilia if clinical and morphological findings align. Our report underscores the association between genotype and phenotype within MDS/MPN and that genomic signatures should guide categorization of these entities.
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Affiliation(s)
- Tania Jain
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
| | - Alisha D Ware
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD, USA; Department of Pathology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - William Brian Dalton
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Sergiu Pasca
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Hua-Ling Tsai
- Division of Biostatistics and Bioinformatics, Johns Hopkins/Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | | | - Lukasz P Gondek
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Rena R Xian
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD, USA
| | | | - Mark J Levis
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
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21
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Fontana D, Elli EM, Pagni F, Piazza R. Myelodysplastic Syndromes/Myeloproliferative Overlap Neoplasms and Differential Diagnosis in the WHO and ICC 2022 Era: A Focused Review. Cancers (Basel) 2023; 15:3175. [PMID: 37370785 DOI: 10.3390/cancers15123175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/05/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
The myelodysplastic syndromes/myeloproliferative neoplasms (MDS/MPN) category comprises a varied group of myeloid neoplastic diseases characterized by clinical and pathologic overlapping features of both myelodysplastic and myeloproliferative neoplasms. For these reasons, these tumors are challenging in terms of diagnosis. The recent World Health Organization (WHO) 2022 classification and the International Consensus Classification (ICC) made changes in the classification of MDS/MPN compared to the previous 2016 WHO classification and improved the diagnostic criteria of these entities. The aim of this review is to describe the main entities reported in the more recent classifications, focusing on chronic myelomonocytic leukemia (CMML), MDS/MPN with neutrophilia (or atypical CML [aCML]), and MDS/MPN with SF3B1 mutation and thrombocytosis/MDS/MPN with ring sideroblasts and thrombocytosis. A particular emphasis is given to the differential diagnosis and analysis of subtle divergences and semantic differences between the WHO classification and the ICC for these entities.
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Affiliation(s)
- Diletta Fontana
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Elena M Elli
- Hematology Division and Bone Marrow Unit, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- Hematology Division and Bone Marrow Unit, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
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22
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Zaghi M, Banfi F, Massimino L, Volpin M, Bellini E, Brusco S, Merelli I, Barone C, Bruni M, Bossini L, Lamparelli LA, Pintado L, D'Aliberti D, Spinelli S, Mologni L, Colasante G, Ungaro F, Cioni JM, Azzoni E, Piazza R, Montini E, Broccoli V, Sessa A. Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition. Nat Commun 2023; 14:3212. [PMID: 37270547 DOI: 10.1038/s41467-023-39043-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/23/2023] [Indexed: 06/05/2023] Open
Abstract
Within the chromatin, distal elements interact with promoters to regulate specific transcriptional programs. Histone acetylation, interfering with the net charges of the nucleosomes, is a key player in this regulation. Here, we report that the oncoprotein SET is a critical determinant for the levels of histone acetylation within enhancers. We disclose that a condition in which SET is accumulated, the severe Schinzel-Giedion Syndrome (SGS), is characterized by a failure in the usage of the distal regulatory regions typically employed during fate commitment. This is accompanied by the usage of alternative enhancers leading to a massive rewiring of the distal control of the gene transcription. This represents a (mal)adaptive mechanism that, on one side, allows to achieve a certain degree of differentiation, while on the other affects the fine and corrected maturation of the cells. Thus, we propose the differential in cis-regulation as a contributing factor to the pathological basis of SGS and possibly other the SET-related disorders in humans.
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Affiliation(s)
- Mattia Zaghi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Federica Banfi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
- CNR Institute of Neuroscience, 20129, Milan, Italy
| | - Luca Massimino
- Esperimental Gastroenterology Unit, Division of Immunology, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Monica Volpin
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget); IRCCS, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Edoardo Bellini
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Simone Brusco
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
- CNR Institute of Neuroscience, 20129, Milan, Italy
| | - Ivan Merelli
- CNR Institute of Biomedical Technologies, 20090, Segrate, Italy
| | - Cristiana Barone
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Michela Bruni
- RNA biology of the Neuron Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Linda Bossini
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Luigi Antonio Lamparelli
- Esperimental Gastroenterology Unit, Division of Immunology, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Laura Pintado
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Deborah D'Aliberti
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Silvia Spinelli
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Luca Mologni
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Gaia Colasante
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Federica Ungaro
- Esperimental Gastroenterology Unit, Division of Immunology, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Jean-Michel Cioni
- RNA biology of the Neuron Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Emanuele Azzoni
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Rocco Piazza
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget); IRCCS, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Vania Broccoli
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
- CNR Institute of Neuroscience, 20129, Milan, Italy
| | - Alessandro Sessa
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy.
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23
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Carreño-Tarragona G, Álvarez-Larrán A, Harrison C, Martínez-Ávila JC, Hernández-Boluda JC, Ferrer-Marín F, Radia DH, Mora E, Francis S, González-Martínez T, Goddard K, Pérez-Encinas M, Narayanan S, Raya JM, Singh V, Gutiérrez X, Toth P, Amat-Martínez P, Mcilwaine L, Alobaidi M, Mayani K, McGregor A, Stuckey R, Psaila B, Segura A, Alvares C, Davidson K, Osorio S, Cutting R, Sweeney CP, Rufián L, Moreno L, Cuenca I, Smith J, Morales ML, Gil-Manso R, Koutsavlis I, Wang L, Mead AJ, Rozman M, Martínez-López J, Ayala R, Cross NCP. CNL and aCML should be considered as a single entity based on molecular profiles and outcomes. Blood Adv 2023; 7:1672-1681. [PMID: 36375042 PMCID: PMC10182308 DOI: 10.1182/bloodadvances.2022008204] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/13/2022] [Accepted: 09/27/2022] [Indexed: 01/11/2023] Open
Abstract
Chronic neutrophilic leukemia (CNL) and atypical chronic myeloid leukemia (aCML) are rare myeloid disorders that are challenging with regard to diagnosis and clinical management. To study the similarities and differences between these disorders, we undertook a multicenter international study of one of the largest case series (CNL, n = 24; aCML, n = 37 cases, respectively), focusing on the clinical and mutational profiles (n = 53 with molecular data) of these diseases. We found no differences in clinical presentations or outcomes of both entities. As previously described, both CNL and aCML share a complex mutational profile with mutations in genes involved in epigenetic regulation, splicing, and signaling pathways. Apart from CSF3R, only EZH2 and TET2 were differentially mutated between them. The molecular profiles support the notion of CNL and aCML being a continuum of the same disease that may fit best within the myelodysplastic/myeloproliferative neoplasms. We identified 4 high-risk mutated genes, specifically CEBPA (β = 2.26, hazard ratio [HR] = 9.54, P = .003), EZH2 (β = 1.12, HR = 3.062, P = .009), NRAS (β = 1.29, HR = 3.63, P = .048), and U2AF1 (β = 1.75, HR = 5.74, P = .013) using multivariate analysis. Our findings underscore the relevance of molecular-risk classification in CNL/aCML as well as the importance of CSF3R mutations in these diseases.
