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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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Jones AG, Aquilino M, Tinker RJ, Duncan L, Jenkins Z, Carvill GL, DeWard SJ, Grange DK, Hajianpour MJ, Halliday BJ, Holder-Espinasse M, Horvath J, Maitz S, Nigro V, Morleo M, Paul V, Spencer C, Esterhuizen AI, Polster T, Spano A, Gómez-Lozano I, Kumar A, Poke G, Phillips JA, Underhill HR, Gimenez G, Namba T, Robertson SP. Clustered de novo start-loss variants in GLUL result in a developmental and epileptic encephalopathy via stabilization of glutamine synthetase. Am J Hum Genet 2024; 111:729-741. [PMID: 38579670 PMCID: PMC11023914 DOI: 10.1016/j.ajhg.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 04/07/2024] Open
Abstract
Glutamine synthetase (GS), encoded by GLUL, catalyzes the conversion of glutamate to glutamine. GS is pivotal for the generation of the neurotransmitters glutamate and gamma-aminobutyric acid and is the primary mechanism of ammonia detoxification in the brain. GS levels are regulated post-translationally by an N-terminal degron that enables the ubiquitin-mediated degradation of GS in a glutamine-induced manner. GS deficiency in humans is known to lead to neurological defects and death in infancy, yet how dysregulation of the degron-mediated control of GS levels might affect neurodevelopment is unknown. We ascertained nine individuals with severe developmental delay, seizures, and white matter abnormalities but normal plasma and cerebrospinal fluid biochemistry with de novo variants in GLUL. Seven out of nine were start-loss variants and two out of nine disrupted 5' UTR splicing resulting in splice exclusion of the initiation codon. Using transfection-based expression systems and mass spectrometry, these variants were shown to lead to translation initiation of GS from methionine 18, downstream of the N-terminal degron motif, resulting in a protein that is stable and enzymatically competent but insensitive to negative feedback by glutamine. Analysis of human single-cell transcriptomes demonstrated that GLUL is widely expressed in neuro- and glial-progenitor cells and mature astrocytes but not in post-mitotic neurons. One individual with a start-loss GLUL variant demonstrated periventricular nodular heterotopia, a neuronal migration disorder, yet overexpression of stabilized GS in mice using in utero electroporation demonstrated no migratory deficits. These findings underline the importance of tight regulation of glutamine metabolism during neurodevelopment in humans.
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Affiliation(s)
- Amy G Jones
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Matilde Aquilino
- Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Rory J Tinker
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Laura Duncan
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Zandra Jenkins
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Gemma L Carvill
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | | | | | - Benjamin J Halliday
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | | | | | - Silvia Maitz
- Medical Genetics Service, Oncology Department of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy
| | - Manuela Morleo
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy
| | | | - Careni Spencer
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Department of Medicine, Division of Human Genetics, Groote Schuur Hospital, Cape Town, South Africa
| | - Alina I Esterhuizen
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Tilman Polster
- Department of Epileptology (Krankenhaus Mara, Bethel Epilepsy Center) Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Alice Spano
- Maggiore Della Carità Hospital, Novara, Italy
| | - Inés Gómez-Lozano
- Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Abhishek Kumar
- Centre for Protein Research, University of Otago, Dunedin, New Zealand
| | - Gemma Poke
- Genetics Health Service New Zealand, Wellington Hospital, Wellington, New Zealand
| | | | | | - Gregory Gimenez
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Takashi Namba
- Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Stephen P Robertson
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Lomeli C. S, Kristin B. A. Epigenetic regulation of craniofacial development and disease. Birth Defects Res 2024; 116:e2271. [PMID: 37964651 PMCID: PMC10872612 DOI: 10.1002/bdr2.2271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND The formation of the craniofacial complex relies on proper neural crest development. The gene regulatory networks (GRNs) and signaling pathways orchestrating this process have been extensively studied. These GRNs and signaling cascades are tightly regulated as alterations to any stage of neural crest development can lead to common congenital birth defects, including multiple syndromes affecting facial morphology as well as nonsyndromic facial defects, such as cleft lip with or without cleft palate. Epigenetic factors add a hierarchy to the regulation of transcriptional networks and influence the spatiotemporal activation or repression of specific gene regulatory cascades; however less is known about their exact mechanisms in controlling precise gene regulation. AIMS In this review, we discuss the role of epigenetic factors during neural crest development, specifically during craniofacial development and how compromised activities of these regulators contribute to congenital defects that affect the craniofacial complex.
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Affiliation(s)
- Shull Lomeli C.
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Artinger Kristin B.
