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Sun W, Zhang X, Bai X, Du K, Chen L, Wang H, Jia X, Lai S. miR-889-3p Facilitates the Browning Process of White Adipocyte Precursors by Targeting the SON Gene. Int J Mol Sci 2023; 24:17580. [PMID: 38139409 PMCID: PMC10743546 DOI: 10.3390/ijms242417580] [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: 10/31/2023] [Revised: 12/02/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
It is well-established that beige/brown adipose tissue can dissipate stored energy through thermogenesis; hence, the browning of white adipocytes (WAT) has garnered significant interest in contemporary research. Our preceding investigations have identified a marked downregulation of miR-889-3p concurrent with the natural maturation of brown adipose tissue. However, the specific role and underlying molecular mechanisms of miR-889-3p in the browning process of white adipose tissue warrant further elucidation. In this research, we initially delved into the potential role of miR-889-3p in preadipocyte growth via flow cytometry and CCK-8 assay, revealing that miR-889-3p can stimulate preadipocyte growth. To validate the potential contribution of miR-889-3p in the browning process of white adipose tissue, we established an in vitro rabbit white adipocyte browning induction, which exhibited a significant upregulation of miR-889-3p during the browning process. RT-qPCR and Western blot analysis indicated that miR-889-3p overexpression significantly amplified the mRNA levels of UCP1, PRDM16, and CIDEA, as well as UCP1 protein levels. Furthermore, miR-889-3p overexpression fostered intracellular triglyceride accumulation. Conversely, the downregulation of miR-889-3p hindered the browning of rabbit preadipocytes. Subsequently, based on target gene prediction and luciferase reporter gene determination, we demonstrated that miR-889-3p directly targets the 3'-UTR region of SON. Lastly, we observed that inhibiting SON could facilitate the browning of rabbit preadipocytes. In conclusion, our findings suggest that miR-889-3p facilitates the browning process of white adipocyte precursors by specifically targeting the SON gene.
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Affiliation(s)
- Wenqiang Sun
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
| | - Xiaoxiao Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
| | - Xue Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
| | - Kun Du
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
| | - Li Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
| | - Haoding Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
| | - Xianbo Jia
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
| | - Songjia Lai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
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2
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Vukadin L, Park B, Mohamed M, Li H, Elkholy A, Torrelli-Diljohn A, Kim JH, Jeong K, Murphy JM, Harvey CA, Dunlap S, Gehrs L, Lee H, Kim HG, Lee SN, Stanford D, Barrington RA, Foote JB, Sorace AG, Welner RS, Hildreth BE, Lim STS, Ahn EYE. A mouse model of ZTTK syndrome reveals indispensable SON functions in organ development and hematopoiesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.19.567732. [PMID: 38014320 PMCID: PMC10680872 DOI: 10.1101/2023.11.19.567732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Rare diseases are underrepresented in biomedical research, leading to insufficient awareness. Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome is a rare disease caused by genetic alterations that result in heterozygous loss-of-function of SON. While ZTTK syndrome patients suffer from numerous symptoms, the lack of model organisms hamper our understanding of both SON and this complex syndrome. Here, we developed Son haploinsufficiency (Son+/-) mice as a model of ZTTK syndrome and identified the indispensable roles of Son in organ development and hematopoiesis. Son+/- mice recapitulated clinical symptoms of ZTTK syndrome, including growth retardation, cognitive impairment, skeletal abnormalities, and kidney agenesis. Furthermore, we identified hematopoietic abnormalities in Son+/- mice, similar to those observed in human patients. Surface marker analyses and single-cell transcriptome profiling of hematopoietic stem and progenitor cells revealed that Son haploinsufficiency inclines cell fate toward the myeloid lineage but compromises lymphoid lineage development by reducing key genes required for lymphoid and B cell lineage specification. Additionally, Son haploinsufficiency causes inappropriate activation of erythroid genes and impaired erythroid maturation. These findings highlight the importance of the full gene dosage of Son in organ development and hematopoiesis. Our model serves as an invaluable research tool for this rare disease and related disorders associated with SON dysfunction.