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MESH Headings
- Humans
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/diagnosis
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/genetics
- Leukemia, Neutrophilic, Chronic/diagnosis
- Leukemia, Neutrophilic, Chronic/genetics
- Epigenesis, Genetic
- Myelodysplastic-Myeloproliferative Diseases/genetics
- Mutation
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Affiliation(s)
- Gonzalo Carreño-Tarragona
- Hematology Department, Hospital Universitario 12 de Octubre, I+12, Centro Nacional de Investigaciones Oncológicas, Complutense University, Centro de Investigación Biomédica en Red de Oncología, Madrid, Spain
| | | | - Claire Harrison
- Hematology Department, Guy’s and St. Thomas NHS Foundation Trust, London, United Kingdom
| | - José Carlos Martínez-Ávila
- Agricultural Economics, Statistics and Business Management Department, Escuela Técnica Superior de Ingeniería Agrónomica, Alimentaria y Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Francisca Ferrer-Marín
- Hematology Department, Hospital Morales Meseguer, Centro de Investigación Biomédica en Red de Enfermedades Raras, Universidad Católica San Antonio de Murcia, Murcia, Spain
| | - Deepti H. Radia
- Hematology Department, Guy’s and St. Thomas NHS Foundation Trust, London, United Kingdom
| | - Elvira Mora
- Hematology Department, Hospital Universitario La Fe, Valencia, Spain
| | - Sebastian Francis
- Hematology Department, Sheffield Hospital, Sheffield, United Kingdom
| | | | - Kathryn Goddard
- Hematology Department, Rotherham Hospital, Rotherham, United Kingdom
| | - Manuel Pérez-Encinas
- Hematology Department, Hospital Clínico Universitario, Santiago de Compostela, Spain
| | - Srinivasan Narayanan
- Hematology Department, University Hospital Southampton, Southampton, United Kingdom
| | - José María Raya
- Hematology Department, Hospital Universitario de Canarias, Tenerife, Spain
| | - Vikram Singh
- The Clatterbridge Cancer Centre, Liverpool, United Kingdom
| | - Xabier Gutiérrez
- Hematology Department, Hospital Universitario 12 de Octubre, I+12, Centro Nacional de Investigaciones Oncológicas, Complutense University, Centro de Investigación Biomédica en Red de Oncología, Madrid, Spain
| | - Peter Toth
- Hematology Department, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
| | | | - Louisa Mcilwaine
- Hematology Department, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Magda Alobaidi
- Department of Haematology, Chelsea and Westminster NHS Trust West Middlesex Hospital, London, United Kingdom
| | - Karan Mayani
- Hematology Department, Hospital General de La Palma, Santa Cruz de Tenerife, Spain
| | - Andrew McGregor
- Department of Haematology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | - Ruth Stuckey
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Bethan Psaila
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Department of Haematology, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
| | - Adrián Segura
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Caroline Alvares
- Hematology Department, University Hospital of Wales, Cardiff, United Kingdom
| | - Kerri Davidson
- Hematology Department, Kirkcaldy Hospital, Fife, Scotland
| | - Santiago Osorio
- Hematology Department, Hospital Universitario Gregorio Marañón, Madrid, Spain
| | - Robert Cutting
- Hematology Department, Doncaster Hospital, Doncaster, Yorkshire, England
| | - Caroline P. Sweeney
- Hematology Department, Vale of Leven Hospital, Alexandria, West Dunbartonshire, Scotland
| | - Laura Rufián
- Hematology Department, Hospital Universitario 12 de Octubre, I+12, Centro Nacional de Investigaciones Oncológicas, Complutense University, Centro de Investigación Biomédica en Red de Oncología, Madrid, Spain
| | - Laura Moreno
- Hematology Department, Hospital Universitario 12 de Octubre, I+12, Centro Nacional de Investigaciones Oncológicas, Complutense University, Centro de Investigación Biomédica en Red de Oncología, Madrid, Spain
| | - Isabel Cuenca
- Hematology Department, Hospital Universitario 12 de Octubre, I+12, Centro Nacional de Investigaciones Oncológicas, Complutense University, Centro de Investigación Biomédica en Red de Oncología, Madrid, Spain
| | - Jeffery Smith
- The Clatterbridge Cancer Centre, Liverpool, United Kingdom
| | - María Luz Morales
- Hematology Department, Hospital Universitario 12 de Octubre, I+12, Centro Nacional de Investigaciones Oncológicas, Complutense University, Centro de Investigación Biomédica en Red de Oncología, Madrid, Spain
| | - Rodrigo Gil-Manso
- Hematology Department, Hospital Universitario 12 de Octubre, I+12, Centro Nacional de Investigaciones Oncológicas, Complutense University, Centro de Investigación Biomédica en Red de Oncología, Madrid, Spain
| | - Ioannis Koutsavlis
- Hematology Department, Western General Hospital, Edinburgh, United Kingdom
| | - Lihui Wang
- Haemato-Oncology Diagnostic Service, Liverpool Clinical Laboratories, Liverpool University Hospital, Liverpool, United Kingdom
| | - Adam J. Mead
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - María Rozman
- Hemopathology Unit, Hospital Clínic, Barcelona, Spain
| | - Joaquín Martínez-López
- Hematology Department, Hospital Universitario 12 de Octubre, I+12, Centro Nacional de Investigaciones Oncológicas, Complutense University, Centro de Investigación Biomédica en Red de Oncología, Madrid, Spain
| | - Rosa Ayala
- Hematology Department, Hospital Universitario 12 de Octubre, I+12, Centro Nacional de Investigaciones Oncológicas, Complutense University, Centro de Investigación Biomédica en Red de Oncología, Madrid, Spain
| | - Nicholas C. P. Cross
- Wessex Regional Genetics Laboratory, Salisbury, United Kingdom
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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24
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Wang H, Gao Y, Qin L, Zhang M, Shi W, Feng Z, Guo L, Zhu B, Liao S. Identification of a novel de novo mutation of SETBP1 and new findings of SETBP1 in tumorgenesis. Orphanet J Rare Dis 2023; 18:107. [PMID: 37150818 PMCID: PMC10165755 DOI: 10.1186/s13023-023-02705-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 04/20/2023] [Indexed: 05/09/2023] Open
Abstract
BACKGROUND In the past decade, SETBP1 has attracted a lot of interest on that the same gene with different type or level (germline or somatic) of variants could provoke different pathologic consequences such as Schinzel-Giedon syndrome, SETBP1 Haploinsufficiency Disorder (SETBP1-HD) and myeloid malignancies. Whole exome sequencing was conducted to detect the etiology of a pregnant woman with mental retardation. As a new oncogene and potential marker of myeloid malignancies, somatic SETBP1 variants in other cancers were rarely studied. We performed a pan-cancer analysis of SETBP1 gene in different cancers for the first time. RESULTS A novel heterozygous mutation of the SETBP1 gene (c.1724_1727del, p.D575Vfs*4) was found in the patient and the fetus and the mutation was predicted to result in a truncated protein. Reduced SETBP1 expression was associated with SETBP1-HD. The pan-cancer analysis of SETBP1 showed that SETBP1 overexpression should be given special attention in Bladder Urothelial Carcinoma (BLCA) and Stomach adenocarcinoma (STAD). CONCLUSIONS The de novo SETBP1 mutation was the genetic cause of SETBP1-HD in the family. BLCA and STAD might be related to SETBP1 overexpression.
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Affiliation(s)
- Hongdan Wang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China.
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China.
| | - Yue Gao
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Litao Qin
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Mengting Zhang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Weili Shi
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Zhanqi Feng
- Department of Urology, The First People's Hospital of Zhengzhou, Zhengzhou, China
| | - Liangjie Guo
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.
| | - Shixiu Liao
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China.
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25
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Sun Y, Wang Q, Zhang X, Zhang Z, Wang Q, Cen J, Zhu M, Pan J, Liu D, Wu D, Cai Y, Chen S. Molecular genetics and management of world health organization defined atypical chronic myeloid leukemia. Ann Hematol 2023; 102:777-785. [PMID: 36735076 DOI: 10.1007/s00277-023-05106-8] [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: 10/23/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023]
Abstract
Atypical chronic myeloid leukemia (CML) is a rare BCR::ABL1-negative hematopoietic stem cell disease characterized by granulocytic proliferation and granulocytic dysplasia. Due to both the challenging diagnosis and the rarity of atypical CML, comprehensive molecular annotation-based analyses of this disease population have been scarce, and it is currently difficult to identify the optimal treatment for atypical CML. To explore atypical CML genomic landscape and treatment options, we performed a systematic retrospective of the clinical data and outcomes of 31 atypical CML patients. We observed that the molecular landscape of atypical CML was highly heterogeneous, with multiple molecular events driving its pathogenesis. Patients with atypical CML had a low response to current therapies, with an overall response rate (ORR) of 33.3% to hypomethylating agent (HMA)-based therapy. The current treatment strategies, including hematopoietic stem cell transplantation (HSCT), did not improve overall survival (OS) in atypical CML patients, with a median survival of 20 months. Thus, the benefits from HSCT and candidates for HSCT remain to be further evaluated. Acute myeloid leukemia (AML)-like chemotherapy followed by bridging allogeneic HSCT may be an ideal regimen for suitable individuals. The large-scale and prospective clinical studies will help to address the dilemma.