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Whitlock JH, Wilk EJ, Howton TC, Clark AD, Lasseigne BN. The landscape of SETBP1 gene expression and transcription factor activity across human tissues. bioRxiv 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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Chopra M, Modi ME, Dies KA, Chamberlin NL, Buttermore ED, Brewster SJ, Prock L, Sahin M. GENE TARGET: A framework for evaluating Mendelian neurodevelopmental disorders for gene therapy. Mol Ther Methods Clin Dev 2022; 27:32-46. [PMID: 36156879 DOI: 10.1016/j.omtm.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Interest in gene-based therapies for neurodevelopmental disorders is increasing exponentially, driven by the rise in recognition of underlying genetic etiology, progress in genomic technology, and recent proof of concept in several disorders. The current prioritization of one genetic disorder over another for development of therapies is driven by competing interests of pharmaceutical companies, advocacy groups, and academic scientists. Although these are all valid perspectives, a consolidated framework will facilitate more efficient and rational gene therapy development. Here we outline features of Mendelian neurodevelopmental disorders that warrant consideration when determining suitability for gene therapy. These features fit into four broad domains: genetics, preclinical validation, clinical considerations, and ethics. We propose a simple mnemonic, GENE TARGET, to remember these features and illustrate how they could be scored using a preliminary scoring rubric. In this suggested rubric, for a given disorder, scores for each feature may be added up to a composite GENE TARGET suitability (GTS) score. In addition to proposing a systematic method to evaluate and compare disorders, our framework helps identify gaps in the translational pipeline for a given disorder, which can inform prioritization of future research efforts.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Fang F, Liu C, Li Q, Xu R, Zhang T, Shen X. The Role of SETBP1 in Gastric Cancer: Friend or Foe. Front Oncol 2022; 12:908943. [PMID: 35898891 PMCID: PMC9309353 DOI: 10.3389/fonc.2022.908943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundGastric cancer (GC) remains a common disease with a poor prognosis worldwide. The SET binding protein 1 (SETBP1) has been implicated in the pathogenesis of several cancers and plays a dual role as an oncogene and a tumor suppressor gene. However, the role and underlying mechanism of SETBP1 in GC remain unclear.Materials and MethodsWe used next-generation RNA sequencing (RNA-seq) data from The Cancer Genome Atlas (TCGA) to explore the correlation between SETBP1 expression and tumor progression. We then quantified SETBP1 expression in GC cells with real-time quantitative polymerase chain reactions (RT-qPCR). The chi-square test and logistic regression were used to assess the correlation between SETBP1 expression and clinicopathological features. Kaplan-Meier survival analysis and Cox proportional hazards regression model were used to assess the relationship between SETBP1 expression and survival. Finally, gene set enrichment analyses (GSEA) were used to examine GC-related signaling pathways in low and high SETBP1 expressing samples.ResultsWe found SETBP1 expression levels in GC tissues to be significantly lower than in adjacent non-tumor tissues in the TCGA database. In addition, SETBP1 expression differed significantly between groups classified by tumor differentiation. Furthermore, SETBP1 expression in diffuse-type GC was significantly higher than in intestinal-type GC. However, it did not differ significantly across pathological- or T-stage groups. RT-qPCR and comprehensive meta-analysis showed that SETBP1 expression is downregulated in GC cells and tissues. Interestingly, SETBP1 expression in poorly- or un-differentiated GC cells was higher than in well-differentiated GC cells. Moreover, the chi-square test and logistic regression analyses showed that SETBP1 expression correlates significantly with tumor differentiation. Kaplan–Meier curves indicated that patients with relatively high SETBP1 expression had a poor prognosis. Multivariate analyses indicated that SETBP1 expression might be an important predictor of poor overall survival in GC patients. GSEA indicated that 20 signaling pathways were significantly enriched in samples with high and low SETBP1 expression.ConclusionSETBP1 may play a dual role in GC progression.
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Affiliation(s)
- Fujin Fang
- Key Laboratory of Environmental Medical Engineering and Education Ministry, School of Public Health, Southeast University, Nanjing, China
- Department of Preventive Medicine, School of Public Health, Southeast University, Nanjing, China
| | - Chengyou Liu
- Department of Medical Engineering, Nanjing First Hospital, Nanjing, China
| | - Qiong Li
- Key Laboratory of Environmental Medical Engineering and Education Ministry, School of Public Health, Southeast University, Nanjing, China
- Department of Preventive Medicine, School of Public Health, Southeast University, Nanjing, China
| | - Rui Xu
- Key Laboratory of Environmental Medical Engineering and Education Ministry, School of Public Health, Southeast University, Nanjing, China
- Department of Preventive Medicine, School of Public Health, Southeast University, Nanjing, China
| | - Tiantian Zhang
- Department of Clinical Laboratory, The Third People’s Hospital of Bengbu, Bengbu, China
| | - Xiaobing Shen
- Key Laboratory of Environmental Medical Engineering and Education Ministry, School of Public Health, Southeast University, Nanjing, China
- Department of Preventive Medicine, School of Public Health, Southeast University, Nanjing, China
- *Correspondence: Xiaobing Shen,
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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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Fiñana C, Gómez-molina N, Alonso-moreno S, Belver L. Genomic and Epigenomic Landscape of Juvenile Myelomonocytic Leukemia. Cancers (Basel) 2022; 14:1335. [PMID: 35267643 PMCID: PMC8909150 DOI: 10.3390/cancers14051335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Yang H, Liu Z, Chen D, Lin W, Wang L, Chen T, Wang R, Yan X. Detection of a novel SETBP1 variant in a Chinese neonate with Schinzel-Giedion syndrome. Front Pediatr 2022; 10:920741. [PMID: 36147799 PMCID: PMC9488805 DOI: 10.3389/fped.2022.920741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 08/12/2022] [Indexed: 11/23/2022] Open
Abstract
Schinzel-Giedion syndrome (SGS) is a multiple malformation syndrome characterized by typical facial features, severe neurodevelopmental delay, and multiple congenital abnormalities. SGS is associated with de novo pathogenic variants in the SETBP1 gene. In specific, SETBP1 variants in over 50 patients with classical or non-classical SGS were clustered within exon 4. A male Chinese neonate with dysmorphic facial features, nervous system disorders, and organ malformations at birth was examined in this study and long-term followed-up. Whole-exome sequencing was performed to identify any underlying pathogenic variants in the proband. Additionally, we reviewed the literature that documents the main clinical features and underlying variants of all patients genetically diagnosed with SGS. The neonate had a characteristic midface retraction, abnormal electroencephalogram waveforms, and genital abnormalities. The patient did not initially develop hydronephrosis or undergo a comprehensive skeletal assessment. Six months after birth, the patient had an epileptic seizure and experienced persistent neurodevelopmental delay with auditory and visual abnormalities. Color Doppler ultrasonography at 18 months revealed hydronephrosis and bilateral widening of the lateral ventricles. The patient died suddenly 20.5 months after birth. Whole-exome sequencing revealed a heterozygous de novo variant (c.2605A > G:p.S869G) in exon 4 degradation sequence in SETBP1. The reported de novo heterozygous variant in SETBP1 (c.2605A > G:p.S869G) broadens the knowledge of the scientific community's on the possible SGS genetic alterations. To the best of our knowledge, this is the first report of SETBP1 variant (c.2605A > G:p.S869G) in SGS. The clinical manifestations of neonatal SGS are atypical, and genetic testing is crucial for diagnosis. Long-term follow-up should be conducted after diagnosis to optimize the therapeutic interventions.