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Affiliation(s)
- Lana Vukadin
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Bohye Park
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mostafa Mohamed
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Huashi Li
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Amr Elkholy
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alex Torrelli-Diljohn
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jung-Hyun Kim
- Metastasis Branch, Division of Cancer Biology, National Cancer Center, Goyang, Gyeonggi-do, Korea
| | - Kyuho Jeong
- Department of Medicine, College of Medicine, Dongguk University, Gyeongju, Korea
| | - James M Murphy
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Caitlin A. Harvey
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sophia Dunlap
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Leah Gehrs
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hanna Lee
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hyung-Gyoon Kim
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Seth N. Lee
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Denise Stanford
- Department of Medicine, Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert A. Barrington
- Department of Microbiology and Immunology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Jeremy B. Foote
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anna G. Sorace
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert S. Welner
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Blake E. Hildreth
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ssang-Taek Steve Lim
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eun-Young Erin Ahn
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
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3
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The Expanding Phenotype of ZTTK Syndrome Due to the Heterozygous Variant of SON Gene Focusing on Liver Involvement: Patient Report and Literature Review. Genes (Basel) 2023; 14:genes14030739. [PMID: 36981010 PMCID: PMC10048019 DOI: 10.3390/genes14030739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
Zhu–Tokita–Takenouchi–Kim (ZTTK) syndrome, an intellectual disability syndrome first described in 2016, is caused by heterozygous loss-of-function variants in SON. Haploinsufficiency in SON may affect multiple genes, including those involved in the development and metabolism of multiple organs. Considering the broad spectrum of SON functions, it is to be expected that pathogenic variants in this gene can cause a wide spectrum of clinical symptoms. We present an additional ZTTK syndrome case due to a de novo heterozygous variant in the SON gene (c.5751_5754delAGTT). The clinical manifestations of our patient were similar to those present in previously reported cases; however, the diagnosis of ZTTK syndrome was delayed for a long time and was carried out during the diagnostic work-up of significant chronic liver disease (CLD). CLD has not yet been reported in any series; therefore, our report provides new information on this rare condition and suggests the expansion of the ZTTK syndrome phenotype, including possible liver involvement. Correspondingly, we recommend screening patients with SON variants specifically for liver involvement from the first years of life. Once the CLD has been diagnosed, an appropriate follow-up is mandatory, especially considering the role of SON as an emerging player in cancer development. Further studies are needed to investigate the role of SON haploinsufficiency as a downregulator of essential genes, thus potentially impairing the normal development and/or functions of multiple organs.
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4
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Establishing the phenotypic spectrum of ZTTK syndrome by analysis of 52 individuals with variants in SON. Eur J Hum Genet 2022; 30:271-281. [PMID: 34521999 PMCID: PMC8904542 DOI: 10.1038/s41431-021-00960-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/16/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022] Open
Abstract
Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome, an intellectual disability syndrome first described in 2016, is caused by heterozygous loss-of-function variants in SON. Its encoded protein promotes pre-mRNA splicing of many genes essential for development. Whereas individual phenotypic traits have previously been linked to erroneous splicing of SON target genes, the phenotypic spectrum and the pathogenicity of missense variants have not been further evaluated. We present the phenotypic abnormalities in 52 individuals, including 17 individuals who have not been reported before. In total, loss-of-function variants were detected in 49 individuals (de novo in 47, inheritance unknown in 2), and in 3, a missense variant was observed (2 de novo, 1 inheritance unknown). Phenotypic abnormalities, systematically collected and analyzed in Human Phenotype Ontology, were found in all organ systems. Significant inter-individual phenotypic variability was observed, even in individuals with the same recurrent variant (n = 13). SON haploinsufficiency was previously shown to lead to downregulation of downstream genes, contributing to specific phenotypic features. Similar functional analysis for one missense variant, however, suggests a different mechanism than for heterozygous loss-of-function. Although small in numbers and while pathogenicity of these variants is not certain, these data allow for speculation whether de novo missense variants cause ZTTK syndrome via another mechanism, or a separate overlapping syndrome. In conclusion, heterozygous loss-of-function variants in SON define a recognizable syndrome, ZTTK, associated with a broad, severe phenotypic spectrum, characterized by a large inter-individual variability. These observations provide essential information for affected individuals, parents, and healthcare professionals to ensure appropriate clinical management.
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5
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Stemm-Wolf AJ, O’Toole ET, Sheridan RM, Morgan JT, Pearson CG. The SON RNA splicing factor is required for intracellular trafficking structures that promote centriole assembly and ciliogenesis. Mol Biol Cell 2021; 32:ar4. [PMID: 34406792 PMCID: PMC8684746 DOI: 10.1091/mbc.e21-06-0305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/16/2021] [Accepted: 07/23/2021] [Indexed: 11/11/2022] Open
Abstract
Control of centrosome assembly is critical for cell division, intracellular trafficking, and cilia. Regulation of centrosome number occurs through the precise duplication of centrioles that reside in centrosomes. Here we explored transcriptional control of centriole assembly and find that the RNA splicing factor SON is specifically required for completing procentriole assembly. Whole genome mRNA sequencing identified genes whose splicing and expression are affected by the reduction of SON, with an enrichment in genes involved in the microtubule (MT) cytoskeleton, centrosome, and centriolar satellites. SON is required for the proper splicing and expression of CEP131, which encodes a major centriolar satellite protein and is required to organize the trafficking and MT network around the centrosomes. This study highlights the importance of the distinct MT trafficking network that is intimately associated with nascent centrioles and is responsible for procentriole development and efficient ciliogenesis.
