1
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Oyler HO, Hudac CM, Chung WK, Green Synder L, Robertson S, Srivastava S, Geye T. SETBP1 haploinsufficiency and related disorders clinical and neurobehavioral phenotype study. Clin Genet 2024; 106:448-461. [PMID: 38923504 DOI: 10.1111/cge.14579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
To comprehensively investigate the neurodevelopmental profile and clinical characteristics associated with SETBP1 haploinsufficiency disorder (SETBP1-HD) and SETBP1-related disorders (SETBP1-RD). We reported genetic results on 34 individuals, with behavior and clinical data from 22 with SETBP1-HD and 5 with SETBP1-RD, by assessing results from medical history interviews and standardized adaptive, clinical, and social measures provided from Simons Searchlight. All individuals with SETBP1-HD and SETBP1-RD exhibited neurological impairments including intellectual disability/developmental delay (IDD), attention-deficit/hyperactivity disorder, autism spectrum disorder, and/or seizures, as well as speech and language delays. While restricted interests and repetitive behaviors present challenges, a relative strength was observed in social motivation within both cohorts. Individuals with SETBP1-RD reported a risk for heart issues and compared to SETBP1-HD greater risks for orthopedic and somatic issues with greater difficulty in bowel control. Higher rates for neonatal feeding difficulties and febrile seizures were reported for individuals with SETBP1-HD. Additional prominent characteristics included sleep, vision, and gastrointestinal issues, hypotonia, and high pain tolerance. This characterization of phenotypic overlap (IDD, speech challenges, autistic, and attention deficit traits) and differentiation (somatic and heart issue risks for SETBP1-RD) between the distinct neurodevelopmental disorders SETBP1-HD and SETBP1-RD is critical for medical management and diagnosis.
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Affiliation(s)
| | - Caitlin M Hudac
- Department of Psychology, Carolina Autism and Neurodevelopment Research Center, University of South Carolina, Columbia, South Carolina, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Stephanie Robertson
- Department of Psychology, Tarleton Center for Child Well-Being, Tarleton State University, Stephenville, Texas, USA
| | - Siddharth Srivastava
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Trina Geye
- Department of Psychology, Tarleton State University, Stephenville, Texas, USA
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2
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Alesi V, Genovese S, Roberti MC, Sallicandro E, Di Tommaso S, Loddo S, Orlando V, Pompili D, Calacci C, Mei V, Pisaneschi E, Faggiano MV, Morgia A, Mammì C, Astrea G, Battini R, Priolo M, Dentici ML, Milone R, Novelli A. Structural rearrangements as a recurrent pathogenic mechanism for SETBP1 haploinsufficiency. Hum Genomics 2024; 18:29. [PMID: 38520002 PMCID: PMC10960460 DOI: 10.1186/s40246-024-00600-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 03/15/2024] [Indexed: 03/25/2024] Open
Abstract
Chromosomal structural rearrangements consist of anomalies in genomic architecture that may or may not be associated with genetic material gain and loss. Evaluating the precise breakpoint is crucial from a diagnostic point of view, highlighting possible gene disruption and addressing to appropriate genotype-phenotype association. Structural rearrangements can either occur randomly within the genome or present with a recurrence, mainly due to peculiar genomic features of the surrounding regions. We report about three non-related individuals, harboring chromosomal structural rearrangements interrupting SETBP1, leading to gene haploinsufficiency. Two out of them resulted negative to Chromosomal Microarray Analysis (CMA), being the rearrangement balanced at a microarray resolution. The third one, presenting with a complex three-chromosome rearrangement, had been previously diagnosed with SETBP1 haploinsufficiency due to a partial gene deletion at one of the chromosomal breakpoints. We thoroughly characterized the rearrangements by means of Optical Genome Mapping (OGM) and Whole Genome Sequencing (WGS), providing details about the involved sequences and the underlying mechanisms. We propose structural variants as a recurrent event in SETBP1 haploinsufficiency, which may be overlooked by laboratory routine genomic analyses (CMA and Whole Exome Sequencing) or only partially determined when associated with genomic losses at breakpoints. We finally introduce a possible role of SETBP1 in a Noonan-like phenotype.