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Affiliation(s)
- Hansong Yang
- Department of Neonatology, Quanzhou Maternity and Children's Hospital, Quanzhou, China
| | - Zhiyong Liu
- Department of Neonatology, Quanzhou Maternity and Children's Hospital, Quanzhou, China
| | - Dongmei Chen
- Department of Neonatology, Quanzhou Maternity and Children's Hospital, Quanzhou, China
| | - Weiru Lin
- Department of Ultrasound, Quanzhou Maternity and Children's Hospital, Quanzhou, China
| | - Lin Wang
- Xiamen Genokon Medical Technology Co., Ltd., Xiamen, China
| | - Tianfeng Chen
- Department of Radiology, Quanzhou Maternity and Children's Hospital, Quanzhou, China
| | - Ruiquan Wang
- Department of Neonatology, Quanzhou Maternity and Children's Hospital, Quanzhou, China
| | - Xialin Yan
- Department of Neonatology, Quanzhou Maternity and Children's Hospital, Quanzhou, China
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Li J, Jing Y, Liu Y, Ru Y, Ju M, Zhao Y, Li G. Large chromosomal deletions and impaired homologous recombination repairing in HEK293T cells exposed to polychlorinated biphenyl 153. PeerJ 2021; 9:e11816. [PMID: 34395077 PMCID: PMC8325425 DOI: 10.7717/peerj.11816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/29/2021] [Indexed: 11/25/2022] Open
Abstract
Background Polychlorinated biphenyls (PCBs) are persistent pollutants with carcinogenesis and mutagenesis effects which have been closely associated with PCBs-induced DNA damage. However, the detailed DNA damage events and corresponding pathway alterations under PCBs poisoning is still not well understood. Methods Whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) were used to explore genome wide variations and related pathway changes in HEK293T cells that challenged by 15 µM PCB153 for 96 h in vitro. Double strand breaks (DSBs) were measured by 53BP1 foci detection, altered pathways were confirmed by quantitative real-time PCR (qPCR). Results The results indicated that abundant copy number variations (CNVs), including four duplications and 30 deletions, occurred in PCB153-exposed HEK293T cells. Multiple large fragment deletions (>1 Mb) involving up to 245 Mb regions on many chromosomes. Missense mutations were found in six tumor susceptibility genes, two of which are key members participating in homologous recombination (HR) repair response, BRCA1 and BRCA2. RNA-seq data showed that PCB153 poisoning apparently suppressedHR repairing genes. Besides, 15 µM PCB153 exposure significantly increased 53BP1 foci formation and effectively reduced BRCA1, RAD51B and RAD51C expression, indicating an elevated DSBs and impaired HR repairing. Conclusion This study firstly reported multiple large chromosomal deletions and impaired HR repairing in PCB153-exposed HEK293T cells, which provided a new insight into the understanding of early response and the mechanism underlying PCB153 genotoxicity. The chromosomal instabilities might be related to the impaired HR repairing that induced by PCB153; however, further investigations, especially on actual toxic effects of human body, are needed to confirm such speculation.
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Affiliation(s)
- Jiaci Li
- Tianjin Medical University, Tianjin, China
| | | | - Yi Liu
- Tianjin Medical University, Tianjin, China
| | - Yawei Ru
- Tianjin Medical University, Tianjin, China
| | - Mingyan Ju
- Tianjin Medical University, Tianjin, China
| | - Yuxia Zhao
- Tianjin Medical University, Tianjin, China
| | - Guang Li
- Tianjin Medical University, Tianjin, China
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Verbinnen I, Vaneynde P, Reynhout S, Lenaerts L, Derua R, Houge G, Janssens V. Protein Phosphatase 2A (PP2A) mutations in brain function, development, and neurologic disease. Biochem Soc Trans 2021:BST20201313. [PMID: 34241636 DOI: 10.1042/BST20201313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/15/2022]
Abstract
By removing Ser/Thr-specific phosphorylations in a multitude of protein substrates in diverse tissues, Protein Phosphatase type 2A (PP2A) enzymes play essential regulatory roles in cellular signalling and physiology, including in brain function and development. Here, we review current knowledge on PP2A gene mutations causally involved in neurodevelopmental disorders and intellectual disability, focusing on PPP2CA, PPP2R1A and PPP2R5D. We provide insights into the impact of these mutations on PP2A structure, substrate specificity and potential function in neurobiology and brain development.
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19
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Banfi F, Rubio A, Zaghi M, Massimino L, Fagnocchi G, Bellini E, Luoni M, Cancellieri C, Bagliani A, Di Resta C, Maffezzini C, Ianielli A, Ferrari M, Piazza R, Mologni L, Broccoli V, Sessa A. SETBP1 accumulation induces P53 inhibition and genotoxic stress in neural progenitors underlying neurodegeneration in Schinzel-Giedion syndrome. Nat Commun 2021; 12:4050. [PMID: 34193871 PMCID: PMC8245514 DOI: 10.1038/s41467-021-24391-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 06/18/2021] [Indexed: 02/06/2023] Open
Abstract
The investigation of genetic forms of juvenile neurodegeneration could shed light on the causative mechanisms of neuronal loss. Schinzel-Giedion syndrome (SGS) is a fatal developmental syndrome caused by mutations in the SETBP1 gene, inducing the accumulation of its protein product. SGS features multi-organ involvement with severe intellectual and physical deficits due, at least in part, to early neurodegeneration. Here we introduce a human SGS model that displays disease-relevant phenotypes. We show that SGS neural progenitors exhibit aberrant proliferation, deregulation of oncogenes and suppressors, unresolved DNA damage, and resistance to apoptosis. Mechanistically, we demonstrate that high SETBP1 levels inhibit P53 function through the stabilization of SET, which in turn hinders P53 acetylation. We find that the inheritance of unresolved DNA damage in SGS neurons triggers the neurodegenerative process that can be alleviated either by PARP-1 inhibition or by NAD + supplementation. These results implicate that neuronal death in SGS originates from developmental alterations mainly in safeguarding cell identity and homeostasis.