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Affiliation(s)
- Alexander J. Stemm-Wolf
- Department of Cell and Developmental Biology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045
| | | | - Ryan M. Sheridan
- RNA Biosciences Initiative (RBI), University of Colorado, Anschutz Medical Campus, Aurora, CO 80045
| | - Jacob T. Morgan
- Department of Cell and Developmental Biology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045
| | - Chad G. Pearson
- Department of Cell and Developmental Biology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045
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6
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Kim JH, Jeong K, Li J, Murphy JM, Vukadin L, Stone JK, Richard A, Tran J, Gillespie GY, Flemington EK, Sobol RW, Lim STS, Ahn EYE. SON drives oncogenic RNA splicing in glioblastoma by regulating PTBP1/PTBP2 switching and RBFOX2 activity. Nat Commun 2021; 12:5551. [PMID: 34548489 PMCID: PMC8455679 DOI: 10.1038/s41467-021-25892-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/01/2021] [Indexed: 12/15/2022] Open
Abstract
While dysregulation of RNA splicing has been recognized as an emerging target for cancer therapy, the functional significance of RNA splicing and individual splicing factors in brain tumors is poorly understood. Here, we identify SON as a master regulator that activates PTBP1-mediated oncogenic splicing while suppressing RBFOX2-mediated non-oncogenic neuronal splicing in glioblastoma multiforme (GBM). SON is overexpressed in GBM patients and SON knockdown causes failure in intron removal from the PTBP1 transcript, resulting in PTBP1 downregulation and inhibition of its downstream oncogenic splicing. Furthermore, SON forms a complex with hnRNP A2B1 and antagonizes RBFOX2, which leads to skipping of RBFOX2-targeted cassette exons, including the PTBP2 neuronal exon. SON knockdown inhibits proliferation and clonogenicity of GBM cells in vitro and significantly suppresses tumor growth in orthotopic xenografts in vivo. Collectively, our study reveals that SON-mediated RNA splicing is a GBM vulnerability, implicating SON as a potential therapeutic target in brain tumors.
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Affiliation(s)
- Jung-Hyun Kim
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Kyuho Jeong
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Jianfeng Li
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - James M Murphy
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Lana Vukadin
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joshua K Stone
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Alexander Richard
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Johnny Tran
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - G Yancey Gillespie
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Erik K Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA.
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA.
| | - Ssang-Teak Steve Lim
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA.
| | - Eun-Young Erin Ahn
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.
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7
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SON inhibits megakaryocytic differentiation via repressing RUNX1 and the megakaryocytic gene expression program in acute megakaryoblastic leukemia. Cancer Gene Ther 2021; 28:1000-1015. [PMID: 33247227 PMCID: PMC8155101 DOI: 10.1038/s41417-020-00262-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/07/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023]
Abstract
A high incidence of acute megakaryoblastic leukemia (AMKL) in Down syndrome patients implies that chromosome 21 genes have a pivotal role in AMKL development, but the functional contribution of individual genes remains elusive. Here, we report that SON, a chromosome 21-encoded DNA- and RNA-binding protein, inhibits megakaryocytic differentiation by suppressing RUNX1 and the megakaryocytic gene expression program. As megakaryocytic progenitors differentiate, SON expression is drastically reduced, with mature megakaryocytes having the lowest levels. In contrast, AMKL cells express an aberrantly high level of SON, and knockdown of SON induced the onset of megakaryocytic differentiation in AMKL cell lines. Genome-wide transcriptome analyses revealed that SON knockdown turns on the expression of pro-megakaryocytic genes while reducing erythroid gene expression. Mechanistically, SON represses RUNX1 expression by directly binding to the proximal promoter and two enhancer regions, the known +23 kb enhancer and the novel +139 kb enhancer, at the RUNX1 locus to suppress H3K4 methylation. In addition, SON represses the expression of the AP-1 complex subunits JUN, JUNB, and FOSB which are required for late megakaryocytic gene expression. Our findings define SON as a negative regulator of RUNX1 and megakaryocytic differentiation, implicating SON overexpression in impaired differentiation during AMKL development.
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Kushary ST, Revah-Politi A, Barua S, Ganapathi M, Accogli A, Aggarwal V, Brunetti-Pierri N, Cappuccio G, Capra V, Fagerberg CR, Gazdagh G, Guzman E, Hadonou M, Harrison V, Havelund K, Iancu D, Kraus A, Lippa NC, Mansukhani M, McBrian D, McEntagart M, Pacio-Míguez M, Palomares-Bralo M, Pottinger C, Ruivenkamp CAL, Sacco O, Santen GWE, Santos-Simarro F, Scala M, Short J, Sørensen KP, Woods CG, Anyane Yeboa K. ZTTK syndrome: Clinical and molecular findings of 15 cases and a review of the literature. Am J Med Genet A 2021; 185:3740-3753. [PMID: 34331327 DOI: 10.1002/ajmg.a.62445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/21/2021] [Accepted: 07/09/2021] [Indexed: 11/10/2022]
Abstract
Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome is caused by de novo loss-of-function variants in the SON gene (MIM #617140). This multisystemic disorder is characterized by intellectual disability, seizures, abnormal brain imaging, variable dysmorphic features, and various congenital anomalies. The wide application and increasing accessibility of whole exome sequencing (WES) has helped to identify new cases of ZTTK syndrome over the last few years. To date, there have been approximately 45 cases reported in the literature. Here, we describe 15 additional individuals with variants in the SON gene, including those with missense variants bringing the total number of known cases to 60. We have reviewed the clinical and molecular data of these new cases and all previously reported cases to further delineate the most common as well as emerging clinical findings related to this syndrome. Furthermore, we aim to delineate any genotype-phenotype correlations specifically for a recurring pathogenic four base pair deletion (c.5753_5756del) along with discussing the impact of missense variants seen in the SON gene.