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Affiliation(s)
- V Alesi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146, Rome, Italy
| | - S Genovese
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146, Rome, Italy.
| | - M C Roberti
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146, Rome, Italy
| | - E Sallicandro
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146, Rome, Italy
| | - S Di Tommaso
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146, Rome, Italy
| | - S Loddo
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146, Rome, Italy
| | - V Orlando
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146, Rome, Italy
| | - D Pompili
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146, Rome, Italy
| | - C Calacci
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146, Rome, Italy
| | - V Mei
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146, Rome, Italy
| | - E Pisaneschi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146, Rome, Italy
| | - M V Faggiano
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146, Rome, Italy
| | - A Morgia
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146, Rome, Italy
| | - C Mammì
- Operative Unit of Medical Genetics, Great Metropolitan Hospital of Reggio Calabria, 89100, Reggio Calabria, Italy
| | - G Astrea
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125, Pisa, Italy
| | - R Battini
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125, Pisa, Italy
- Department of Clinical and Experimental Medicine, University of Pisa, 56100, Pisa, Italy
| | - M Priolo
- Operative Unit of Medical Genetics, Great Metropolitan Hospital of Reggio Calabria, 89100, Reggio Calabria, Italy
| | - M L Dentici
- Medical Genetics Unit, Bambino Gesù Children Hospital, IRCCS, 00146, Rome, Italy
| | - R Milone
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125, Pisa, Italy
| | - A Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146, Rome, Italy
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Ganesh VS, Riquin K, Chatron N, Lamar KM, Aziz MC, Monin P, O’Leary M, Goodrich JK, Garimella KV, England E, Yoon E, Weisburd B, Aguet F, Bacino CA, Murdock DR, Dai H, Rosenfeld JA, Emrick LT, Ketkar S, Sarusi Y, Sanlaville D, Kayani S, Broadbent B, Isidor B, Pengam A, Cogné B, MacArthur DG, Ulitsky I, Carvill GL, O’Donnell-Luria A. Novel syndromic neurodevelopmental disorder caused by de novo deletion of CHASERR, a long noncoding RNA. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.31.24301497. [PMID: 38496558 PMCID: PMC10942497 DOI: 10.1101/2024.01.31.24301497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Genes encoding long non-coding RNAs (lncRNAs) comprise a large fraction of the human genome, yet haploinsufficiency of a lncRNA has not been shown to cause a Mendelian disease. CHASERR is a highly conserved human lncRNA adjacent to CHD2-a coding gene in which de novo loss-of-function variants cause developmental and epileptic encephalopathy. Here we report three unrelated individuals each harboring an ultra-rare heterozygous de novo deletion in the CHASERR locus. We report similarities in severe developmental delay, facial dysmorphisms, and cerebral dysmyelination in these individuals, distinguishing them from the phenotypic spectrum of CHD2 haploinsufficiency. We demonstrate reduced CHASERR mRNA expression and corresponding increased CHD2 mRNA and protein in whole blood and patient-derived cell lines-specifically increased expression of the CHD2 allele in cis with the CHASERR deletion, as predicted from a prior mouse model of Chaserr haploinsufficiency. We show for the first time that de novo structural variants facilitated by Alu-mediated non-allelic homologous recombination led to deletion of a non-coding element (the lncRNA CHASERR) to cause a rare syndromic neurodevelopmental disorder. We also demonstrate that CHD2 has bidirectional dosage sensitivity in human disease. This work highlights the need to carefully evaluate other lncRNAs, particularly those upstream of genes associated with Mendelian disorders.
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Affiliation(s)
- Vijay S. Ganesh
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kevin Riquin
- Nantes Université, CHU de Nantes, CNRS, INSERM, L’institut du Thorax, Nantes, France
| | - Nicolas Chatron
- Institut Neuromyogène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Equipe Métabolisme énergétique et développement neuronal, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
- Service de génétique, Hospices Civils de Lyon, Lyon, France
| | - Kay-Marie Lamar
- Departments of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Miriam C. Aziz
- Departments of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Pauline Monin
- Service de génétique, Hospices Civils de Lyon, Lyon, France
| | - Melanie O’Leary
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia K. Goodrich
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kiran V. Garimella
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eleina England
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Esther Yoon
- Departments of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Ben Weisburd
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Francois Aguet
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David R. Murdock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lisa T. Emrick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shamika Ketkar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Yael Sarusi
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Damien Sanlaville
- Institut Neuromyogène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Equipe Métabolisme énergétique et développement neuronal, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