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Affiliation(s)
- Yingxin Sun
- Department of Hematology, First Affiliated Hospital of Soochow University, Soochow University, Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Suzhou, China.,Department of Thrombosis and Hemostasis, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Qinrong Wang
- Department of Hematology, First Affiliated Hospital of Soochow University, Soochow University, Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Suzhou, China.,Department of Thrombosis and Hemostasis, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Xingxia Zhang
- Department of Hematology, Huai'an Hospital Affiliated to Xuzhou Medical College and Huai'an Second People's Hospital, Huai'an, China
| | - Zhiyu Zhang
- Department of Hematology, First Affiliated Hospital of Soochow University, Soochow University, Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Suzhou, China.,Department of Thrombosis and Hemostasis, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Qian Wang
- Department of Hematology, First Affiliated Hospital of Soochow University, Soochow University, Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Suzhou, China.,Department of Thrombosis and Hemostasis, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Jiannong Cen
- Department of Hematology, First Affiliated Hospital of Soochow University, Soochow University, Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Suzhou, China.,Department of Thrombosis and Hemostasis, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Mingqing Zhu
- Department of Hematology, First Affiliated Hospital of Soochow University, Soochow University, Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Suzhou, China.,Department of Thrombosis and Hemostasis, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Jinlan Pan
- Department of Hematology, First Affiliated Hospital of Soochow University, Soochow University, Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Suzhou, China.,Department of Thrombosis and Hemostasis, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Dandan Liu
- Department of Hematology, First Affiliated Hospital of Soochow University, Soochow University, Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Suzhou, China.,Department of Thrombosis and Hemostasis, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Depei Wu
- Department of Hematology, First Affiliated Hospital of Soochow University, Soochow University, Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Suzhou, China.,Department of Thrombosis and Hemostasis, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Yifeng Cai
- Department of Hematology, Affiliated Hospital of Nantong University, Nantong University, Nantong, China.
| | - Suning Chen
- Department of Hematology, First Affiliated Hospital of Soochow University, Soochow University, Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, Suzhou, China. .,Department of Thrombosis and Hemostasis, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China.
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26
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Patnaik MM, Tefferi A. Atypical chronic myeloid leukemia and myelodysplastic/myeloproliferative neoplasm, not otherwise specified: 2023 update on diagnosis, risk stratification, and management. Am J Hematol 2023; 98:681-689. [PMID: 36601682 DOI: 10.1002/ajh.26828] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023]
Abstract
DISEASE OVERVIEW Atypical chronic myeloid leukemia (aCML) and myelodysplastic/myeloproliferative (MDS/MPN) neoplasms, not otherwise specified (NOS), are MDS/MPN overlap neoplasms characterized by leukocytosis, in the absence of monocytosis and eosinophilia, with <20% blasts in the blood and bone marrow. DIAGNOSIS aCML, previously known as aCML, BCR::ABL1 negative, was renamed as aCML by the ICC classification, and as MDS/MPN with neutrophilia by the 5th edition of the WHO classification. This entity is characterized by dysplastic neutrophilia with immature myeloid cells comprising ≥10% of the white blood cell count, with prominent dysgranulopoiesis. MDS/MPN-NOS consists of MDS/MPN overlap neoplasms not meeting criteria for defined categories such as chronic myelomonocytic leukemia (CMML), MDS/MPN-ring sideroblasts-thrombocytosis (MDS/MPN-RS-T), and aCML. MUTATIONS AND KARYOTYPE Cytogenetic abnormalities are seen in 40-50% of patients in both categories. In aCML, somatic mutations commonly encountered include ASXL1, SETBP1, ETNK1, and EZH2 whereas MDS/MPN-NOS can be further stratified by mutational profiles into CMML-like, MDS/MPN-RS-T-like, aCML-like, TP35-mutated, and "others", respectively. RISK STRATIFICATION The Mayo Clinic aCML model stratifies patients based on age >67 years, hemoglobin <10 g/dl, and the presence of TET2 mutations into low-risk (0-1 points) and high-risk (>2 points) groups, with median survivals of 18 and 7 months, respectively. MDS/MPN-NOS patients have traditionally been risk stratified using MDS risk models such as IPSS and IPSS-R. TREATMENT Leukocytosis and anemia are managed like lower risk MPN and MDS. DNMT inhibitors have been used in both entities with suboptimal response rates. Allogeneic stem cell transplant remains the only curative strategy but is associated with high morbidity and mortality.
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MESH Headings
- Humans
- Aged
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/diagnosis
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/genetics
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/therapy
- Myelodysplastic Syndromes/diagnosis
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/therapy
- Leukocytosis
- Myelodysplastic-Myeloproliferative Diseases/diagnosis
- Myelodysplastic-Myeloproliferative Diseases/genetics
- Myelodysplastic-Myeloproliferative Diseases/therapy
- Leukemia, Myelomonocytic, Chronic/diagnosis
- Leukemia, Myelomonocytic, Chronic/genetics
- Leukemia, Myelomonocytic, Chronic/therapy
- Thrombocytosis/genetics
- Mutation
- Risk Assessment
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Affiliation(s)
- Mrinal M Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Ayalew Tefferi
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
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Cardo LF, de la Fuente DC, Li M. Impaired neurogenesis and neural progenitor fate choice in a human stem cell model of SETBP1 disorder. Mol Autism 2023; 14:8. [PMID: 36805818 PMCID: PMC9940404 DOI: 10.1186/s13229-023-00540-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/07/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Disruptions of SETBP1 (SET binding protein 1) on 18q12.3 by heterozygous gene deletion or loss-of-function variants cause SETBP1 disorder. Clinical features are frequently associated with moderate to severe intellectual disability, autistic traits and speech and motor delays. Despite the association of SETBP1 with neurodevelopmental disorders, little is known about its role in brain development. METHODS Using CRISPR/Cas9 genome editing technology, we generated a SETBP1 deletion model in human embryonic stem cells (hESCs) and examined the effects of SETBP1-deficiency in neural progenitors (NPCs) and neurons derived from these stem cells using a battery of cellular assays, genome-wide transcriptomic profiling and drug-based phenotypic rescue. RESULTS Neural induction occurred efficiently in all SETBP1 deletion models as indicated by uniform transition into neural rosettes. However, SETBP1-deficient NPCs exhibited an extended proliferative window and a decrease in neurogenesis coupled with a deficiency in their ability to acquire ventral forebrain fate. Genome-wide transcriptome profiling and protein biochemical analysis revealed enhanced activation of Wnt/β-catenin signaling in SETBP1 deleted cells. Crucially, treatment of the SETBP1-deficient NPCs with a small molecule Wnt inhibitor XAV939 restored hyper canonical β-catenin activity and restored both cortical and MGE neuronal differentiation. LIMITATIONS The current study is based on analysis of isogenic hESC lines with genome-edited SETBP1 deletion and further studies would benefit from the use of patient-derived iPSC lines that may harbor additional genetic risk that aggravate brain pathology of SETBP1 disorder. CONCLUSIONS We identified an important role for SETBP1 in controlling forebrain progenitor expansion and neurogenic differentiation. Our study establishes a novel regulatory link between SETBP1 and Wnt/β-catenin signaling during human cortical neurogenesis and provides mechanistic insights into structural abnormalities and potential therapeutic avenues for SETBP1 disorder.
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Affiliation(s)
- Lucia F Cardo
- Neuroscience and Mental Health Innovation Institute, School of Medicine and School of Bioscience, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK.
| | - Daniel C de la Fuente
- Neuroscience and Mental Health Innovation Institute, School of Medicine and School of Bioscience, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Meng Li
- Neuroscience and Mental Health Innovation Institute, School of Medicine and School of Bioscience, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK.
