1
|
Wang Y, Czap MS, Kim H, Lu H, Liu J, Chang Y, Romanienko PJ, Montagna C, Shen Z. The Mammalian KU70 C-terminus SAP Domain Is Required to Repair Exogenous DNA Damage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.30.601420. [PMID: 38979328 PMCID: PMC11230462 DOI: 10.1101/2024.06.30.601420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The mammalian non-homologous end joining (NHEJ) is required for V(D)J recombination as well as coping with exogenously induced DNA double strand breaks (DSBs). Initiated by the binding of KU70/KU80 (KU) dimer to DNA ends and the subsequent recruitment of the DNA- dependent protein kinase catalytic subunit (DNA-PKcs), NHEJ plays a key role in DNA repair. While there has been significant structural understandings of how KU70 participates in NHEJ, the specific function of its highly conserved C-terminal SAP domain remains elusive. In this study, we developed a novel mouse model by deleting the SAP domain but preserving the KU70 nuclear localization and its dimerization ability with KU80. We found that the KU70 SAP deletion did not affect the V(D)J recombination or animal development but significantly impaired the animals and cells in repairing exogenously induced DSBs. We further showed an inability of KU70-ΔSAP cells to retain the DNA Ligase IV (LIG4) and other NHEJ co-factors on chromatin, and a spreading pattern of DSB marker γH2AX in KU70-ΔSAP cells after DNA damage. Our findings suggest that a specific inhibition of the SAP function may offer an opportunity to modulate cell sensitivity to therapeutic DSB-inducing agents without interfering with the developmental function of KU70. KeyPoints Generation of a novel transgenic mouse line lacking the C-terminal conserved KU70-SAP domainKU70-SAP defends against exogenous DSBs, but unessential for development and V(D)J recombinationKU70-SAP aids in recruiting and retaining NHEJ components, such as LIG4, to DSB sites.
Collapse
|
2
|
Wang Y, Shen Z. Unmasking the mammalian SET domain-containing protein 4. NAR Cancer 2022; 4:zcac021. [PMID: 35854936 PMCID: PMC9277757 DOI: 10.1093/narcan/zcac021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
SET domain-containing protein 4 (SETD4) is a member of a unique class of protein lysine methyltransferases. Here, we introduce the basic features of SETD4 and summarize the key findings from recent studies with emphases on its roles in tissue development and tumorigenesis, and its methylation substrates. SETD4 is expressed in stem/progenitor cells. Ablation of Setd4+ cells impedes the repopulation of acinar cells after pancreatic injury. Setd4 deletion in mice promotes the recovery of radiation-induced bone marrow (BM) failure by boosting the function of BM niche, facilitates the generation of endothelial cells and neovascularization of capillary vessels in the heart, enhances the proliferation of BM mesenchymal stem cells and disrupts the TLR4 signaling in BM-derived macrophages. SETD4 expression is also associated with the maintenance of quiescent breast cancer stem cells. While mouse Setd4 knockout delays radiation-induced T-lymphoma formation, elevated SETD4 expression has been observed in some proliferative cancer cells and is associated with a pro-survival potential. Oncogenic fusions of SETD4 have also been identified in cancer, albeit rare. In addition, SETD4 methylates lysine-570 in the C-terminal globular domain of KU70, which enables KU70 translocation to cytoplasm to suppress apoptosis.