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MESH Headings
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/metabolism
- Abnormalities, Multiple/pathology
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cells, Cultured
- Craniofacial Abnormalities/genetics
- Craniofacial Abnormalities/metabolism
- Craniofacial Abnormalities/pathology
- DNA Damage
- Hand Deformities, Congenital/genetics
- Hand Deformities, Congenital/metabolism
- Hand Deformities, Congenital/pathology
- Heredodegenerative Disorders, Nervous System/genetics
- Heredodegenerative Disorders, Nervous System/metabolism
- Heredodegenerative Disorders, Nervous System/pathology
- Humans
- Intellectual Disability/genetics
- Intellectual Disability/metabolism
- Intellectual Disability/pathology
- Mutation
- Nails, Malformed/genetics
- Nails, Malformed/metabolism
- Nails, Malformed/pathology
- Neural Stem Cells/metabolism
- Neural Stem Cells/pathology
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Organoids
- Tumor Suppressor Protein p53/antagonists & inhibitors
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Affiliation(s)
- Federica Banfi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- CNR Institute of Neuroscience, Milan, Italy
| | - Alicia Rubio
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- CNR Institute of Neuroscience, Milan, Italy
| | - Mattia Zaghi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Massimino
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Fagnocchi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Edoardo Bellini
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Mirko Luoni
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Cinzia Cancellieri
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Human Induced Pluripotent Stem Cells service, Istituto Italiano di Oncologia Molecolare (IFOM), Milan, Italy
| | - Anna Bagliani
- Medical Oncology Unit, ASST Ovest Milanese, Legnano Hospital, Legnano, Italy
| | - Chiara Di Resta
- Vita-Salute San Raffaele University, Milan, Italy
- Unit of Genomics for human disease diagnosis, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Camilla Maffezzini
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angelo Ianielli
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- CNR Institute of Neuroscience, Milan, Italy
| | | | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Luca Mologni
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Vania Broccoli
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- CNR Institute of Neuroscience, Milan, Italy
| | - Alessandro Sessa
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy.
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20
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Leonardi E, Bettella E, Pelizza MF, Aspromonte MC, Polli R, Boniver C, Sartori S, Milani D, Murgia A. Identification of SETBP1 Mutations by Gene Panel Sequencing in Individuals With Intellectual Disability or With "Developmental and Epileptic Encephalopathy". Front Neurol 2021; 11:593446. [PMID: 33391157 PMCID: PMC7772201 DOI: 10.3389/fneur.2020.593446] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/16/2020] [Indexed: 11/17/2022] Open
Abstract
SETBP1 mutations are associated with the Schinzel-Giedion syndrome (SGS), characterized by profound neurodevelopmental delay, typical facial features, and multiple congenital malformations (OMIM 269150). Refractory epilepsy is a common feature of SGS. Loss of function mutations have been typically associated with a distinct and milder phenotype characterized by intellectual disability and expressive speech impairment. Here we report three variants of SETBP1, two novel de novo truncating mutations, identified by NGS analysis of an Intellectual Disability gene panel in 600 subjects with non-specific neurodevelopmental disorders, and one missense identified by a developmental epilepsy gene panel tested in 56 pediatric epileptic cases. The three individuals carrying the identified SETBP1 variants presented mild to severe developmental delay and lacked the cardinal features of classical SGS. One of these subjects, carrying the c.1765C>T (p.Arg589*) mutation, had mild Intellectual Disability with speech delay; the second one carrying the c.2199_2203del (p.Glu734Alafs19*) mutation had generalized epilepsy, responsive to treatment, and moderate Intellectual Disability; the third patient showed a severe cognitive defects and had a history of drug resistant epilepsy with West syndrome evolved into a Lennox-Gastaut syndrome. This latter subject carries the missense c.2572G>A (p.Glu858Lys) variant, which is absent from the control population, reported as de novo in a subject with ASD, and located close to the SETBP1 hot spot for SGS-associated mutations. Our findings contribute to further characterizing the associated phenotypes and suggest inclusion of SETBP1 in the list of prioritized genes for the genetic diagnosis of overlapping phenotypes ranging from non-specific neurodevelopmental disorders to “developmental and epileptic encephalopathy” (DEE).
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Affiliation(s)
- Emanuela Leonardi
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città Della Speranza, Padua, Italy
| | - Elisa Bettella
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città Della Speranza, Padua, Italy
| | - Maria Federica Pelizza
- Paediatric Neurology and Neurophysiology Unit, Department of Woman and Child Health, University Hospital of Padova, Padua, Italy
| | - Maria Cristina Aspromonte
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città Della Speranza, Padua, Italy
| | - Roberta Polli
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città Della Speranza, Padua, Italy
| | - Clementina Boniver
- Paediatric Neurology and Neurophysiology Unit, Department of Woman and Child Health, University Hospital of Padova, Padua, Italy
| | - Stefano Sartori
- Paediatric Neurology and Neurophysiology Unit, Department of Woman and Child Health, University Hospital of Padova, Padua, Italy
| | - Donatella Milani
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessandra Murgia
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica (IRP), Città Della Speranza, Padua, Italy
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21
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Provenzano A, La Barbera A, Scagnet M, Pagliazzi A, Traficante G, Pantaleo M, Tiberi L, Vergani D, Kurtas NE, Guarducci S, Bargiacchi S, Forzano G, Artuso R, Palazzo V, Kura A, Giordano F, di Feo D, Mortilla M, De Filippi C, Mattei G, Garavelli L, Giusti B, Genitori L, Zuffardi O, Giglio S. Chiari 1 malformation and exome sequencing in 51 trios: the emerging role of rare missense variants in chromatin-remodeling genes. Hum Genet 2020; 140:625-647. [PMID: 33337535 PMCID: PMC7981314 DOI: 10.1007/s00439-020-02231-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/20/2020] [Indexed: 02/07/2023]
Abstract
Type 1 Chiari malformation (C1M) is characterized by cerebellar tonsillar herniation of 3–5 mm or more, the frequency of which is presumably much higher than one in 1000 births, as previously believed. Its etiology remains undefined, although a genetic basis is strongly supported by C1M presence in numerous genetic syndromes associated with different genes. Whole-exome sequencing (WES) in 51 between isolated and syndromic pediatric cases and their relatives was performed after confirmation of the defect by brain magnetic resonance image (MRI). Moreover, in all the cases showing an inherited candidate variant, brain MRI was performed in both parents and not only in the carrier one to investigate whether the defect segregated with the variant. More than half of the variants were Missense and belonged to the same chromatin-remodeling genes whose protein truncation variants are associated with severe neurodevelopmental syndromes. In the remaining cases, variants have been detected in genes with a role in cranial bone sutures, microcephaly, neural tube defects, and RASopathy. This study shows that the frequency of C1M is widely underestimated, in fact many of the variants, in particular those in the chromatin-remodeling genes, were inherited from a parent with C1M, either asymptomatic or with mild symptoms. In addition, C1M is a Mendelian trait, in most cases inherited as dominant. Finally, we demonstrate that modifications of the genes that regulate chromatin architecture can cause localized anatomical alterations, with symptoms of varying degrees.