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28
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Li Y, Liu Y, Gao X, Zhao W, Zhou F, Liu H, Wang W. Identification of novel PIEZO1::CBFA2T3 and INO80C::SETBP1 fusion genes in an acute myeloid leukemia patient by RNA-seq. Mol Biol Rep 2023; 50:1961-1966. [PMID: 36472727 DOI: 10.1007/s11033-022-08138-x] [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: 07/22/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Fusion genes are recurrent molecular aberrations in acute myeloid leukemia, with significant diagnostic and therapeutic value. The identification of novel fusion genes provides advanced biomarkers for diagnosis and facilitates the discovery of drug targets. METHODS Bone marrow sample was extracted from an acute myeloid leukemia patient and RNA-sequencing was performed. Several bioinformatic methods, including differential analysis and Gene Set Enrichment Analysis (GSEA) pathway analyses were conducted based on the expression data. RESULTS Two novel fusion genes, PIEZO1::CBFA2T3 and INO80C::SETBP1, were identified by RNA-seq. Differential analysis found that SETBP1 and CBFA2T3 were overexpressed, and GSEA analysis showed the activation of immune-related pathways. These findings indicate dysfunction of the fusion related- genes and possible pathogenic effect of the fusion genes. CONCLUSION We reported a male AML patient with presence of PIEZO1::CBFA2T3 and INO80C::SETBP1 fusion genes.
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Affiliation(s)
- Yanling Li
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yao Liu
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinyu Gao
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Weiwei Zhao
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fanghui Zhou
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hongxing Liu
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, 065201, China.
- Beijing Lu Daopei Institute of Hematology, Beijing, 100076, China.
- Division of Pathology & Laboratory Medicine, Beijing Lu Daopei Hospital, Beijing, 100076, China.
| | - Wei Wang
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
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29
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Prakash S, Arber DA, Bueso-Ramos C, Hasserjian RP, Orazi A. Advances in myelodysplastic/myeloproliferative neoplasms. Virchows Arch 2023; 482:69-83. [PMID: 36469102 DOI: 10.1007/s00428-022-03465-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/07/2022]
Abstract
The myelodysplastic syndrome/myeloproliferative neoplasms (MDS/MPN) category includes a heterogeneous group of diseases characterized by the co-occurrence of clinical and pathologic features of both myelodysplastic and myeloproliferative neoplasms. The recently published International Consensus Classification of myeloid neoplasms revised the entities included in the MDS/MPN category as well as criteria for their diagnosis. In addition to the presence of one or more increased peripheral blood cell counts as evidence of myeloproliferative features, concomitant cytopenia as evidence of ineffective hematopoiesis is now an explicit requirement to diagnose the diseases included in this category. The increasing availability of modern gene sequencing has allowed better understanding of the biologic characteristics of these myeloid neoplasms. The presence of specific mutations in the appropriate clinicopathologic context is now included in the diagnostic criteria for some of MDS/MPN entities. In this review, we highlight what has changed in the diagnostic criteria of MDS/MPN from the WHO 2016 classification while providing practical guidance in diagnosing these diseases.
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Affiliation(s)
- Sonam Prakash
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Daniel A Arber
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Carlos Bueso-Ramos
- Division of Pathology and Laboratory Medicine, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert P Hasserjian
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Attilio Orazi
- Department of Pathology, Texas Tech University Health Sciences Center, El Paso, TX, USA.
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30
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Islam SA, Díaz-Gay M, Wu Y, Barnes M, Vangara R, Bergstrom EN, He Y, Vella M, Wang J, Teague JW, Clapham P, Moody S, Senkin S, Li YR, Riva L, Zhang T, Gruber AJ, Steele CD, Otlu B, Khandekar A, Abbasi A, Humphreys L, Syulyukina N, Brady SW, Alexandrov BS, Pillay N, Zhang J, Adams DJ, Martincorena I, Wedge DC, Landi MT, Brennan P, Stratton MR, Rozen SG, Alexandrov LB. Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor. CELL GENOMICS 2022; 2:None. [PMID: 36388765 PMCID: PMC9646490 DOI: 10.1016/j.xgen.2022.100179] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 04/10/2022] [Accepted: 08/31/2022] [Indexed: 12/09/2022]
Abstract
Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues.
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Affiliation(s)
- S.M. Ashiqul Islam
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yang Wu
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yudou He
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Mike Vella
- NVIDIA Corporation, 2788 San Tomas Expressway, Santa Clara, CA 95051, USA
| | - Jingwei Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Jon W. Teague
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Peter Clapham
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sergey Senkin
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Yun Rose Li
- Departments of Radiation Oncology and Cancer Genetics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Laura Riva
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Andreas J. Gruber
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
- Department of Biology, University of Konstanz, Universitaetsstrasse 10, D-78464 Konstanz, Germany
| | - Christopher D. Steele
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Laura Humphreys
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | | | - Samuel W. Brady
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Boian S. Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - David J. Adams
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - David C. Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Michael R. Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Steven G. Rozen
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
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Moyo TK, Mendler JH, Itzykson R, Kishtagari A, Solary E, Seegmiller AC, Gerds AT, Ayers GD, Dezern AE, Nazha A, Valent P, van de Loosdrecht AA, Onida F, Pleyer L, Cirici BX, Tibes R, Geissler K, Komrokji RS, Zhang J, Germing U, Steensma DP, Wiseman DH, Pfeilstöecker M, Elena C, Cross NCP, Kiladjian JJ, Luebbert M, Mesa RA, Montalban-Bravo G, Sanz GF, Platzbecker U, Patnaik MM, Padron E, Santini V, Fenaux P, Savona MR. The ABNL-MARRO 001 study: a phase 1–2 study of randomly allocated active myeloid target compound combinations in MDS/MPN overlap syndromes. BMC Cancer 2022; 22:1013. [PMID: 36153475 PMCID: PMC9509596 DOI: 10.1186/s12885-022-10073-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 09/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background Myelodysplastic/myeloproliferative neoplasms (MDS/MPN) comprise several rare hematologic malignancies with shared concomitant dysplastic and proliferative clinicopathologic features of bone marrow failure and propensity of acute leukemic transformation, and have significant impact on patient quality of life. The only approved disease-modifying therapies for any of the MDS/MPN are DNA methyltransferase inhibitors (DNMTi) for patients with dysplastic CMML, and still, outcomes are generally poor, making this an important area of unmet clinical need. Due to both the rarity and the heterogeneous nature of MDS/MPN, they have been challenging to study in dedicated prospective studies. Thus, refining first-line treatment strategies has been difficult, and optimal salvage treatments following DNMTi failure have also not been rigorously studied. ABNL-MARRO (A Basket study of Novel therapy for untreated MDS/MPN and Relapsed/Refractory Overlap Syndromes) is an international cooperation that leverages the expertise of the MDS/MPN International Working Group (IWG) and provides the framework for collaborative studies to advance treatment of MDS/MPN and to explore clinical and pathologic markers of disease severity, prognosis, and treatment response. Methods ABNL MARRO 001 (AM-001) is an open label, randomly allocated phase 1/2 study that will test novel treatment combinations in MDS/MPNs, beginning with the novel targeted agent itacitinib, a selective JAK1 inhibitor, combined with ASTX727, a fixed dose oral combination of the DNMTi decitabine and the cytidine deaminase inhibitor cedazuridine to improve decitabine bioavailability. Discussion Beyond the primary objectives of the study to evaluate the safety and efficacy of novel treatment combinations in MDS/MPN, the study will (i) Establish the ABNL MARRO infrastructure for future prospective studies, (ii) Forge innovative scientific research that will improve our understanding of pathogenetic mechanisms of disease, and (iii) Inform the clinical application of diagnostic criteria, risk stratification and prognostication tools, as well as response assessments in this heterogeneous patient population. Trial registration This trial was registered with ClinicalTrials.gov on August 19, 2019 (Registration No. NCT04061421).
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32
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Liu L, Feng X, Liu S, Zhou Y, Dong X, Yao H, Tan B. Whole-genome sequencing combined RNA-sequencing analysis of patients with mutations in SET binding protein 1. Front Neurosci 2022; 16:980000. [PMID: 36161179 PMCID: PMC9490002 DOI: 10.3389/fnins.2022.980000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
SET binding protein 1 (SETBP1) is essential for human development, and pathogenic germline variants in SETBP1 lead to a recognizable developmental syndrome and variable clinical features. In this study, we assessed a patient with facial dysmorphism, intellectual disability and delayed motor development. Whole genome sequencing identified a novel de novo variation of the SETBP1 (c.2631C > A; p. S877R) gene, which is located in the SKI domain, as a likely pathogenic variant for the proband’s phenotype. RNA sequencing was performed to investigate the potential molecular mechanism of the novel variation in SETBP1. In total, 77 and 38 genes were identified with aberrant expression and splicing, respectively. Moreover, the biological functions of these genes were involved in DNA/protein binding, expression regulation, and the cell cycle, which may advance our understanding of the pathogenesis of SETBP1 in vivo.