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Affiliation(s)
- Sulagna Tina Kushary
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Anya Revah-Politi
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Subit Barua
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Vimla Aggarwal
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Gerarda Cappuccio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Valeria Capra
- IRCCS 'G. Gaslini' Children's Hospital, Genoa, Italy
| | | | - Gabriella Gazdagh
- West of Scotland Centre for Genomic Medicine, Laboratory Medicine Building, Queen Elizabeth University Hospital, Glasgow, UK
| | - Edwin Guzman
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Medard Hadonou
- St. George's Genomics Service, St. George's University Hospitals NHS FT, London, UK
| | | | - Kathrine Havelund
- HC Andersen Children's Hospital, Odense University Hospital, Odense, Denmark
| | | | - Alison Kraus
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Natalie C Lippa
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Mahesh Mansukhani
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Danielle McBrian
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Meriel McEntagart
- Department of Medical Genetics, St. George's University Hospital NHS FT, London, UK
| | - Marta Pacio-Míguez
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - María Palomares-Bralo
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Carrie Pottinger
- Department of Clinical Genetics, All Wales Genomic Medicine Service, Maelor Hospital, Wrexham, UK
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Fernando Santos-Simarro
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | | | - John Short
- St. George's Genomics Service, St. George's University Hospitals NHS FT, London, UK
| | - Kristina P Sørensen
- HC Andersen Children's Hospital, Odense University Hospital, Odense, Denmark
| | - Christopher G Woods
- Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
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- Wellcome Trust Sanger Institute, Cambridge, UK
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- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Kwame Anyane Yeboa
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
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9
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Yang L, Yang F. A de novo heterozygous variant in the SON gene is associated with Zhu-Tokita-Takenouchi-Kim syndrome. Mol Genet Genomic Med 2020; 8:e1496. [PMID: 32926520 PMCID: PMC7667370 DOI: 10.1002/mgg3.1496] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/30/2020] [Accepted: 08/21/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Zhu-Tokita-Takenouchi-Kim (ZTTK, OMIM# 617140) syndrome is a rare, autosomal dominant genetic disorder caused by heterozygous variants in the SON gene (OMIM#182465, GenBank#NC_000021.9). There are only 33 cases and 26 causative SON variants reported to date since the first report in 2015. Here, we report a new case of ZTTK syndrome and a de novo disease-causing SON variant. METHODS We conducted whole-exome sequencing (WES) to obtain genetic data of the patient. The clinical and genetic data of the patient were analyzed. RESULTS The clinical features of our patient were strikingly similar to previously reported cases. Notably, our patient had unique presentations, including a bridged palmar crease in the left hand and growth hormone deficiency. The c.5297del de novo variant in SON causes an amino change (p.Ser1766Leufs*7). CONCLUSION Our report expands the mutant spectrum of the SON gene and refines the genotype-phenotype map of ZTTK syndrome. Our findings also highlighted the importance of WES for early diagnosis of ZTTK syndrome, which may improve diagnostic procedures for affected individuals.
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Affiliation(s)
- Lianlian Yang
- Department of Child Health, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Fan Yang
- Department of Child Health, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
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10
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Chiu C, Loth S, Kuhlen M, Ginzel S, Schaper J, Rosenbaum T, Pietsch T, Borkhardt A, Hoell JI. Mutated SON putatively causes a cancer syndrome comprising high-risk medulloblastoma combined with café-au-lait spots. Fam Cancer 2019; 18:353-358. [PMID: 30680470 DOI: 10.1007/s10689-019-00121-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Medulloblastoma is the most frequent malignant brain tumor in childhood. This highly malignant neoplasm occurs usually before 10 years of age and more frequently in boys. The 5-year event-free survival rate for high-risk medulloblastoma is low at 62% despite a multimodal therapy including surgical resection, radiation therapy and chemotherapy. We report the case of a boy, who was born to consanguineous parents. Prominently, he had multiple café-au-lait spots. At the age of 3 years he was diagnosed with a high-risk metastatic medulloblastoma. The patient died only 11 months after diagnosis of a fulminant relapse presenting as meningeal and spinal dissemination. Whole-exome sequencing of germline DNA was employed to detect the underlying mutation for this putative cancer syndrome presenting with the combination of medulloblastoma and skin alterations. After screening all possible homozygous gene SNVs, we identified a mutation of SON, an essential protein in cell cycle regulation and cell proliferation, as the most likely genetic cause.