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Affiliation(s)
- Aldesia Provenzano
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy.
| | - Andrea La Barbera
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Mirko Scagnet
- Department of Neurosurgery, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Angelica Pagliazzi
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Marilena Pantaleo
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Lucia Tiberi
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Debora Vergani
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Nehir Edibe Kurtas
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Silvia Guarducci
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Giulia Forzano
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Rosangela Artuso
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Viviana Palazzo
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Ada Kura
- Department of Experimental and Clinical Medicine, Atherothrombotic Diseases Center, University of Florence, Careggi Hospital, Florence, Italy
| | - Flavio Giordano
- Department of Neurosurgery, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Daniele di Feo
- Department of Radiology, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Marzia Mortilla
- Department of Radiology, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Claudio De Filippi
- Department of Radiology, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Gianluca Mattei
- Department of Information Engineering, University of Florence, Florence, Italy
| | - Livia Garavelli
- Medical Genetics Unit, Department of Mother and Child, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Betti Giusti
- Department of Experimental and Clinical Medicine, Atherothrombotic Diseases Center, University of Florence, Careggi Hospital, Florence, Italy
| | - Lorenzo Genitori
- Department of Neurosurgery, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Orsetta Zuffardi
- Unit of Medical Genetics, Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Sabrina Giglio
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy.,Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
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22
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Leone MP, Palumbo P, Palumbo O, Di Muro E, Chetta M, Laforgia N, Resta N, Stella A, Castellana S, Mazza T, Castori M, Carella M, Bukvic N. The recurrent SETBP1 c.2608G > A, p.(Gly870Ser) variant in a patient with Schinzel-Giedion syndrome: an illustrative case of the utility of whole exome sequencing in a critically ill neonate. Ital J Pediatr 2020; 46:74. [PMID: 32460883 PMCID: PMC7254667 DOI: 10.1186/s13052-020-00839-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
Background Schinzel-Giedion syndrome (SGS) is a multiple malformation syndrome mainly characterized by severe intellectual disability, distinctive facial features, and multiple congenital anomalies, including skeletal abnormalities, genitourinary and renal malformations, cardiac defects, as well as an increased pediatric cancer risk. Recently, SGS has been associated with de novo heterozygous deleterious variants in the SETBP1 gene; to date, nine different variants, clustering in exon 4 of SETBP1, have been identified in 25 patients. Case presentation In this study, by using Whole Exome Sequencing (WES), we identified a patient with a recurrent missense mutation in SETBP1, the c.2608G > A, p.(Gly870Ser) variant, previously reported as likely pathogenic. This finding allowed us to confirm the suspected clinical diagnosis of SGS. Clinical features of patients carrying the same variant, including our patient, were evaluated by a review of medical records. Conclusions Our study confirms SGS as a severe disorder potentially presenting at birth as a critically ill neonate and demonstrates the causal role of the c.2608G > A, p.(Gly870Ser) variant in the etiology of the syndrome. Moreover, although the cohort of SETBP1-patients reported in the literature is still small, our study reports for the first time the prevalence of the variant (about 27%, 7/26). Finally, given the heterogeneity of clinical presentations of affected patients hospitalized in Neonatal Intensive Care Units (NICU) and/or Pediatric Intensive Care Units (PICU), in agreement with emerging data from the literature, we suggest that WES should be used in the diagnosis of unexplained syndromic conditions, and even as part of a standard first-line diagnostic approach, as it would allow a better diagnosis, counseling and management of affected patients and their families.
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Affiliation(s)
- Maria Pia Leone
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Pietro Palumbo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Orazio Palumbo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Ester Di Muro
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Massimiliano Chetta
- Division of Medical and Laboratory Genetics, Azienda Ospedaliera di Rilievo Nazionale "Antonio Cardarelli", Naples, Italy
| | - Nicola Laforgia
- Division of Neonatology and Neonatal Intensive Care, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, Bari, Italy
| | - Nicoletta Resta
- Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO), University of Bari "Aldo Moro", Bari, Italy
| | - Alessandro Stella
- Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO), University of Bari "Aldo Moro", Bari, Italy
| | - Stefano Castellana
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy.
| | - Nenad Bukvic
- Division of Medical Genetics, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, Bari, Italy
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23
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Sullivan JA, Stong N, Baugh EH, McDonald MT, Takeuchi A, Shashi V. A pathogenic variant in the SETBP1 hotspot results in a forme-fruste Schinzel-Giedion syndrome. Am J Med Genet A 2020; 182:1947-1951. [PMID: 32445275 DOI: 10.1002/ajmg.a.61630] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022]
Abstract
Schinzel-Giedion syndrome (SGS; OMIM 269150) is an ultra-rare genetic disorder associated with a distinctive facial gestalt, congenital malformations, severe intellectual disability, and a progressive neurological course. The prognosis for SGS is poor, with survival beyond the first decade rare. Germline, de novo heterozygous variants in the SETBP1 gene cause SGS with the pathogenic variants associated with the SGS phenotype missense and confined to exon 4 of the gene, clustered in a four amino acid (12 bp) hotspot in the SKI homologous region of the SETBP1 protein. We report a patient with a de novo I871S variant within the SKI homologous region, which has been associated with the severe phenotype previously; but our patient has fewer features of SGS and a milder course. This is the first report of a forme-fruste phenotype in a patient with a pathogenic variant within the SGS hotspot on the SETBP1 gene and it highlights the importance of considering atypical clinical presentations in the context of severe ultra-rare genetic disorders.