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Affiliation(s)
- Li Liu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaoshu Feng
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Sihan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Yanqiu Zhou
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaojing Dong
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Yao
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Hong Yao,
| | - Bo Tan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Bo Tan,
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Hergott CB, Kim AS. Molecular Diagnostic Testing for Hematopoietic Neoplasms: Linking Pathogenic Drivers to Personalized Diagnosis. Clin Lab Med 2022; 42:325-347. [PMID: 36150815 DOI: 10.1016/j.cll.2022.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular diagnostics inhabit an increasingly central role in characterizing hematopoietic malignancies. This brief review summarizes the genomic targets important for many major categories of hematopoietic neoplasia by focusing on disease pathogenesis. In myeloid disease, recurrent mutations in key functional classes drive clonal hematopoiesis, on which additional variants can specify clinical presentation and accelerate progression. Lymphoblastic leukemias are frequently initiated by oncogenic fusions that block lymphoid maturation while, in concert with additional mutations, driving proliferation. The links between genetic aberrations and lymphoma patient outcomes have been clarified substantially through the clustering of genomic profiles. Finally, the addition of next-generation sequencing strategies to cytogenetics is refining risk stratification for plasma cell myeloma. In all categories, molecular diagnostics shed light on the unique mechanistic underpinnings of each individual malignancy, thereby empowering more rational, personalized care for these patients.
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Affiliation(s)
- Christopher B Hergott
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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Carratt SA, Kong GL, Curtiss BM, Schonrock Z, Maloney L, Maniaci BN, Blaylock HZ, Baris A, Druker BJ, Braun TP, Maxson JE. Mutated SETBP1 activates transcription of Myc programs to accelerate CSF3R-driven myeloproliferative neoplasms. Blood 2022; 140:644-658. [PMID: 35482940 PMCID: PMC9373012 DOI: 10.1182/blood.2021014777] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/15/2022] [Indexed: 11/20/2022] Open
Abstract
Colony stimulating factor 3 receptor (CSF3R) mutations lead to JAK pathway activation and are the molecular hallmark of chronic neutrophilic leukemia (CNL). Approximately half of patients with CNL also have mutations in SET binding protein 1 (SETBP1). In this study, we developed models of SETBP1-mutated leukemia to understand the role that SETBP1 plays in CNL. SETBP1 mutations promote self-renewal of CSF3R-mutated hematopoietic progenitors in vitro and prevent cells from undergoing terminal differentiation. In vivo, SETBP1 mutations accelerate leukemia progression, leading to the rapid development of hepatosplenomegaly and granulocytosis. Through transcriptomic and epigenomic profiling, we found that SETBP1 enhances progenitor-associated programs, most strongly upregulating Myc and Myc target genes. This upregulation of Myc can be reversed by LSD1 inhibitors. In summary, we found that SETBP1 mutations promote aggressive hematopoietic cell expansion when expressed with mutated CSF3R through the upregulation of Myc-associated gene expression programs.
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Affiliation(s)
- Sarah A Carratt
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Garth L Kong
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Brittany M Curtiss
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Zachary Schonrock
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Lauren Maloney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Breanna N Maniaci
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Hunter Z Blaylock
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Adrian Baris
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Theodore P Braun
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Julia E Maxson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
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Symeonidis A, Chondropoulos S, Verigou E, Lazaris V, Kourakli A, Tsirigotis P. Allogeneic Hematopoietic Stem Cell Transplantation for Mixed or Overlap Myelodysplastic/Myeloproliferative Disorders. Front Oncol 2022; 12:884723. [PMID: 35992818 PMCID: PMC9389581 DOI: 10.3389/fonc.2022.884723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/23/2022] [Indexed: 12/30/2022] Open
Abstract
Chronic myelomonocytic leukemia (CMML) and the remaining, less frequent hybrid, mixed, or overlap myelodysplastic syndromes/myeloproliferative neoplasms (MDSs/MPNs) are difficult to treat neoplastic hematological disorders, exhibiting substantial clinical and prognostic heterogeneity, for which clear therapeutic guidelines or effective treatment options are still missing. CMML has an overall survival ranging from a few months to several years. Although patients with proliferative or dysplastic features may benefit from hydroxyurea and hypomethylating agent treatment, respectively, none of these treatments can establish long-term remission and prevent the inevitable transformation to acute leukemia. Novel targeted treatment approaches are emerging but are still under investigation. Therefore, currently, allogeneic stem cell transplantation (allo-SCT) remains the only treatment modality with a curative potential, but its widespread application is limited, due to significant morbidity and mortality associated with the procedure, especially in the elderly and in patients with comorbidities. Recognition of patient eligibility for allo-SCT is crucial, and the procedure should be addressed to patients with a good performance status without severe comorbidities and mainly to those in intermediate- to high-risk category, with a suitable stem cell donor available. The issues of best timing for performing transplantation, patient and donor eligibility, the type of conditioning regimen, and the outcomes after various allo-SCT procedures are the topics of this review.
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Affiliation(s)
- Argiris Symeonidis
- University of Patras Medical School, Hematology Division, Patras, Greece
- *Correspondence: Argiris Symeonidis, ; orcid.org/0000-0002-0543-046X
| | | | - Evgenia Verigou
- Hematology Division, General University Hospital of Patras, Rion of Patras, Greece
| | - Vasileios Lazaris
- Hematology Division, General University Hospital of Patras, Rion of Patras, Greece
| | - Alexandra Kourakli
- Hematology Division, General University Hospital of Patras, Rion of Patras, Greece
| | - Panagiotis Tsirigotis
- Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
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Kar SP, Quiros PM, Gu M, Jiang T, Mitchell J, Langdon R, Iyer V, Barcena C, Vijayabaskar MS, Fabre MA, Carter P, Petrovski S, Burgess S, Vassiliou GS. Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis. Nat Genet 2022; 54:1155-1166. [PMID: 35835912 PMCID: PMC9355874 DOI: 10.1038/s41588-022-01121-z] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/06/2022] [Indexed: 12/14/2022]
Abstract
Clonal hematopoiesis (CH), the clonal expansion of a blood stem cell and its progeny driven by somatic driver mutations, affects over a third of people, yet remains poorly understood. Here we analyze genetic data from 200,453 UK Biobank participants to map the landscape of inherited predisposition to CH, increasing the number of germline associations with CH in European-ancestry populations from 4 to 14. Genes at new loci implicate DNA damage repair (PARP1, ATM, CHEK2), hematopoietic stem cell migration/homing (CD164) and myeloid oncogenesis (SETBP1). Several associations were CH-subtype-specific including variants at TCL1A and CD164 that had opposite associations with DNMT3A- versus TET2-mutant CH, the two most common CH subtypes, proposing key roles for these two loci in CH development. Mendelian randomization analyses showed that smoking and longer leukocyte telomere length are causal risk factors for CH and that genetic predisposition to CH increases risks of myeloproliferative neoplasia, nonhematological malignancies, atrial fibrillation and blood epigenetic ageing.