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Affiliation(s)
- Celine Chiu
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Stefanie Loth
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Michaela Kuhlen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Sebastian Ginzel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Jörg Schaper
- Department of Diagnostic and Interventional Radiology, Medical Faculty, University of Duesseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Thorsten Rosenbaum
- Department of Pediatrics, Sana Kliniken Duisburg, Zu den Rehwiesen 9, 47055, Duisburg, Germany
| | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, DZNE German Center for Neurodegenerative Diseases, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Jessica I Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Children's Hospital, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany.
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11
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Yang Y, Xu L, Yu Z, Huang H, Yang L. Clinical and genetic analysis of ZTTK syndrome caused by SON heterozygous mutation c.394C>T. Mol Genet Genomic Med 2019; 7:e953. [PMID: 31557424 PMCID: PMC6825855 DOI: 10.1002/mgg3.953] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 08/11/2019] [Accepted: 08/12/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The present study aims to summarize the clinical and genetic characteristics of ZTTK syndrome. METHODS The clinical and genetic data of a Chinese girl with severe growth and development delay, intellectual disability, and facial features were analyzed. Original articles on ZTTK syndrome published up to November 20l8 were identified from PubMed, Human Gene Mutation Database, Online Mendelian Inheritance in Man, China National Knowledge Infrastructure, and WanFang databases using the keywords "ZTTK syndrome" and "SON". RESULTS The patient was born small for gestational age, and had poor academic performance, delayed language development, and motor retardation. The patient's height was 113 cm (less than -3 SD), and had moles on the back skin and possessed facial features. A novel heterozygous mutation c.394C>T (p.Q132X) of SON was found in this patient, but the parents were normal. CONCLUSION The patient's clinical phenotype was consistent with ZTTK syndrome. The novel heterozygous mutation c.394C>T (p.Q132X) of SON was its pathogenic mutation, which has not been reported at home and abroad.
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Affiliation(s)
- Yu Yang
- Department of Endocrinology, Metabolism, and Genetics, Affiliated Children's Hospital of Nanchang university, Nanchang shi, Jiangxi Sheng, people's Republic of China, Nanchang, Jiangxi, China
| | - Lei Xu
- Department of Endocrinology, Metabolism, and Genetics, Affiliated Children's Hospital of Nanchang university, Nanchang shi, Jiangxi Sheng, people's Republic of China, Nanchang, Jiangxi, China
| | - Zhen Yu
- Department of Endocrinology, Metabolism, and Genetics, Affiliated Children's Hospital of Nanchang university, Nanchang shi, Jiangxi Sheng, people's Republic of China, Nanchang, Jiangxi, China
| | - Hui Huang
- Central Laboratory, Non-directly Affiliated Hospital of Nanchang University, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
| | - Li Yang
- Department of Endocrinology, Metabolism, and Genetics, Affiliated Children's Hospital of Nanchang university, Nanchang shi, Jiangxi Sheng, people's Republic of China, Nanchang, Jiangxi, China
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12
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Ji M, Yao Y, Liu A, Shi L, Chen D, Tang L, Yang G, Liang X, Peng J, Shao C. lncRNA H19 binds VGF and promotes pNEN progression via PI3K/AKT/CREB signaling. Endocr Relat Cancer 2019; 26:643-658. [PMID: 31117050 DOI: 10.1530/erc-18-0552] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 04/30/2019] [Indexed: 12/12/2022]
Abstract
Pancreatic neuroendocrine neoplasms (pNENs) are endocrine tumors arising in pancreas and is the most common neuroendocrine tumors. Mounting evidence indicates lncRNA H19 could be a determinant of tumor progression. However, the expression and mechanism of H19 and the relevant genes mediated by H19 in pNENs remain undefined. Microarray analysis was conducted to identify the differentially expressed lncRNAs in pNENs. H19 expression was analyzed in 39 paired pNEN tissues by qPCR. The biological role of H19 was determined by functional experiments. RNA pulldown, mass spectroscopy and RNA immunoprecipitation were performed to confirm the interaction between H19 and VGF. RNA-seq assays were performed after knockdown H19 or VGF. H19 was significantly upregulated in pNEN tissues with malignant behaviors, and the upregulation predicted poor prognosis in pNENs. In vitro and in vivo data showed that H19 overexpression promoted tumor growth and metastasis, whereas H19 knockdown led to the opposite phenotypes. H19 interacted with VGF, which was significantly upregulated in pNENs, and higher VGF expression was markedly related to poor differentiation and advanced stage. Furthermore, VGF was downregulated when H19 was knocked down, and VGF promoted cell proliferation, migration and invasion. Mechanistic investigations revealed that H19 activated PI3K/AKT/CREB signaling and promoted pNEN progression by interacting with VGF. These findings indicate that H19 is a promising prognostic factor in pNENs with malignant behaviors and functions as an oncogene via the VGF-mediated PI3K/AKT/CREB pathway. In addition, our study implies that VGF may also serve as a candidate prognostic biomarker and therapeutic target in pNENs.