Collapse
Affiliation(s)
- Yuan Wang
- Rutgers Cancer Institute of New Jersey, Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School , 195 Little Albany Street , New Brunswick, NJ 08901, USA
| | - Zhiyuan Shen
- Rutgers Cancer Institute of New Jersey, Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School , 195 Little Albany Street , New Brunswick, NJ 08901, USA
| |
Collapse
|
3
|
Wang Y, Liu B, Lu H, Liu J, Romanienko PJ, Montelione GT, Shen Z. SETD4-mediated KU70 methylation suppresses apoptosis. Cell Rep 2022; 39:110794. [PMID: 35545041 PMCID: PMC9201767 DOI: 10.1016/j.celrep.2022.110794] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/28/2021] [Accepted: 04/15/2022] [Indexed: 12/12/2022] Open
Abstract
The mammalian KU70 is a pleiotropic protein functioning in DNA repair and cytoplasmic suppression of apoptosis. We report a regulatory mechanism by which KU70’s cytoplasmic function is enabled due to a methylation at K570 of KU70 by SET-domain-containing protein 4 (SETD4). While SETD4 silencing reduces the level of methylated KU70, over-expression of SETD4 enhances methylation of KU70. Mutations of Y272 and Y284 of SETD4 abrogate methylation of KU70. Although SETD4 is predominantly a nuclear protein, the methylated KU70 is enriched in the cytoplasm. SETD4 knockdown enhances staurosporine (STS)-induced apoptosis and cell killing. Over-expression of the wild-type (WT) SETD4, but not the SETD4-Y272/Y284F mutant, suppresses STS-induced apoptosis. The KU70-K570R (mouse Ku70-K568R) mutation dampens the anti-apoptosis activity of KU70. Our study identifies KU70 as a non-histone substrate of SETD4, discovers a post-translational modification of KU70, and uncovers a role for SETD4 and KU70-K570 methylation in the suppression of apoptosis. Wang et al. identify the methylation of mammalian KU70 by SETD4. This post-translational modification is critical for KU70 localization to the cytoplasm and subsequent suppression of apoptosis.
Collapse
Affiliation(s)
- Yuan Wang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA
| | - Bochao Liu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA
| | - Huimei Lu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA
| | - Jingmei Liu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA
| | - Peter J Romanienko
- Genome Editing Shared Resource, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180, USA
| | - Zhiyuan Shen
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901, USA.
| |
Collapse
|
4
|
Jürgens L, Manske F, Hubert E, Kischka T, Flötotto L, Klaas O, Shabardina V, Schliemann C, Makalowski W, Wethmar K. Somatic Functional Deletions of Upstream Open Reading Frame-Associated Initiation and Termination Codons in Human Cancer. Biomedicines 2021; 9:biomedicines9060618. [PMID: 34072580 PMCID: PMC8227997 DOI: 10.3390/biomedicines9060618] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/22/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022] Open
Abstract
Upstream open reading frame (uORF)-mediated translational control has emerged as an important regulatory mechanism in human health and disease. However, a systematic search for cancer-associated somatic uORF mutations has not been performed. Here, we analyzed the genetic variability at canonical (uAUG) and alternative translational initiation sites (aTISs), as well as the associated upstream termination codons (uStops) in 3394 whole-exome-sequencing datasets from patient samples of breast, colon, lung, prostate, and skin cancer and of acute myeloid leukemia, provided by The Cancer Genome Atlas research network. We found that 66.5% of patient samples were affected by at least one of 5277 recurrent uORF-associated somatic single nucleotide variants altering 446 uAUG, 347 uStop, and 4733 aTIS codons. While twelve uORF variants were detected in all entities, 17 variants occurred in all five types of solid cancer analyzed here. Highest frequencies of individual somatic variants in the TLSs of NBPF20 and CHCHD2 reached 10.1% among LAML and 8.1% among skin cancer patients, respectively. Functional evaluation by dual luciferase reporter assays identified 19 uORF variants causing significant translational deregulation of the associated main coding sequence, ranging from 1.73-fold induction for an AUG.1 > UUG variant in SETD4 to 0.006-fold repression for a CUG.6 > GUG variant in HLA-DRB1. These data suggest that somatic uORF mutations are highly prevalent in human malignancies and that defective translational regulation of protein expression may contribute to the onset or progression of cancer.