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Affiliation(s)
- Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Marie T McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Akihito Takeuchi
- Department of Neonatology, Okayama Medical Center, National Hospital Organization, Okayama, Japan
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
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24
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Li HR, Gao J, Jin C, Jiang JH, Ding JY. Downregulation of SETBP1 promoted non-small cell lung cancer progression by inducing cellular EMT and disordered immune status. Am J Transl Res 2020; 12:447-462. [PMID: 32194895 PMCID: PMC7061827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
PURPOSE SET binding protein 1 (SETBP1) has involved in cancer pathogenesis like leukemic malignancies and breast cancer. But the role and the underlying mechanism in NSCLC remain unclear. METHODS RT-PCR and western blotting were used for determining the expression level of SETBP1 in NSCLC. The clinical values of SETBP1 expression were evaluated by tissue microarray and immunohistochemistry. CCK-8, transwell and Matrigel assays were used to assess NSCLC cells proliferation, migration and invasion ability. The analysis of EMT markers was carried out by RT-PCR, western blotting and immunofluorescence. Bioinformatics analysis revealed the relationship between SETBP1 expression and tumor-associated immune cells. RESULTS SETBP1 expression was significantly downregulated in NSCLC tissues than matched peri-tumors and NSCLC patients with the decreased level of SETBP1 had worse OS. Downregulation of SETBP1 expression induced EMT to promote NSCLC cells proliferation, migration and invasion by the activation of ERK1/2 signal pathway. Aberrant SETBP1 expression was companied by disordered immune status of NSCLC patients and might be involved in regulation of polarization of tumor-associated macrophages. CONCLUSION SETBP1 can act as a tumor suppressor to reduce the progression of NSCLC and can be used for a prognostic biomarker in NSCLC. Aberrant SETBP1 expression was companied by disordered immune status of NSCLC patients.
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Affiliation(s)
- Hao-Ran Li
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University Shanghai 200032, P. R. China
| | - Jian Gao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University Shanghai 200032, P. R. China
| | - Chun Jin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University Shanghai 200032, P. R. China
| | - Jia-Hao Jiang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University Shanghai 200032, P. R. China
| | - Jian-Yong Ding
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University Shanghai 200032, P. R. China
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25
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Arriazu E, Vicente C, Pippa R, Peris I, Martínez-Balsalobre E, García-Ramírez P, Marcotegui N, Igea A, Alignani D, Rifón J, Mateos MC, Cayuela ML, Nebreda AR, Odero MD. A new regulatory mechanism of protein phosphatase 2A activity via SET in acute myeloid leukemia. Blood Cancer J 2020; 10:3. [PMID: 31913266 DOI: 10.1038/s41408-019-0270-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 12/04/2019] [Accepted: 12/12/2019] [Indexed: 12/11/2022] Open
Abstract
Acute myeloid leukemia (AML) is an aggressive hematologic malignancy. Although novel emerging drugs are available, the overall prognosis remains poor and new therapeutic approaches are required. PP2A phosphatase is a key regulator of cell homeostasis and is recurrently inactivated in AML. The anticancer activity of several PP2A-activating drugs (e.g., FTY720) depends on their interaction with the SET oncoprotein, an endogenous PP2A inhibitor that is overexpressed in 30% of AML cases. Elucidation of SET regulatory mechanisms may therefore provide novel targeted therapies for SET-overexpressing AMLs. Here, we show that upregulation of protein kinase p38β is a common event in AML. We provide evidence that p38β potentiates SET-mediated PP2A inactivation by two mechanisms: facilitating SET cytoplasmic translocation through CK2 phosphorylation, and directly binding to and stabilizing the SET protein. We demonstrate the importance of this new regulatory mechanism in primary AML cells from patients and in zebrafish xenograft models. Accordingly, combination of the CK2 inhibitor CX-4945, which retains SET in the nucleus, and FTY720, which disrupts the SET-PP2A binding in the cytoplasm, significantly reduces the viability and migration of AML cells. In conclusion, we show that the p38β/CK2/SET axis represents a new potential therapeutic pathway in AML patients with SET-dependent PP2A inactivation.
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26
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Eder-Azanza L, Hurtado C, Navarro-Herrera D, Calavia D, Novo FJ, Vizmanos JL. Analysis of genes encoding epigenetic regulators in myeloproliferative neoplasms: Coexistence of a novel SETBP1 mutation in a patient with a p.V617F JAK2 positive myelofibrosis. Mol Clin Oncol 2019; 10:639-643. [PMID: 31031980 DOI: 10.3892/mco.2019.1840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 03/18/2019] [Indexed: 12/28/2022] Open
Abstract
In recent years it has been shown that the causes of chronic myeloproliferative neoplasms (MPNs) are more complex than a simple signaling aberration and many other mutated genes affecting different cell processes have been described. For instance, mutations in genes encoding epigenetic regulators are more frequent than expected. One of the latest genes described as mutated is SET binding protein 1 (SETBP1). In silico tools have revealed that there are several human SETBP1 paralogous to nuclear receptor binding SET domain protein 1 (NSD1), NSD2 and NSD3, for example, which are also involved in the development of other hematological malignancies. Therefore, the present study analyzed the mutational status of NSD1, NSD2, NSD3 and SETBP1 in BCR-ABL1 negative MPNs with or without Janus kinase 2 (JAK2) p.V617F mutation. The present study revealed that the NSD genes are not frequently mutated in MPNs. However, a novel SETBP1 mutation was identified in a patient with p.V617F JAK2 positive primary myelofibrosis. These results provide further insight into the genetic complexity of MPNs.
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Affiliation(s)
- Laura Eder-Azanza
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, E-31008 Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), E-31008 Pamplona, Spain
| | - Cristina Hurtado
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, E-31008 Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), E-31008 Pamplona, Spain
| | - David Navarro-Herrera
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, E-31008 Pamplona, Spain
| | - Diego Calavia
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, E-31008 Pamplona, Spain
| | - Francisco Javier Novo
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, E-31008 Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), E-31008 Pamplona, Spain
| | - José Luis Vizmanos
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, E-31008 Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), E-31008 Pamplona, Spain
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27
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Morgan AT, Webster R. Aetiology of childhood apraxia of speech: A clinical practice update for paediatricians. J Paediatr Child Health 2018; 54:1090-1095. [PMID: 30294994 DOI: 10.1111/jpc.14150] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 06/18/2018] [Indexed: 02/03/2023]
Abstract
Childhood apraxia of speech (CAS) is a rare disorder of childhood that can leave a watermark of the impacts throughout the lifetime. Since being first described in the 1950s, aetiological insights have been limited. At a neurobiological level, clinical MRI scans fail to reveal overt neural anomalies in individual cases with CAS, although quantitative MRI methods have revealed subtle brain anomalies at a group level. Dramatic insights, however, occurred in the past decade from the discovery of genetic pathways underlying the phenotype. Several single genes and copy number-variant conditions are now associated with CAS either in relative isolation, as in the case of FOXP2 variants, or most typically in association with other neurodevelopmental conditions, such as epilepsy, intellectual disability, motor impairment and autism. CAS requires careful differential diagnosis from other childhood speech disorders, but when a severe and persistent diagnosis is confirmed, a genetic aetiology should increasingly be pursued.