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Affiliation(s)
- Meng Ji
- Department of General Surgery (Department of Pancreatic-Biliary Surgery), Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai, China
| | - Yanli Yao
- Glycochemistry & Glycobiology Lab, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Anan Liu
- Department of General Surgery (Department of Pancreatic-Biliary Surgery), Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai, China
| | - Ligang Shi
- Department of General Surgery (Department of Pancreatic-Biliary Surgery), Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai, China
| | - Danlei Chen
- Department of General Surgery (Department of Pancreatic-Biliary Surgery), Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai, China
| | - Liang Tang
- Department of General Surgery (Department of Pancreatic-Biliary Surgery), Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai, China
| | - Guang Yang
- Department of General Surgery (Department of Pancreatic-Biliary Surgery), Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai, China
| | - Xing Liang
- Department of General Surgery (Department of Pancreatic-Biliary Surgery), Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai, China
| | - Junfeng Peng
- Department of General Surgery (Department of Pancreatic-Biliary Surgery), Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai, China
| | - Chenghao Shao
- Department of General Surgery (Department of Pancreatic-Biliary Surgery), Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai, China
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13
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Myung JK, Yeo SG, Kim KH, Baek KS, Shin D, Kim JH, Cho JY, Yoo BC. Proteins that interact with calgranulin B in the human colon cancer cell line HCT-116. Oncotarget 2017; 8:6819-6832. [PMID: 28036279 PMCID: PMC5351672 DOI: 10.18632/oncotarget.14301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/12/2016] [Indexed: 11/25/2022] Open
Abstract
Calgranulin B is released from immune cells and can be internalized into colon cancer cells to prevent proliferation. The present study aimed to identify proteins that interact with calgranulin B to suppress the proliferation of colon cancer cells, and to obtain information on the underlying anti-tumor mechanism(s) of calgranulin B. Calgranulin B expression was induced in colon cancer cell line HCT-116 by infection with calgranulin B-FLAG expressing lentivirus, and it led to a significant suppression of cell proliferation. Proteins that interacted with calgranulin B were obtained by immunoprecipitation using whole homogenate of lentivirus-infected HCT-116 cells which expressing calgranulin B-FLAG, and identified using liquid chromatography-mass spectrometry/mass spectrometry analysis. A total of 454 proteins were identified that potentially interact with calgranulin B, and most identified proteins were associated with RNA processing, post-transcriptional modifications and the EIF2 signaling pathway. Direct interaction of calgranulin B with flotillin-1, dynein intermediate chain 1, and CD59 glycoprotein has been confirmed, and the molecules N-myc proto-oncogene protein, rapamycin-insensitive companion of mTOR, and myc proto-oncogene protein were shown to regulate calgranulin B-interacting proteins. Our results provide new insight and useful information to explain the possible mechanism(s) underlying the role of calgranulin B as an anti-tumor effector in colon cancer cells.
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Affiliation(s)
- Jae Kyung Myung
- Department of System Cancer Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Seung-Gu Yeo
- Department of Radiation Oncology, Soonchunhyang University College of Medicine, Cheonan, Korea
| | - Kyung Hee Kim
- Colorectal Cancer Branch, Research Institute, National Cancer Center, Goyang, Korea.,Omics Core, Research Institute, National Cancer Center, Goyang, Korea
| | - Kwang-Soo Baek
- Colorectal Cancer Branch, Research Institute, National Cancer Center, Goyang, Korea.,Department of Genetic Engineering, Sungkyunkwan University, Suwon, Korea
| | - Daye Shin
- Department of System Cancer Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea.,Cancer Cell and Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, Korea
| | - Jong Heon Kim
- Department of System Cancer Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea.,Cancer Cell and Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, Korea
| | - Jae Youl Cho
- Department of Genetic Engineering, Sungkyunkwan University, Suwon, Korea
| | - Byong Chul Yoo
- Colorectal Cancer Branch, Research Institute, National Cancer Center, Goyang, Korea
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14
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Kim JH, Shinde D, Reijnders M, Hauser N, Belmonte R, Wilson G, Bosch D, Bubulya P, Shashi V, Petrovski S, Stone J, Park E, Veltman J, Sinnema M, Stumpel C, Draaisma J, Nicolai J, Yntema H, Lindstrom K, de Vries B, Jewett T, Santoro S, Vogt J, Bachman K, Seeley A, Krokosky A, Turner C, Rohena L, Hempel M, Kortüm F, Lessel D, Neu A, Strom T, Wieczorek D, Bramswig N, Laccone F, Behunova J, Rehder H, Gordon C, Rio M, Romana S, Tang S, El-Khechen D, Cho M, McWalter K, Douglas G, Baskin B, Begtrup A, Funari T, Schoch K, Stegmann A, Stevens S, Zhang DE, Traver D, Yao X, MacArthur D, Brunner H, Mancini G, Myers R, Owen L, Lim ST, Stachura D, Vissers L, Ahn EY, Vissers LELM, Ahn EYE. De Novo Mutations in SON Disrupt RNA Splicing of Genes Essential for Brain Development and Metabolism, Causing an Intellectual-Disability Syndrome. Am J Hum Genet 2016; 99:711-719. [PMID: 27545680 PMCID: PMC5011044 DOI: 10.1016/j.ajhg.2016.06.029] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/24/2016] [Indexed: 12/01/2022] Open
Abstract
The overall understanding of the molecular etiologies of intellectual disability (ID) and developmental delay (DD) is increasing as next-generation sequencing technologies identify genetic variants in individuals with such disorders. However, detailed analyses conclusively confirming these variants, as well as the underlying molecular mechanisms explaining the diseases, are often lacking. Here, we report on an ID syndrome caused by de novo heterozygous loss-of-function (LoF) mutations in SON. The syndrome is characterized by ID and/or DD, malformations of the cerebral cortex, epilepsy, vision problems, musculoskeletal abnormalities, and congenital malformations. Knockdown of son in zebrafish resulted in severe malformation of the spine, brain, and eyes. Importantly, analyses of RNA from affected individuals revealed that genes critical for neuronal migration and cortex organization (TUBG1, FLNA, PNKP, WDR62, PSMD3, and HDAC6) and metabolism (PCK2, PFKL, IDH2, ACY1, and ADA) are significantly downregulated because of the accumulation of mis-spliced transcripts resulting from erroneous SON-mediated RNA splicing. Our data highlight SON as a master regulator governing neurodevelopment and demonstrate the importance of SON-mediated RNA splicing in human development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
| | - Eun-Young Erin Ahn
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA.