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Affiliation(s)
- Siddhartha P Kar
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Section of Translational Epidemiology, Division of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Pedro M Quiros
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.
| | - Muxin Gu
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tao Jiang
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge, UK
| | - Jonathan Mitchell
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ryan Langdon
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Section of Translational Epidemiology, Division of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Vivek Iyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Clea Barcena
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - M S Vijayabaskar
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Margarete A Fabre
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Paul Carter
- Division of Cardiovascular Medicine, Department of Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Stephen Burgess
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - George S Vassiliou
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
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Elsayed M, Harry S, Nanua S, Zaidi S, Habib MH, Raza S. Trametinib: Could It Be a Promising Drug to Treat Atypical Chronic Myeloid Leukemia? Cureus 2022; 14:e26619. [PMID: 35949766 PMCID: PMC9356656 DOI: 10.7759/cureus.26619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2022] [Indexed: 12/03/2022] Open
Abstract
Atypical chronic myeloid leukemia (aCML) is a rare disease that is currently classified under the myelodysplastic (MDS)/myeloproliferative neoplasm (MPN) disease spectrum. MDS/MPN diseases are characterized by the absence of the Philadelphia (Ph) chromosome and the overlap between bone marrow fibrosis and dysplastic features. The Ph chromosome, resulting from BCR-ABL1 translocation, helps to distinguish aCML from chronic myeloid leukemia (CML). The currently reported incidence of aCML is imprecise because aCML is diagnosed primarily based on morphological features and other unspecified laboratory findings, and there is an especially high chance of under-diagnosis of aCML and other MDS/MPN diseases. Recent advances in next-generation sequencing (NGS) have allowed a greater understanding of the nature of aCML, providing better opportunities to achieve higher diagnostic accuracy and for the use of more targeted treatment to achieve better outcomes. Herein, we present a case of a 68-year-old woman who came to our hospital complaining of shortness of breath, fatigue, and weakness, who was found to have significantly increased leukocytosis, hepatosplenomegaly, and was negative for the Ph chromosome. Further investigations with NGS revealed mutations in ASXL1, GATA2, NRAS, and SRSF2 but not CSF3R. In addition to this, peripheral smear and bone marrow aspiration findings were suggestive of aCML based on specific morphological findings. Since the patient was ineligible for a stem cell transplant (SCT), symptomatic treatment was started with cell transfusion; however, the patient continued to have symptomatic anemia that required multiple transfusions. A trial with trametinib, a mitogen-activated protein kinase kinase (MEK) inhibitor, was later started as a targeted therapy based on one of her genetic mutations. Interestingly, the patient’s blood counts stabilized, she reported feeling better, and she did not need any blood transfusions for four consecutive months during treatment with trametinib. Unfortunately, our patient later died from sepsis resulting from secondary infections. In light of the significant advancements in NGS, clinicians should always consider utilizing it as a helpful tool to not only establish a rare diagnosis of aCML but also to offer the best available targeted therapy when applicable. This might alleviate the burden associated with the poor prognosis of aCML.
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Wagner U, Wong C, Camenisch U, Zimmermann K, Rechsteiner M, Valtcheva N, Theocharides A, Widmer CC, Manz MG, Moch H, Wild PJ, Balabanov S. Comprehensive Validation of Diagnostic Next-Generation Sequencing Panels for Acute Myeloid Leukemia Patients. J Mol Diagn 2022; 24:935-954. [PMID: 35718092 DOI: 10.1016/j.jmoldx.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/11/2022] [Accepted: 05/06/2022] [Indexed: 11/28/2022] Open
Abstract
Next-generation sequencing has greatly advanced the molecular diagnostics of malignant hematological diseases and provides useful information for clinical decision making. Studies have shown that certain mutations are associated with prognosis and have a direct impact on treatment of affected patients. Therefore, reliable detection of pathogenic variants is critically important. In this study, we aimed to compare four sequencing panels with different characteristics, from number of genes covered to technical aspects of library preparation and data analysis workflows, to find the panel with the best clinical utility for myeloid neoplasms with a special focus on acute myeloid leukemia. Using the Acrometrix Oncology Hotspot Control DNA and DNA from acute myeloid leukemia patients, we evaluated panel performance in terms of coverage, precision, recall, and reproducibility and tested different bioinformatics tools that can be used for the evaluation of any next-generation sequencing panel. Taken together, our results support the reliability of the Acrometrix Oncology Hotspot Control to validate and compare sequencing panels for hematological diseases and show which panel-software combination (platform) has the best performance.
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Affiliation(s)
- Ulrich Wagner
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Christine Wong
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Ulrike Camenisch
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Kathrin Zimmermann
- Division of Medical Oncology and Hematology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Markus Rechsteiner
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Nadejda Valtcheva
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Alexandre Theocharides
- Division of Medical Oncology and Hematology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Corinne C Widmer
- Division of Medical Oncology and Hematology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Markus G Manz
- Division of Medical Oncology and Hematology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Peter J Wild
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany; Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany; Wildlab, University Hospital Frankfurt MVZ GmbH, Frankfurt am Main, Germany.
| | - Stefan Balabanov
- Division of Medical Oncology and Hematology, University Hospital and University of Zurich, Zurich, Switzerland.
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Antonyan L, Ernst C. Putative Roles of SETBP1 Dosage on the SET Oncogene to Affect Brain Development. Front Neurosci 2022; 16:813430. [PMID: 35685777 PMCID: PMC9173722 DOI: 10.3389/fnins.2022.813430] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/19/2022] [Indexed: 12/24/2022] Open
Abstract
Mutations in SET BINDING PROTEIN 1 (SETBP1) cause two different clinically distinguishable diseases called Schinzel–Giedion syndrome (SGS) or SETBP1 deficiency syndrome (SDD). Both disorders are disorders of protein dosage, where SGS is caused by decreased rate of protein breakdown due to mutations in a proteosome targeting domain, and SDD is caused by heterozygous loss-of-function mutations leading to haploinsufficiency. While phenotypes of affected individuals support a role for SETBP1 in brain development, little is known about the mechanisms that might underlie this. The binding partner which gave SETBP1 its name is SET and there is extensive literature on this important oncogene in non-neural tissues. Here we describe different molecular complexes in which SET is involved as well as the role of these complexes in brain development. Based on this information, we postulate how SETBP1 protein dosage might influence these SET-containing molecular pathways and affect brain development. We examine the roles of SET and SETBP1 in acetylation inhibition, phosphatase activity, DNA repair, and cell cycle control. This work provides testable hypotheses for how altered SETBP1 protein dosage affects brain development.
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40
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Enjeti AK, Agarwal R, Blombery P, Chee L, Chua CC, Grigg A, Hamad N, Iland H, Lane S, Perkins A, Singhal D, Tate C, Tiong IS, Ross DM. Panel-based gene testing in myelodysplastic/myeloproliferative neoplasm- overlap syndromes: Australasian Leukaemia and Lymphoma Group (ALLG) consensus statement. Pathology 2022; 54:389-398. [DOI: 10.1016/j.pathol.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 11/30/2022]
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Genomic and Epigenomic Landscape of Juvenile Myelomonocytic Leukemia. Cancers (Basel) 2022; 14:cancers14051335. [PMID: 35267643 PMCID: PMC8909150 DOI: 10.3390/cancers14051335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Juvenile myelomonocytic leukemia (JMML) is a rare pediatric myelodysplastic/myeloproliferative neoplasm characterized by the constitutive activation of the RAS pathway. In spite of the recent progresses in the molecular characterization of JMML, this disease is still a clinical challenge due to its heterogeneity, difficult diagnosis, poor prognosis, and the lack of curative treatment options other than hematopoietic stem cell transplantation (HSCT). In this review, we will provide a detailed overview of the genetic and epigenetic alterations occurring in JMML, and discuss their clinical relevance in terms of disease prognosis and risk of relapse after HSCT. We will also present the most recent advances on novel preclinical and clinical therapeutic approaches directed against JMML molecular targets. Finally, we will outline future research perspectives to further explore the oncogenic mechanism driving JMML leukemogenesis and progression, with special attention to the application of single-cell next-generation sequencing technologies. Abstract Juvenile myelomonocytic leukemia (JMML) is a rare myelodysplastic/myeloproliferative neoplasm of early childhood. Most of JMML patients experience an aggressive clinical course of the disease and require hematopoietic stem cell transplantation, which is currently the only curative treatment. JMML is characterized by RAS signaling hyperactivation, which is mainly driven by mutations in one of five genes of the RAS pathway, including PTPN11, KRAS, NRAS, NF1, and CBL. These driving mutations define different disease subtypes with specific clinico-biological features. Secondary mutations affecting other genes inside and outside the RAS pathway contribute to JMML pathogenesis and are associated with a poorer prognosis. In addition to these genetic alterations, JMML commonly presents aberrant epigenetic profiles that strongly correlate with the clinical outcome of the patients. This observation led to the recent publication of an international JMML stratification consensus, which defines three JMML clinical groups based on DNA methylation status. Although the characterization of the genomic and epigenomic landscapes in JMML has significantly contributed to better understand the molecular mechanisms driving the disease, our knowledge on JMML origin, cell identity, and intratumor and interpatient heterogeneity is still scarce. The application of new single-cell sequencing technologies will be critical to address these questions in the future.