- Service de génétique, Hospices Civils de Lyon, Lyon, France
| | - Saima Kayani
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Bertrand Isidor
- Nantes Université, CHU de Nantes, CNRS, INSERM, L’institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique médicale, F-44000 Nantes, France
| | - Alisée Pengam
- Nantes Université, CHU de Nantes, Service de Génétique médicale, F-44000 Nantes, France
| | - Benjamin Cogné
- Nantes Université, CHU de Nantes, CNRS, INSERM, L’institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique médicale, F-44000 Nantes, France
| | - Daniel G. MacArthur
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, Australia
- Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Igor Ulitsky
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Gemma L. Carvill
- Departments of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Anne O’Donnell-Luria
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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4
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Whitlock JH, Wilk EJ, Howton TC, Clark AD, Lasseigne BN. The landscape of SETBP1 gene expression and transcription factor activity across human tissues. PLoS One 2024; 19:e0296328. [PMID: 38165902 PMCID: PMC10760659 DOI: 10.1371/journal.pone.0296328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/11/2023] [Indexed: 01/04/2024] Open
Abstract
The SET binding protein 1 (SETBP1) gene encodes a transcription factor (TF) involved in various cellular processes. Variants in SETBP1 can result in three different diseases determined by the introduction (germline vs. somatic) and location of the variant. Germline variants cause the ultra-rare pediatric Schinzel Giedion Syndrome (SGS) and SETBP1 haploinsufficiency disorder (SETBP1-HD), characterized by severe multisystemic abnormalities with neurodegeneration or a less severe brain phenotype accompanied by hypotonia and strabismus, respectively. Somatic variants in SETBP1 are associated with hematological malignancies and cancer development in other tissues in adults. To better understand the tissue-specific mechanisms involving SETBP1, we analyzed publicly available RNA-sequencing (RNA-seq) data from the Genotype-Tissue Expression (GTEx) project. We found SETBP1 and its known target genes were widely expressed across 31 adult human tissues. K-means clustering identified three distinct expression patterns of SETBP1 targets across tissues. Functional enrichment analysis (FEA) of each cluster revealed gene sets related to transcriptional regulation, DNA binding, and mitochondrial function. TF activity analysis of SETBP1 and its target TFs revealed tissue-specific TF activity, underscoring the role of tissue context-driven regulation and suggesting its impact in SETBP1-associated disease. In addition to uncovering tissue-specific molecular signatures of SETBP1 expression and TF activity, we provide a Shiny web application to facilitate exploring TF activity across human tissues for 758 TFs. This study provides insight into the landscape of SETBP1 expression and TF activity across 31 non-diseased human tissues and reveals tissue-specific expression and activity of SETBP1 and its targets. In conjunction with the web application we constructed, our framework enables researchers to generate hypotheses related to the role tissue backgrounds play with respect to gene expression and TF activity in different disease contexts.
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Affiliation(s)
- Jordan H. Whitlock
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Elizabeth J. Wilk
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Amanda D. Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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5
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Giudice V, Serio B, Errichiello S, Ferrara I, Galdiero A, Bertolini A, Visconti R, De Novellis D, Guariglia R, Luponio S, Morini D, Della Corte AM, Sessa AM, Verdesca F, Langella M, Izzo B, Selleri C. Subclones with variants of uncertain clinical significance might contribute to ineffective hemopoiesis and leukemia predisposition. Eur J Haematol 2023; 111:729-741. [PMID: 37501402 DOI: 10.1111/ejh.14069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND Splicing modifications, genomic instability, and hypomethylation are central mechanisms promoting myelodysplasia and acute myeloid leukemia (AML). In this real-life retrospective study, to elucidate pathophysiology of clonal hemopoiesis in hematological malignancies, we investigated clinical significance of mutations in leukemia-related genes of known pathogenetic significance and of variants of uncertain clinical significance (VUS) in a cohort of patients with MDS and AML. METHODS A total of 59 consecutive subjects diagnosed with MDS, 48 with AML, and 17 with clonal cytopenia with unknown significance were screened for somatic mutations in AML-related genes by next-generation sequencing. RESULTS We showed that TET2, SETBP1, ASXL1, EZH2, RUNX1, SRSF2, DNMT3A, and IDH1/2 were commonly mutated. MDS patients also showed a high genetic complexity, especially for SETBP1. Moreover, the presence of SETBP1 wild-type or two or more simultaneous VUS variants identified a subgroup of AML and MDS patients with better outcome, while the presence of single SETBP1 VUS variant was related to a worse prognosis, regardless TET2 mutational status. CONCLUSIONS In conclusions, we linked both pathogenic and VUS variants in AML-related genes to clonal hematopoiesis; therefore, we proposed to consider those variants as prognostic markers in leukemia and myelodysplasia. However, further studies in larger prospective cohorts are required to validate our results.