Collapse
Affiliation(s)
- Lara Jürgens
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Felix Manske
- Faculty of Medicine, Institute of Bioinformatics, University of Münster, 48149 Münster, Germany; (F.M.); (T.K.); (W.M.)
| | - Elvira Hubert
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Tabea Kischka
- Faculty of Medicine, Institute of Bioinformatics, University of Münster, 48149 Münster, Germany; (F.M.); (T.K.); (W.M.)
| | - Lea Flötotto
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Oliver Klaas
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Victoria Shabardina
- Institute of Evolutionary Biology, CSIC-Unversitat Pompeu Frabra, 08002 Barcelona, Spain;
| | - Christoph Schliemann
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Wojciech Makalowski
- Faculty of Medicine, Institute of Bioinformatics, University of Münster, 48149 Münster, Germany; (F.M.); (T.K.); (W.M.)
| | - Klaus Wethmar
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
- Correspondence: ; Tel.: +49-251-8347587; Fax: +49-251-8347588
| |
Collapse
|
5
|
Hernández HG, Hernández-Castañeda AA, Pieschacón MP, Arboleda H. ZNF718, HOXA4, and ZFP57 are differentially methylated in periodontitis in comparison with periodontal health: Epigenome-wide DNA methylation pilot study. J Periodontal Res 2021; 56:710-725. [PMID: 33660869 DOI: 10.1111/jre.12868] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 02/07/2021] [Accepted: 02/14/2021] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To investigate the differences in the epigenomic patterns of DNA methylation in peripheral leukocytes between patients with periodontitis and gingivally healthy controls evaluating its functional meaning by functional enrichment analysis. BACKGROUND The DNA methylation profiling of peripheral leukocytes as immune-related tissue potentially relevant as a source of biomarkers between periodontitis patients and gingivally healthy subjects has not been investigated. METHODS A DNA methylation epigenome-wide study of peripheral leukocytes was conducted using the Illumina MethylationEPIC platform in sixteen subjects, eight diagnosed with periodontitis patients and eight age-matched and sex-matched periodontally healthy controls. A trained periodontist performed the clinical evaluation. Global DNA methylation was estimated using methylation-sensitive high-resolution melting in LINE1. Routine cell count cytometry and metabolic laboratory tests were also performed. The analysis of differentially methylated positions (DMPs) and differentially methylated regions (DMRs) was made using R/Bioconductor environment considering leukocyte populations assessed in both routine cell counts and using the FlowSorted.Blood.EPIC package. Finally, a DMP and DMR intersection analysis was performed. Functional enrichment analysis was carried out with the differentially methylated genes found in DMP. RESULTS DMP analysis identified 81 differentially hypermethylated genes and 21 differentially hypomethylated genes. Importantly, the intersection analysis showed that zinc finger protein 718 (ZNF718) and homeobox A4 (HOXA4) were differentially hypermethylated and zinc finger protein 57 (ZFP57) was differentially hypomethylated in periodontitis. The functional enrichment analysis found clearly immune-related ontologies such as "detection of bacterium" and "antigen processing and presentation." CONCLUSION The results of this study propose three new periodontitis-related genes: ZNF718, HOXA4, and ZFP57 but also evidence the suitability and relevance of studying leukocytes' DNA methylome for biological interpretation of systemic immune-related epigenetic patterns in periodontitis.