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Tefferi A, Gangat N, Pardanani A, Crispino JD. Myelofibrosis: Genetic Characteristics and the Emerging Therapeutic Landscape. Cancer Res 2022; 82:749-763. [PMID: 34911786 PMCID: PMC9306313 DOI: 10.1158/0008-5472.can-21-2930] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/18/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023]
Abstract
Primary myelofibrosis (PMF) is one of three myeloproliferative neoplasms (MPN) that are morphologically and molecularly inter-related, the other two being polycythemia vera (PV) and essential thrombocythemia (ET). MPNs are characterized by JAK-STAT-activating JAK2, CALR, or MPL mutations that give rise to stem cell-derived clonal myeloproliferation, which is prone to leukemic and, in case of PV and ET, fibrotic transformation. Abnormal megakaryocyte proliferation is accompanied by bone marrow fibrosis and characterizes PMF, while the clinical phenotype is pathogenetically linked to ineffective hematopoiesis and aberrant cytokine expression. Among MPN-associated driver mutations, type 1-like CALR mutation has been associated with favorable prognosis in PMF, while ASXL1, SRSF2, U2AF1-Q157, EZH2, CBL, and K/NRAS mutations have been shown to be prognostically detrimental. Such information has enabled development of exclusively genetic (GIPSS) and clinically integrated (MIPSSv2) prognostic models that facilitate individualized treatment decisions. Allogeneic stem cell transplantation remains the only treatment modality in MF with the potential to prolong survival, whereas drug therapy, including JAK2 inhibitors, is directed mostly at the inflammatory component of the disease and is therefore palliative in nature. Similarly, disease-modifying activity remains elusive for currently available investigational drugs, while their additional value in symptom management awaits controlled confirmation. There is a need for genetic characterization of clinical observations followed by in vitro and in vivo preclinical studies that will hopefully identify therapies that target the malignant clone in MF to improve patient outcomes.
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Affiliation(s)
- Ayalew Tefferi
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, Minnesota.,Corresponding Author: Ayalew Tefferi, Division of Hematology, Department of Medicine, Mayo Clinic, 200 First St SW, Rochester, MN 55905. Phone: 507-284-2511; Fax: 507-266-4972; E-mail:
| | - Naseema Gangat
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Animesh Pardanani
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - John D. Crispino
- Division of Experimental Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee
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Kohyanagi N, Kitamura N, Tanaka K, Mizuno T, Fujiwara N, Ohama T, Sato K. The protein level of the tumor-promoting factor SET is regulated by cell density. J Biochem 2022; 171:295-303. [PMID: 35076073 DOI: 10.1093/jb/mvab125] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/15/2021] [Indexed: 11/14/2022] Open
Abstract
SET/I2PP2A is a multifunctional protein that acts as an intrinsic inhibitor of the tumor suppressor protein phosphatase 2A and as a histone chaperone. Increased SET levels have been observed in various cancers; however, the underlying molecular mechanisms remain unclear. In this study, we found that SET protein accumulates with the increasing density of cultured cells. This phenomenon was observed not only in cancer cell lines but also in non-cancer cell lines. The mRNA levels of SET were not affected by the cell density. Proteasome inhibition decreased SET levels, whereas autophagy inhibition led to SET accumulation, indicating the involvement of autophagy. The mRNA and protein expression of SETBP1, which stabilizes the SET protein, increased with cell density. The decrease in SET level due to the loss of SETBP1 was more pronounced in wild-type cells than that in autophagy-deficient cells. These results have revealed a mechanism underlying the regulation of SET level, wherein increased cell density induces SETBP1 expression and protects SET from autophagy.
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Affiliation(s)
- Naoki Kohyanagi
- Laboratory of Veterinary Pharmacology and Laboratory of Molecular Diagnostics
| | - Nao Kitamura
- Laboratory of Veterinary Pharmacology and Laboratory of Molecular Diagnostics
| | - Keiko Tanaka
- Laboratory of Veterinary Pharmacology and Laboratory of Molecular Diagnostics
| | - Takuya Mizuno
- Laboratory of Molecular Diagnostics and Therapeutics, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan
| | - Nobuyuki Fujiwara
- Laboratory of Drug Discovery and Pharmacology, Faculty of Veterinary Medicine, Okayama University of Science, 794-8555 Ehime, Japan
| | - Takashi Ohama
- Laboratory of Veterinary Pharmacology and Laboratory of Molecular Diagnostics
| | - Koichi Sato
- Laboratory of Veterinary Pharmacology and Laboratory of Molecular Diagnostics
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Nguyen N, Gudmundsson KO, Soltis AR, Oakley K, Roy KR, Han Y, Gurnari C, Maciejewski JP, Crouch G, Ernst P, Dalgard CL, Du Y. Recruitment of MLL1 complex is essential for SETBP1 to induce myeloid transformation. iScience 2022; 25:103679. [PMID: 35036869 PMCID: PMC8749219 DOI: 10.1016/j.isci.2021.103679] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/26/2021] [Accepted: 12/21/2021] [Indexed: 12/12/2022] Open
Abstract
Abnormal activation of SETBP1 due to overexpression or missense mutations occurs frequently in various myeloid neoplasms and associates with poor prognosis. Direct activation of Hoxa9/Hoxa10/Myb transcription by SETBP1 and its missense mutants is essential for their transforming capability; however, the underlying epigenetic mechanisms remain elusive. We found that both SETBP1 and its missense mutant SETBP1(D/N) directly interact with histone methyltransferase MLL1. Using a combination of ChIP-seq and RNA-seq analysis in primary hematopoietic stem and progenitor cells, we uncovered extensive overlap in their genomic occupancy and their cooperation in activating many oncogenic transcription factor genes including Hoxa9/Hoxa10/Myb and a large group of ribosomal protein genes. Genetic ablation of Mll1 as well as treatment with an inhibitor of the MLL1 complex OICR-9429 abrogated Setbp1/Setbp1(D/N)-induced transcriptional activation and transformation. Thus, the MLL1 complex plays a critical role in Setbp1-induced transcriptional activation and transformation and represents a promising target for treating myeloid neoplasms with SETBP1 activation.
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Affiliation(s)
- Nhu Nguyen
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Kristbjorn O. Gudmundsson
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Anthony R. Soltis
- The American Genome Center (TAGC), Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Kevin Oakley
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Kartik R. Roy
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Yufen Han
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jaroslaw P. Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Gary Crouch
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Patricia Ernst
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pharmacology, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Clifton L. Dalgard
- The American Genome Center (TAGC), Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Yang Du
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
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45
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Mori N, Ohwashi-Miyazaki M, Yoshinaga K, Ogasawara T, Marshall S, Shiseki M, Sakura H, Tanaka J. Genetic alterations in patients with chronic leucocytosis and persistent thrombocytosis. J Genet 2022. [DOI: 10.1007/s12041-021-01354-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Diaz-Colunga J, Diaz-Uriarte R. Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next? PLoS Comput Biol 2021; 17:e1009055. [PMID: 34932572 PMCID: PMC8730404 DOI: 10.1371/journal.pcbi.1009055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 01/05/2022] [Accepted: 11/25/2021] [Indexed: 12/13/2022] Open
Abstract
Accurate prediction of tumor progression is key for adaptive therapy and precision medicine. Cancer progression models (CPMs) can be used to infer dependencies in mutation accumulation from cross-sectional data and provide predictions of tumor progression paths. However, their performance when predicting complete evolutionary trajectories is limited by violations of assumptions and the size of available data sets. Instead of predicting full tumor progression paths, here we focus on short-term predictions, more relevant for diagnostic and therapeutic purposes. We examine whether five distinct CPMs can be used to answer the question "Given that a genotype with n mutations has been observed, what genotype with n + 1 mutations is next in the path of tumor progression?" or, shortly, "What genotype comes next?". Using simulated data we find that under specific combinations of genotype and fitness landscape characteristics CPMs can provide predictions of short-term evolution that closely match the true probabilities, and that some genotype characteristics can be much more relevant than global features. Application of these methods to 25 cancer data sets shows that their use is hampered by a lack of information needed to make principled decisions about method choice. Fruitful use of these methods for short-term predictions requires adapting method's use to local genotype characteristics and obtaining reliable indicators of performance; it will also be necessary to clarify the interpretation of the method's results when key assumptions do not hold.