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Affiliation(s)
- Angela T Morgan
- Speech and Language, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Audiology and Speech Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard Webster
- Department of Neurology and Neurosurgery, Children's Hospital, Sydney, New South Wales, Australia
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28
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Piazza R, Magistroni V, Redaelli S, Mauri M, Massimino L, Sessa A, Peronaci M, Lalowski M, Soliymani R, Mezzatesta C, Pirola A, Banfi F, Rubio A, Rea D, Stagno F, Usala E, Martino B, Campiotti L, Merli M, Passamonti F, Onida F, Morotti A, Pavesi F, Bregni M, Broccoli V, Baumann M, Gambacorti-Passerini C. SETBP1 induces transcription of a network of development genes by acting as an epigenetic hub. Nat Commun 2018; 9:2192. [PMID: 29875417 PMCID: PMC5989213 DOI: 10.1038/s41467-018-04462-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/27/2018] [Indexed: 12/21/2022] Open
Abstract
SETBP1 variants occur as somatic mutations in several hematological malignancies such as atypical chronic myeloid leukemia and as de novo germline mutations in the Schinzel–Giedion syndrome. Here we show that SETBP1 binds to gDNA in AT-rich promoter regions, causing activation of gene expression through recruitment of a HCF1/KMT2A/PHF8 epigenetic complex. Deletion of two AT-hooks abrogates the binding of SETBP1 to gDNA and impairs target gene upregulation. Genes controlled by SETBP1 such as MECOM are significantly upregulated in leukemias containing SETBP1 mutations. Gene ontology analysis of deregulated SETBP1 target genes indicates that they are also key controllers of visceral organ development and brain morphogenesis. In line with these findings, in utero brain electroporation of mutated SETBP1 causes impairment of mouse neurogenesis with a profound delay in neuronal migration. In summary, this work unveils a SETBP1 function that directly affects gene transcription and clarifies the mechanism operating in myeloid malignancies and in the Schinzel–Giedion syndrome caused by SETBP1 mutations. SETBP1 variants occur as somatic mutations in several malignancies and as de novo germline mutations in developmental disorders. Here the authors provide evidence that SETBP1 binds to gDNA in AT-rich promoter regions to promote target gene upregulation, indicating SETBP1 functions directly to regulate transcription.
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Affiliation(s)
- Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca and San Gerardo hospital, 20900, Monza, Italy.
| | - Vera Magistroni
- Department of Medicine and Surgery, University of Milano-Bicocca and San Gerardo hospital, 20900, Monza, Italy
| | - Sara Redaelli
- Department of Medicine and Surgery, University of Milano-Bicocca and San Gerardo hospital, 20900, Monza, Italy
| | - Mario Mauri
- Department of Medicine and Surgery, University of Milano-Bicocca and San Gerardo hospital, 20900, Monza, Italy
| | - Luca Massimino
- Department of Medicine and Surgery, University of Milano-Bicocca and San Gerardo hospital, 20900, Monza, Italy
| | - Alessandro Sessa
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Marco Peronaci
- Department of Medicine and Surgery, University of Milano-Bicocca and San Gerardo hospital, 20900, Monza, Italy
| | - Maciej Lalowski
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, Meilahti Clinical Proteomics Core Facility, University of Helsinki, 00290, Helsinki, Finland
| | - Rabah Soliymani
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, Meilahti Clinical Proteomics Core Facility, University of Helsinki, 00290, Helsinki, Finland
| | - Caterina Mezzatesta
- Department of Medicine and Surgery, University of Milano-Bicocca and San Gerardo hospital, 20900, Monza, Italy
| | - Alessandra Pirola
- Department of Medicine and Surgery, University of Milano-Bicocca and San Gerardo hospital, 20900, Monza, Italy
| | - Federica Banfi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Alicia Rubio
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Delphine Rea
- Service d'Hématologie Adulte, Hôpital Saint-Louis, 75010, Paris, France
| | - Fabio Stagno
- Chair and Hematology Section, Ferrarotto Hospital, AOU Policlinico, 95123, Catania, Italy
| | - Emilio Usala
- Azienda Brotzu U.O. Ematologia e CTMO, Ospedale Businco, 09121, Cagliari, Italy
| | - Bruno Martino
- UO Ematologia Azienda Ospedaliera "BIANCHI MELACRINO MORELLI", 89124, Reggio Calabria, Italy
| | - Leonardo Campiotti
- Dipartimento Medicina Clinica e Sperimentale, Università Insubria, 21100, Varese, Italy
| | - Michele Merli
- Division of Hematology, University Hospital Ospedale di Circolo e Fondazione Macchi, 21100, Varese, Italy
| | - Francesco Passamonti
- Hematology, Dipartimento di Medicina Clinica e Sperimentale, University of Varese, 21100, Varese, Italy
| | - Francesco Onida
- BMT Center - Oncohematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, 20122, Milan, Italy
| | - Alessandro Morotti
- Department of Clinical and Biological Sciences, University of Torino, 10043, Orbassano (Torino), Italy
| | - Francesca Pavesi
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Marco Bregni
- Oncology Unit, ASST Valle Olona, Ospedale di Circolo di Busto Arsizio, 21052, Busto Arsizio, Italy
| | - Vania Broccoli
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy.,CNR Institute of Neuroscience, 20129, Milan, Italy
| | - Marc Baumann
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, Meilahti Clinical Proteomics Core Facility, University of Helsinki, 00290, Helsinki, Finland
| | - Carlo Gambacorti-Passerini
- Department of Medicine and Surgery, University of Milano-Bicocca and San Gerardo hospital, 20900, Monza, Italy
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Stevens SJ, van der Schoot V, Leduc MS, Rinne T, Lalani SR, Weiss MM, van Hagen JM, Lachmeijer AM, Stockler-Ipsiroglu SG, Lehman A, Brunner HG. De novo mutations in the SET
nuclear proto-oncogene, encoding a component of the inhibitor of histone acetyltransferases (INHAT) complex in patients with nonsyndromic intellectual disability. Hum Mutat 2018; 39:1014-1023. [DOI: 10.1002/humu.23541] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/12/2018] [Accepted: 04/20/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Servi J.C. Stevens
- Department of Clinical Genetics; Maastricht University Medical Centre; Maastricht the Netherlands
| | - Vyne van der Schoot
- Department of Clinical Genetics; Maastricht University Medical Centre; Maastricht the Netherlands
| | - Magalie S. Leduc
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
- Baylor Genetics; Houston Texas USA
| | - Tuula Rinne
- Department of Genetics; Radboud University Medical Centre; Nijmegen the Netherlands