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Affiliation(s)
- Valentina Giudice
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery, and Dentistry, University of Salerno, Baronissi, Italy
| | - Bianca Serio
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Santa Errichiello
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Idalucia Ferrara
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Alessandra Galdiero
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Angela Bertolini
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Roberta Visconti
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Danilo De Novellis
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery, and Dentistry, University of Salerno, Baronissi, Italy
| | - Roberto Guariglia
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Serena Luponio
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Denise Morini
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Anna Maria Della Corte
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Anna Maria Sessa
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Francesco Verdesca
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Maddalena Langella
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Barbara Izzo
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Carmine Selleri
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery, and Dentistry, University of Salerno, Baronissi, Italy
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6
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Whitlock JH, Soelter TM, Howton TC, Wilk EJ, Oza VH, Lasseigne BN. Cell-type-specific gene expression and regulation in the cerebral cortex and kidney of atypical Setbp1 S858R Schinzel Giedion Syndrome mice. J Cell Mol Med 2023; 27:3565-3577. [PMID: 37872881 PMCID: PMC10660642 DOI: 10.1111/jcmm.18001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/27/2023] [Accepted: 10/05/2023] [Indexed: 10/25/2023] Open
Abstract
Schinzel Giedion Syndrome (SGS) is an ultra-rare autosomal dominant Mendelian disease presenting with abnormalities spanning multiple organ systems. The most notable phenotypes involve severe developmental delay, progressive brain atrophy, and drug-resistant seizures. SGS is caused by spontaneous variants in SETBP1, which encodes for the epigenetic hub SETBP1 transcription factor (TF). SETBP1 variants causing classical SGS cluster at the degron, disrupting SETBP1 protein degradation and resulting in toxic accumulation, while those located outside cause milder atypical SGS. Due to the multisystem phenotype, we evaluated gene expression and regulatory programs altered in atypical SGS by snRNA-seq of the cerebral cortex and kidney of Setbp1S858R heterozygous mice (corresponds to the human likely pathogenic SETBP1S867R variant) compared to matched wild-type mice by constructing cell-type-specific regulatory networks. Setbp1 was differentially expressed in excitatory neurons, but known SETBP1 targets were differentially expressed and regulated in many cell types. Our findings suggest molecular drivers underlying neurodevelopmental phenotypes in classical SGS also drive atypical SGS, persist after birth, and are present in the kidney. Our results indicate SETBP1's role as an epigenetic hub leads to cell-type-specific differences in TF activity, gene targeting, and regulatory rewiring. This research provides a framework for investigating cell-type-specific variant impact on gene expression and regulation.
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Affiliation(s)
- Jordan H. Whitlock
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Tabea M. Soelter
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Elizabeth J. Wilk
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Vishal H. Oza
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of MedicineThe University of Alabama at BirminghamBirminghamAlabamaUSA
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7
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Whitlock JH, Wilk EJ, Howton TC, Clark AD, Lasseigne BN. The landscape of SETBP1 gene expression and transcription factor activity across human tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.551337. [PMID: 37873221 PMCID: PMC10592643 DOI: 10.1101/2023.08.08.551337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background The SET binding protein 1 (SETBP1) gene encodes a transcription factor (TF) involved in various cellular processes. Distinct SETBP1 variants have been linked to three different diseases. Germline variants cause the ultra-rare pediatric Schinzel Giedion Syndrome (SGS) and SETBP1 haploinsufficiency disorder (SETBP1-HD), characterized by severe multisystemic abnormalities with neurodegeneration or a less severe brain phenotype accompanied by hypotonia and strabismus, respectively. Somatic variants in SETBP1 are associated with hematological malignancies and cancer development in other tissues in adults. Results To better understand the tissue-specific mechanisms involving SETBP1, we analyzed publicly available RNA-sequencing data from the Genotype-Tissue Expression (GTEx) project. We found SETBP1, and its known target genes were widely expressed across 31 adult human tissues. K-means clustering identified three distinct expression patterns of SETBP1 targets across tissues. Functional enrichment analysis (FEA) of each cluster revealed gene sets related to transcription regulation, DNA binding, and mitochondrial function. TF activity analysis of SETBP1 and its target TFs revealed tissue-specific TF activity, underscoring the role of tissue context-driven regulation and suggesting its impact in SETBP1-associated disease. In addition to uncovering tissue-specific molecular signatures of SETBP1 expression and TF activity, we provide a Shiny web application to facilitate exploring TF activity across human tissues for 758 TFs. Conclusions This study provides insight into the landscape of SETBP1 expression and TF activity across 31 non-diseased human tissues and reveals tissue-specific expression and activity of SETBP1 and its targets. In conjunction with the web application we constructed, our framework enables researchers to generate hypotheses related to the role tissue backgrounds play with respect to gene expression and TF activity in different disease contexts.