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Affiliation(s)
- Juan Diaz-Colunga
- Department of Biochemistry, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
- Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (UAM-CSIC), Madrid, Spain
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut, United States of America
| | - Ramon Diaz-Uriarte
- Department of Biochemistry, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
- Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (UAM-CSIC), Madrid, Spain
- * E-mail:
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47
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Avramović V, Frederiksen SD, Brkić M, Tarailo-Graovac M. Driving mosaicism: somatic variants in reference population databases and effect on variant interpretation in rare genetic disease. Hum Genomics 2021; 15:71. [PMID: 34906245 PMCID: PMC8670043 DOI: 10.1186/s40246-021-00371-y] [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: 09/27/2021] [Accepted: 11/29/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Genetic variation databases provide invaluable information on the presence and frequency of genetic variants in the 'untargeted' human population, aggregated with the primary goal to facilitate the interpretation of clinically important variants. The presence of somatic variants in such databases can affect variant assessment in undiagnosed rare disease (RD) patients. Previously, the impact of somatic mosaicism was only considered in relation to two Mendelian disease-associated genes. Here, we expand the analyses to identify additional mosaicism-prone genes in blood-derived reference population databases. RESULTS To identify additional mosaicism-prone genes relevant to RDs, we focused on known/previously established ClinVar pathogenic and likely pathogenic single-nucleotide variants, residing in genes associated with early onset, severe autosomal dominant diseases. We asked whether any of these variants are present in a higher-than-expected frequency in the reference population databases and whether there is evidence of somatic origin (i.e., allelic imbalance) rather than germline heterozygosity (~ half of the reads supporting alternative allele). The mosaicism-prone genes identified were further categorized according to the processes they are involved in. Beyond the previously reported ASXL1 and DNMT3A, we identified 7 additional autosomal dominant RD-associated genes with known pathogenic single-nucleotide variants present in the reference population databases and good evidence of allelic imbalance: BRAF, CBL, FGFR3, IDH2, KRAS, PTPN11 and SETBP1. From this group of 9 genes, the majority (n = 7) was important for hematopoiesis. In addition, 4 of these genes were involved in cell proliferation. Further assessment of the known 156 hematopoietic genes led to identification of 48 genes (21 not yet associated with RDs) with at least some evidence of mosaicism detectable in reference population databases. CONCLUSIONS These results stress the importance of considering genes involved in hematopoiesis and cell proliferation when interpreting the presence and frequency of genetic variants in blood-derived reference population databases, both public and private. This is especially important when considering new variants of uncertain significance in known hematopoietic/cell proliferation RD genes and future novel gene-disease associations involving this class of genes.
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Affiliation(s)
- Vladimir Avramović
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Simona Denise Frederiksen
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Marjana Brkić
- Department of Neurobiology, Institute for Biological Research, University of Belgrade, 11060, Belgrade, Republic of Serbia.,VIB Center for Inflammation Research, Ghent University, 9052, Ghent, Belgium
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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48
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Kuendgen A, Kasprzak A, Germing U. Hybrid or Mixed Myelodysplastic/Myeloproliferative Disorders - Epidemiological Features and Overview. Front Oncol 2021; 11:778741. [PMID: 34869027 PMCID: PMC8635204 DOI: 10.3389/fonc.2021.778741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
The WHO-category Myelodysplastic/Myeloproliferative neoplasms (MDS/MPNs) recognizes a unique group of clonal myeloid malignancies exhibiting overlapping features of myelodysplastic as well as myeloproliferative neoplasms. The group consists of chronic myelomonocytic leukemia (CMML), atypical chronic myeloid leukemia, BCR-ABL1-negative (aCML), juvenile myelomonocytic leukemia (JMML), myelodysplastic/myeloproliferative neoplasm with ringed sideroblasts and thrombocytosis (MDS/MPN-RS-T), and myelodysplastic/myeloproliferative neoplasms, unclassifiable (MDS/MPN-U). The most frequent entity in this category is CMML, while all other diseases are extremely rare. Thus, only very limited data on the epidemiology of these subgroups exists. An appropriate diagnosis and classification can be challenging since the diagnosis is still largely based on morphologic criteria and myelodysplastic as well as myeloproliferative features can be found in various occurrences. The diseases in this category share several features that are common in this specific WHO-category, but also exhibit specific traits for each disease. This review summarizes published data on epidemiological features and offers a brief overview of the main diagnostic criteria and clinical characteristics of the five MDS/MPN subgroups.
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Affiliation(s)
- Andrea Kuendgen
- Department of Hematology, Oncology, and Clinical Immunology, Heinrich-Heine-University Hospital Duesseldorf, Duesseldorf, Germany
| | - Annika Kasprzak
- Department of Hematology, Oncology, and Clinical Immunology, Heinrich-Heine-University Hospital Duesseldorf, Duesseldorf, Germany
| | - Ulrich Germing
- Department of Hematology, Oncology, and Clinical Immunology, Heinrich-Heine-University Hospital Duesseldorf, Duesseldorf, Germany
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49
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Fontana D, Gambacorti-Passerini C, Piazza R. Molecular Pathogenesis of BCR-ABL-Negative Atypical Chronic Myeloid Leukemia. Front Oncol 2021; 11:756348. [PMID: 34858828 PMCID: PMC8631780 DOI: 10.3389/fonc.2021.756348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/22/2021] [Indexed: 11/30/2022] Open
Abstract
Atypical chronic myeloid leukemia is a rare disease whose pathogenesis has long been debated. It currently belongs to the group of myelodysplastic/myeloproliferative disorders. In this review, an overview on the current knowledge about diagnosis, prognosis, and genetics is presented, with a major focus on the recent molecular findings. We describe here the molecular pathogenesis of the disease, focusing on the mechanisms of action of the main mutations as well as on gene expression profiling. We also present the treatment options focusing on emerging targeted therapies.
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Affiliation(s)
- Diletta Fontana
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Carlo Gambacorti-Passerini
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.,Hematology and Clinical Research Unit, San Gerardo Hospital, Monza, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.,Hematology and Clinical Research Unit, San Gerardo Hospital, Monza, Italy.,Bicocca Bioinformatics, Biostatistics and Bioimaging Centre (B4), University of Milano-Bicocca, Milan, Italy
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50
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Carratt SA, Braun TP, Coblentz C, Schonrock Z, Callahan R, Curtiss BM, Maloney L, Foley AC, Maxson JE. Mutant SETBP1 enhances NRAS-driven MAPK pathway activation to promote aggressive leukemia. Leukemia 2021; 35:3594-3599. [PMID: 34002029 PMCID: PMC8595361 DOI: 10.1038/s41375-021-01278-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/12/2021] [Accepted: 04/29/2021] [Indexed: 01/07/2023]
Abstract
Mutations in SET-binding protein 1 (SETBP1) are associated with poor outcomes in myeloid leukemias. In the Ras-driven leukemia, juvenile myelomonocytic leukemia, SETBP1 mutations are enriched in relapsed disease. While some mechanisms for SETBP1-driven oncogenesis have been established, it remains unclear how SETBP1 specifically modulates the biology of Ras-driven leukemias. In this study, we found that when co-expressed with Ras pathway mutations, SETBP1 promoted oncogenic transformation of murine bone marrow in vitro and aggressive myeloid leukemia in vivo. We demonstrate that SETBP1 enhances the NRAS gene expression signature, driving upregulation of mitogen-activated protein kinase (MAPK) signaling and downregulation of differentiation pathways. SETBP1 also enhances NRAS-driven phosphorylation of MAPK proteins. Cells expressing NRAS and SETBP1 are sensitive to inhibitors of the MAPK pathway, and treatment with the MEK inhibitor trametinib conferred a survival benefit in a mouse model of NRAS/SETBP1-mutant disease. Our data demonstrate that despite driving enhanced MAPK signaling, SETBP1-mutant cells remain susceptible to trametinib in vitro and in vivo, providing encouraging preclinical data for the use of trametinib in SETBP1-mutant disease.
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Affiliation(s)
| | | | | | | | | | | | | | - Amy C. Foley
- Oregon Health & Science University, Portland, OR
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