| | - Seema R. Lalani
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
| | - Marjan M. Weiss
- Department of Clinical Genetics; VU University Medical Centre; Amsterdam the Netherlands
| | - Johanna M. van Hagen
- Department of Clinical Genetics; VU University Medical Centre; Amsterdam the Netherlands
| | | | | | - Anna Lehman
- Department of Medical Genetics; British Columbia Children's Hospital; Vancouver Canada
| | - Han G Brunner
- Department of Clinical Genetics; Maastricht University Medical Centre; Maastricht the Netherlands
- Department of Genetics; Radboud University Medical Centre; Nijmegen the Netherlands
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30
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Rocca S, Carrà G, Poggio P, Morotti A, Brancaccio M. Targeting few to help hundreds: JAK, MAPK and ROCK pathways as druggable targets in atypical chronic myeloid leukemia. Mol Cancer 2018; 17:40. [PMID: 29455651 PMCID: PMC5817721 DOI: 10.1186/s12943-018-0774-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/01/2018] [Indexed: 12/19/2022] Open
Abstract
Atypical Chronic Myeloid Leukemia (aCML) is a myeloproliferative neoplasm characterized by neutrophilic leukocytosis and dysgranulopoiesis. From a genetic point of view, aCML shows a heterogeneous mutational landscape with mutations affecting signal transduction proteins but also broad genetic modifiers and chromatin remodelers, making difficult to understand the molecular mechanisms causing the onset of the disease. The JAK-STAT, MAPK and ROCK pathways are known to be responsible for myeloproliferation in physiological conditions and to be aberrantly activated in myeloproliferative diseases. Furthermore, experimental evidences suggest the efficacy of inhibitors targeting these pathways in repressing myeloproliferation, opening the way to deep clinical investigations. However, the activation status of these pathways is rarely analyzed when genetic mutations do not occur in a component of the signaling cascade. Given that mutations in functionally unrelated genes give rise to the same pathology, it is tempting to speculate that alteration in the few signaling pathways mentioned above might be a common feature of pathological myeloproliferation. If so, targeted therapy would be an option to be considered for aCML patients.
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Affiliation(s)
- Stefania Rocca
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126, Torino, Italy
| | - Giovanna Carrà
- Department of Clinical and Biological Sciences, University of Torino, 10043, Orbassano, Italy
| | - Pietro Poggio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126, Torino, Italy
| | - Alessandro Morotti
- Department of Clinical and Biological Sciences, University of Torino, 10043, Orbassano, Italy
| | - Mara Brancaccio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126, Torino, Italy.
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31
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Bulut O, Ince Z, Altunoglu U, Yildirim S, Coban A. Schinzel-Giedion Syndrome with Congenital Megacalycosis in a Turkish Patient: Report of SETBP1 Mutation and Literature Review of the Clinical Features. Case Rep Genet 2017; 2017:3740524. [PMID: 29333303 DOI: 10.1155/2017/3740524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/14/2017] [Indexed: 11/18/2022] Open
Abstract
Schinzel-Giedion syndrome (SGS) is a rare autosomal dominant disorder that results in facial dysmorphism, multiple congenital anomalies, and an increased risk of malignancy. Recently, using exome sequencing, de novo heterozygous mutations in the SETBP1 gene have been identified in patients with SGS. Most affected individuals do not survive after childhood because of the severity of this disorder. Here, we report SETBP1 mutation confirmed by molecular analysis in a case of SGS with congenital megacalycosis.
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32
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Winkelmann N, Schäfer V, Rinke J, Kaiser A, Ernst P, Scholl S, Hochhaus A, Ernst T. Only SETBP1 hotspot mutations are associated with refractory disease in myeloid malignancies. J Cancer Res Clin Oncol 2017; 143:2511-2519. [DOI: 10.1007/s00432-017-2518-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 09/06/2017] [Indexed: 12/22/2022]
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33
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Abstract
SETBP1 is a SET-binding protein regulating self-renewal potential through HOXA-protein activation. Somatic SETBP1 mutations were identified by whole exome sequencing in several phenotypes of myelodysplastic/myeloproliferative neoplasms (MDS/MPN), including atypical chronic myeloid leukemia, chronic myelomonocytic leukemia, and juvenile myelomonocytic leukemia as well as in secondary acute myeloid leukemia (sAML). Surprisingly, its recurrent somatic activated mutations are located at the identical positions of germline mutations reported in congenital Schinzel-Giedion syndrome. In general, somatic SETBP1 mutations have a significant clinical impact on the outcome as poor prognostic factor, due to downstream HOXA-pathway as well as associated aggressive types of chromosomal defects (-7/del(7q) and i(17q)), which is consistent with wild-type SETBP1 activation in aggressive types of acute myeloid leukemia and leukemic evolution. Biologically, mutant SETBP1 attenuates RUNX1 and activates MYB. The studies of mouse models confirmed biological significance of SETBP1 mutations in myeloid leukemogenesis, particularly associated with ASXL1 mutations. SETBP1 is a major oncogene in myeloid neoplasms, which cooperates with various genetic events and causes distinct phenotypes of MDS/MPN and sAML.
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MESH Headings
- Animals
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Chromosome Deletion
- Chromosomes, Human, Pair 7/genetics
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/genetics
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/metabolism
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/mortality
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/therapy
- Leukemia, Myelomonocytic, Chronic/genetics
- Leukemia, Myelomonocytic, Chronic/metabolism
- Leukemia, Myelomonocytic, Chronic/mortality
- Leukemia, Myelomonocytic, Chronic/therapy
- Leukemia, Myelomonocytic, Juvenile
- Mice
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Proto-Oncogene Proteins c-myb/genetics
- Proto-Oncogene Proteins c-myb/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
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Affiliation(s)
- Hideki Makishima
- Department of Pathology and Tumor Biology, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
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