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Affiliation(s)
- Jordan H. Whitlock
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, AL, U.S.A
| | - Elizabeth J. Wilk
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, AL, U.S.A
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, AL, U.S.A
| | - Amanda D. Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, AL, U.S.A
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine The University of Alabama at Birmingham, Birmingham, AL, U.S.A
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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] [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] [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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Starkova T, Polyanichko A, Tomilin AN, Chikhirzhina E. Structure and Functions of HMGB2 Protein. Int J Mol Sci 2023; 24:ijms24098334. [PMID: 37176041 PMCID: PMC10179549 DOI: 10.3390/ijms24098334] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
High-Mobility Group (HMG) chromosomal proteins are the most numerous nuclear non-histone proteins. HMGB domain proteins are the most abundant and well-studied HMG proteins. They are involved in variety of biological processes. HMGB1 and HMGB2 were the first members of HMGB-family to be discovered and are found in all studied eukaryotes. Despite the high degree of homology, HMGB1 and HMGB2 proteins differ from each other both in structure and functions. In contrast to HMGB2, there is a large pool of works devoted to the HMGB1 protein whose structure-function properties have been described in detail in our previous review in 2020. In this review, we attempted to bring together diverse data about the structure and functions of the HMGB2 protein. The review also describes post-translational modifications of the HMGB2 protein and its role in the development of a number of diseases. Particular attention is paid to its interaction with various targets, including DNA and protein partners. The influence of the level of HMGB2 expression on various processes associated with cell differentiation and aging and its ability to mediate the differentiation of embryonic and adult stem cells are also discussed.
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Affiliation(s)
- Tatiana Starkova
- Laboratory of Molecular Biology of Stem Cells, Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Av. 4, 194064 St. Petersburg, Russia
| | - Alexander Polyanichko
- Laboratory of Molecular Biology of Stem Cells, Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Av. 4, 194064 St. Petersburg, Russia
| | - Alexey N Tomilin
- Laboratory of Molecular Biology of Stem Cells, Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Av. 4, 194064 St. Petersburg, Russia
| | - Elena Chikhirzhina
- Laboratory of Molecular Biology of Stem Cells, Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Av. 4, 194064 St. Petersburg, Russia
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Cardo LF, de la Fuente DC, Li M. Impaired neurogenesis and neural progenitor fate choice in a human stem cell model of SETBP1 disorder. Mol Autism 2023; 14:8. [PMID: 36805818 PMCID: PMC9940404 DOI: 10.1186/s13229-023-00540-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/07/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Disruptions of SETBP1 (SET binding protein 1) on 18q12.3 by heterozygous gene deletion or loss-of-function variants cause SETBP1 disorder. Clinical features are frequently associated with moderate to severe intellectual disability, autistic traits and speech and motor delays. Despite the association of SETBP1 with neurodevelopmental disorders, little is known about its role in brain development. METHODS Using CRISPR/Cas9 genome editing technology, we generated a SETBP1 deletion model in human embryonic stem cells (hESCs) and examined the effects of SETBP1-deficiency in neural progenitors (NPCs) and neurons derived from these stem cells using a battery of cellular assays, genome-wide transcriptomic profiling and drug-based phenotypic rescue. RESULTS Neural induction occurred efficiently in all SETBP1 deletion models as indicated by uniform transition into neural rosettes. However, SETBP1-deficient NPCs exhibited an extended proliferative window and a decrease in neurogenesis coupled with a deficiency in their ability to acquire ventral forebrain fate. Genome-wide transcriptome profiling and protein biochemical analysis revealed enhanced activation of Wnt/β-catenin signaling in SETBP1 deleted cells. Crucially, treatment of the SETBP1-deficient NPCs with a small molecule Wnt inhibitor XAV939 restored hyper canonical β-catenin activity and restored both cortical and MGE neuronal differentiation. LIMITATIONS The current study is based on analysis of isogenic hESC lines with genome-edited SETBP1 deletion and further studies would benefit from the use of patient-derived iPSC lines that may harbor additional genetic risk that aggravate brain pathology of SETBP1 disorder. CONCLUSIONS We identified an important role for SETBP1 in controlling forebrain progenitor expansion and neurogenic differentiation. Our study establishes a novel regulatory link between SETBP1 and Wnt/β-catenin signaling during human cortical neurogenesis and provides mechanistic insights into structural abnormalities and potential therapeutic avenues for SETBP1 disorder.
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Affiliation(s)
- Lucia F Cardo
- Neuroscience and Mental Health Innovation Institute, School of Medicine and School of Bioscience, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK.
| | - Daniel C de la Fuente
- Neuroscience and Mental Health Innovation Institute, School of Medicine and School of Bioscience, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Meng Li
- Neuroscience and Mental Health Innovation Institute, School of Medicine and School of Bioscience, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK.
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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] [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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