Collapse
Affiliation(s)
- Hernán G Hernández
- Faculty of Dentistry, Division of Health Sciences, Universidad Santo Tomás, Bucaramanga, Colombia
| | | | - Maria P Pieschacón
- Faculty of Dentistry, Division of Health Sciences, Universidad Santo Tomás, Bucaramanga, Colombia
| | - Humberto Arboleda
- Neurosciences Research Group, Faculty of Medicine and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| |
Collapse
|
6
|
Liao X, Wu C, Shao Z, Zhang S, Zou Y, Wang K, Ha Y, Xing J, Zheng A, Shen Z, Zheng S, Guo J, Jie W. SETD4 in the Proliferation, Migration, Angiogenesis, Myogenic Differentiation and Genomic Methylation of Bone Marrow Mesenchymal Stem Cells. Stem Cell Rev Rep 2021; 17:1374-1389. [PMID: 33506343 DOI: 10.1007/s12015-021-10121-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 11/28/2022]
Abstract
Epigenetic modification is a crucial mechanism affecting the biological function of stem cells. SETD4 is a histone methyltransferase, and its biological role in bone marrow mesenchymal stem cells (BMSCs) is currently unknown. In this study, we employed CRISPR/Cas9 technology edited mouse model and found that SETD4 knockout significantly promoted the proliferation of BMSCs, impaired BMSCs migration and differentiation potentials of lineages of cardiacmyocyte and smooth muscle cell, and even the angiogenesis via paracrine of VEGF. Through Reduced Representation Bisulfite Sequencing (RRBS) method, we verified that the overall genomic methylation of BMSCs in the SETD4 knockout group only was decreased by 0.47 % compared with wild type. However, the changed genomic methylation covers a total of 96,331 differential methylated CpG sites and 8,692 differential methylation regions (DMRs), with part of them settled in promoter regions. Bioinformatic analysis revealed that differential CpG islands and DMRs in promoter impacted 270 GO functions and 34 KEGG signaling pathways, with some closely related to stem cell biology. Mechanismly, SETD4 knockout inhibited sets of monomethylases and dimethylases for histone lysine, along with significant changes in some factors including Nkx2.5, Gata4, Gli2, Grem2, E2f7, Map7, Nr2f2 and Shox2 that associated with stem cell biology. These results are the first to reveal that even though SETD4 changes the genome's overall methylation to a limited extent in BMSCs, it still affects the numerous cellular functions and signaling pathways, implying SETD4-altered genomic methylation serves a crucial molecular role in BMSCs' biological functions.
Collapse
Affiliation(s)
- Xiaomin Liao
- Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang, 524023, China
| | - Caixia Wu
- Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang, 524023, China
| | - Zhongming Shao
- Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang, 524023, China
| | - Shuya Zhang
- Key Laboratory for Tropical Cardiovascular Diseases Research of Hainan Province, The First Affiliated Hospital of Hainan Medical University, Haikou, 571199, China
| | - Yuan Zou
- Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang, 524023, China
| | - Keke Wang
- Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang, 524023, China
| | - Yanping Ha
- Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang, 524023, China
| | - Jingci Xing
- Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang, 524023, China
| | - Axiu Zheng
- Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang, 524023, China
| | - Zhihua Shen
- Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang, 524023, China
| | - Shaojiang Zheng
- Key Laboratory for Tropical Cardiovascular Diseases Research of Hainan Province, The First Affiliated Hospital of Hainan Medical University, Haikou, 571199, China.,Key Laboratory of Emergency and Trauma of Ministry of Education & Research Unit of Island Emergency Medicine of Chinese Academy of Medical Sciences, Hainan Medical University, Haikou, 571199, China
| | - Junli Guo
- Key Laboratory for Tropical Cardiovascular Diseases Research of Hainan Province, The First Affiliated Hospital of Hainan Medical University, Haikou, 571199, China. .,Key Laboratory of Emergency and Trauma of Ministry of Education & Research Unit of Island Emergency Medicine of Chinese Academy of Medical Sciences, Hainan Medical University, Haikou, 571199, China.
| | - Wei Jie
- Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang, 524023, China. .,Key Laboratory for Tropical Cardiovascular Diseases Research of Hainan Province, The First Affiliated Hospital of Hainan Medical University, Haikou, 571199, China. .,Key Laboratory of Emergency and Trauma of Ministry of Education & Research Unit of Island Emergency Medicine of Chinese Academy of Medical Sciences, Hainan Medical University, Haikou, 571199, China.
| |
Collapse
|