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15
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Tokita M, Braxton A, Shao Y, Lewis A, Vincent M, Küry S, Besnard T, Isidor B, Latypova X, Bézieau S, Liu P, Motter C, Melver C, Robin N, Infante E, McGuire M, El-Gharbawy A, Littlejohn R, McLean S, Bi W, Bacino C, Lalani S, Scott D, Eng C, Yang Y, Schaaf C, Walkiewicz M. De Novo Truncating Variants in SON Cause Intellectual Disability, Congenital Malformations, and Failure to Thrive. Am J Hum Genet 2016; 99:720-727. [PMID: 27545676 DOI: 10.1016/j.ajhg.2016.06.035] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/24/2016] [Indexed: 10/21/2022] Open
Abstract
SON is a key component of the spliceosomal complex and a critical mediator of constitutive and alternative splicing. Additionally, SON has been shown to influence cell-cycle progression, genomic integrity, and maintenance of pluripotency in stem cell populations. The clear functional relevance of SON in coordinating essential cellular processes and its presence in diverse human tissues suggests that intact SON might be crucial for normal growth and development. However, the phenotypic effects of deleterious germline variants in SON have not been clearly defined. Herein, we describe seven unrelated individuals with de novo variants in SON and propose that deleterious variants in SON are associated with a severe multisystem disorder characterized by developmental delay, persistent feeding difficulties, and congenital malformations, including brain anomalies.
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16
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Kim JH, Baddoo MC, Park EY, Stone JK, Park H, Butler TW, Huang G, Yan X, Pauli-Behn F, Myers RM, Tan M, Flemington EK, Lim ST, Ahn EYE. SON and Its Alternatively Spliced Isoforms Control MLL Complex-Mediated H3K4me3 and Transcription of Leukemia-Associated Genes. Mol Cell 2016; 61:859-73. [PMID: 26990989 DOI: 10.1016/j.molcel.2016.02.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 12/16/2015] [Accepted: 02/17/2016] [Indexed: 10/22/2022]
Abstract
Dysregulation of MLL complex-mediated histone methylation plays a pivotal role in gene expression associated with diseases, but little is known about cellular factors modulating MLL complex activity. Here, we report that SON, previously known as an RNA splicing factor, controls MLL complex-mediated transcriptional initiation. SON binds to DNA near transcription start sites, interacts with menin, and inhibits MLL complex assembly, resulting in decreased H3K4me3 and transcriptional repression. Importantly, alternatively spliced short isoforms of SON are markedly upregulated in acute myeloid leukemia. The short isoforms compete with full-length SON for chromatin occupancy but lack the menin-binding ability, thereby antagonizing full-length SON function in transcriptional repression while not impairing full-length SON-mediated RNA splicing. Furthermore, overexpression of a short isoform of SON enhances replating potential of hematopoietic progenitors. Our findings define SON as a fine-tuner of the MLL-menin interaction and reveal short SON overexpression as a marker indicating aberrant transcriptional initiation in leukemia.
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Affiliation(s)
- Jung-Hyun Kim
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Melody C Baddoo
- Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA
| | - Eun Young Park
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Joshua K Stone
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Hyeonsoo Park
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA
| | - Thomas W Butler
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Gang Huang
- Division of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaomei Yan
- Division of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | | | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Ming Tan
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | | | - Ssang-Taek Lim
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA
| | - Eun-Young Erin Ahn
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA.
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17
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Tapak L, Saidijam M, Sadeghifar M, Poorolajal J, Mahjub H. Competing risks data analysis with high-dimensional covariates: an application in bladder cancer. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:169-76. [PMID: 25907251 PMCID: PMC4563215 DOI: 10.1016/j.gpb.2015.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 09/27/2014] [Accepted: 10/08/2014] [Indexed: 01/09/2023]
Abstract
Analysis of microarray data is associated with the methodological problems of high dimension and small sample size. Various methods have been used for variable selection in high-dimension and small sample size cases with a single survival endpoint. However, little effort has been directed toward addressing competing risks where there is more than one failure risks. This study compared three typical variable selection techniques including Lasso, elastic net, and likelihood-based boosting for high-dimensional time-to-event data with competing risks. The performance of these methods was evaluated via a simulation study by analyzing a real dataset related to bladder cancer patients using time-dependent receiver operator characteristic (ROC) curve and bootstrap .632+ prediction error curves. The elastic net penalization method was shown to outperform Lasso and boosting. Based on the elastic net, 33 genes out of 1381 genes related to bladder cancer were selected. By fitting to the Fine and Gray model, eight genes were highly significant (P<0.001). Among them, expression of RTN4, SON, IGF1R, SNRPE, PTGR1, PLEK, and ETFDH was associated with a decrease in survival time, whereas SMARCAD1 expression was associated with an increase in survival time. This study indicates that the elastic net has a higher capacity than the Lasso and boosting for the prediction of survival time in bladder cancer patients. Moreover, genes selected by all methods improved the predictive power of the model based on only clinical variables, indicating the value of information contained in the microarray features.
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Affiliation(s)
- Leili Tapak
- Department of Biostatistics and Epidemiology, School of Public Health, Hamadan University of Medical Sciences, Hamadan 65175-4171, Iran
| | - Massoud Saidijam
- Research Center for Molecular Medicine, Department of Molecular Medicine and Genetics, School of Medicine, Hamadan University of Medical Sciences, Hamadan 651783-8695, Iran
| | - Majid Sadeghifar
- Department of Statistics, Bu-Ali Sina University, Hamadan 65175-4171, Iran
| | - Jalal Poorolajal
- Department of Biostatistics and Epidemiology, School of Public Health, Hamadan University of Medical Sciences, Hamadan 65175-4171, Iran; Modeling of Noncommunicable Diseases Research Center, School of Public Health, Hamadan University of Medical Sciences, Hamadan 65178-38695, Iran
| | - Hossein Mahjub
- Department of Biostatistics and Epidemiology, School of Public Health, Hamadan University of Medical Sciences, Hamadan 65175-4171, Iran; Research Center for Health Sciences, School of Public Health, Hamadan University of Medical Sciences, Hamadan 65175-4171, Iran.
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18
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Battini VP, Bubulya A, Bubulya PA. Accurate splicing of HDAC6 pre-mRNA requires SON. Int J Mol Sci 2015; 16:5886-99. [PMID: 25782155 PMCID: PMC4394511 DOI: 10.3390/ijms16035886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/19/2015] [Accepted: 03/03/2015] [Indexed: 11/26/2022] Open
Abstract
Pre-mRNA splicing requires proper splice site selection mediated by many factors including snRNPs and serine-arginine rich (SR) splicing factors. Our lab previously reported that the SR-like protein SON maintains organization of pre-mRNA splicing factors in nuclear speckles as well as splicing of many human transcripts including mRNAs coding for the chromatin-modifying enzymes HDAC6, ADA and SETD8. However, the mechanism by which SON maintains accurate splicing is unknown. To build tools for understanding SON-dependent pre-mRNA splicing, we constructed a minigene reporter plasmid driving expression of the genomic sequence spanning exons 26 through 29 of HDAC6. Following SON depletion, we observed altered splicing of HDAC6 reporter transcripts that showed exclusion of exons 27 and 28, reflecting the splicing patterns of endogenous HDAC6 mRNA. Importantly, loss of HDAC6 biological function was also observed, as indicated by truncated HDAC6 protein and corresponding absence of aggresome assembly activities of HDAC6 binding-of-ubiquitin zinc finger (BUZ) domain. We therefore propose that SON-mediated splicing regulation of HDAC6 is essential for supporting protein degradation pathways that prevent human disease.
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Affiliation(s)
- Vishnu Priya Battini
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA.
| | - Athanasios Bubulya
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA.
| | - Paula A Bubulya
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA.
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19
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Pan K, Lee JTH, Huang Z, Wong CM. Coupling and coordination in gene expression processes with pre-mRNA splicing. Int J Mol Sci 2015; 16:5682-96. [PMID: 25768347 PMCID: PMC4394499 DOI: 10.3390/ijms16035682] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/28/2015] [Accepted: 03/04/2015] [Indexed: 12/13/2022] Open
Abstract
RNA processing is a tightly regulated and highly complex pathway which includes transcription, splicing, editing, transportation, translation and degradation. It has been well-documented that splicing of RNA polymerase II medicated nascent transcripts occurs co-transcriptionally and is functionally coupled to other RNA processing. Recently, increasing experimental evidence indicated that pre-mRNA splicing influences RNA degradation and vice versa. In this review, we summarized the recent findings demonstrating the coupling of these two processes. In addition, we highlighted the importance of splicing in the production of intronic miRNA and circular RNAs, and hence the discovery of the novel mechanisms in the regulation of gene expression.
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