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Perycz M, Dabrowski MJ, Jardanowska-Kotuniak M, Roura AJ, Gielniewski B, Stepniak K, Dramiński M, Ciechomska IA, Kaminska B, Wojtas B. Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors. Acta Neuropathol Commun 2024; 12:72. [PMID: 38711090 DOI: 10.1186/s40478-024-01779-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
The RE1-silencing transcription factor (REST) acts either as a repressor or activator of transcription depending on the genomic and cellular context. REST is a key player in brain cell differentiation by inducing chromatin modifications, including DNA methylation, in a proximity of its binding sites. Its dysfunction may contribute to oncogenesis. Mutations in IDH1/2 significantly change the epigenome contributing to blockade of cell differentiation and glioma development. We aimed at defining how REST modulates gene activation and repression in the context of the IDH mutation-related phenotype in gliomas. We studied the effects of REST knockdown, genome wide occurrence of REST binding sites, and DNA methylation of REST motifs in IDH wild type and IDH mutant gliomas. We found that REST target genes, REST binding patterns, and TF motif occurrence proximal to REST binding sites differed in IDH wild-type and mutant gliomas. Among differentially expressed REST targets were genes involved in glial cell differentiation and extracellular matrix organization, some of which were differentially methylated at promoters or gene bodies. REST knockdown differently impacted invasion of the parental or IDH1 mutant glioma cells. The canonical REST-repressed gene targets showed significant correlation with the GBM NPC-like cellular state. Interestingly, results of REST or KAISO silencing suggested the interplay between these TFs in regulation of REST-activated and repressed targets. The identified gene regulatory networks and putative REST cooperativity with other TFs, such as KAISO, show distinct REST target regulatory networks in IDH-WT and IDH-MUT gliomas, without concomitant DNA methylation changes. We conclude that REST could be an important therapeutic target in gliomas.
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Affiliation(s)
- Malgorzata Perycz
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Michal J Dabrowski
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Marta Jardanowska-Kotuniak
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
- Doctoral School of Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Adria-Jaume Roura
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Bartlomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Karolina Stepniak
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Michał Dramiński
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Iwona A Ciechomska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Bartosz Wojtas
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
- Laboratory of Sequencing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
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Horiguchi H, Xu H, Duvert B, Ciuculescu F, Yao Q, Sinha A, McGuinness M, Harris C, Brendel C, Troeger A, Chiarle R, Williams DA. Deletion of murine Rhoh leads to de-repression of Bcl-6 via decreased KAISO levels and accelerates a malignancy phenotype in a murine model of lymphoma. Small GTPases 2022; 13:267-281. [PMID: 34983288 PMCID: PMC8741284 DOI: 10.1080/21541248.2021.2019503] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
RHOH/TFF, a member of the RAS GTPase super family, has important functions in lymphopoiesis and proximal T cell receptor signalling and has been implicated in a variety of leukaemias and lymphomas. RHOH was initially identified as a translocation partner with BCL-6 in non-Hodgkin lymphoma (NHL), and aberrant somatic hypermutation (SHM) in the 5' untranslated region of the RHOH gene has also been detected in Diffuse Large B-Cell Lymphoma (DLBCL). Recent data suggest a correlation between RhoH expression and disease progression in Acute Myeloid Leukaemia (AML). However, the effects of RHOH mutations and translocations on RhoH expression and malignant transformation remain unknown. We found that aged Rhoh-/- (KO) mice had shortened lifespans and developed B cell derived splenomegaly with an increased Bcl-6 expression profile in splenocytes. We utilized a murine model of Bcl-6 driven DLBCL to further explore the role of RhoH in malignant behaviour by crossing RhohKO mice with Iµ-HABcl-6 transgenic (Bcl-6Tg) mice. The loss of Rhoh in Bcl-6Tg mice led to a more rapid disease progression. Mechanistically, we demonstrated that deletion of Rhoh in these murine lymphoma cells was associated with decreased levels of the RhoH binding partner KAISO, a dual-specific Zinc finger transcription factor, de-repression of KAISO target Bcl-6, and downregulation of the BCL-6 target Blimp-1. Re-expression of RhoH in RhohKOBcl-6Tg lymphoma cell lines reversed these changes in expression profile and reduced proliferation of lymphoma cells in vitro. These findings suggest a previously unidentified regulatory role of RhoH in the proliferation of tumour cells via altered BCL-6 expression. (250).
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Affiliation(s)
- Hiroto Horiguchi
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Haiming Xu
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Beatrice Duvert
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Felicia Ciuculescu
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Qiuming Yao
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Meaghan McGuinness
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Chad Harris
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Christian Brendel
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Stem Cell Institute, Harvard University, Boston, MA, USA
| | - Anja Troeger
- Division of Pediatric Hematology, Oncology and Hematopoietic Stem Cell Transplantation, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Roberto Chiarle
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - David A. Williams
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Stem Cell Institute, Harvard University, Boston, MA, USA,Harvard Medical School, Harvard Initiative for RNA Medicine, Boston, MA, USA,CONTACT David A. Williams Division of Hematology/Oncology, Boston Children’s Hospital, 300 Longwood Ave. Karp 08125.3, Boston, MA02115, USA
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Choi SH, Koh DI, Cho SY, Kim MK, Kim KS, Hur MW. Temporal and differential regulation of KAISO-controlled transcription by phosphorylated and acetylated p53 highlights a crucial regulatory role of apoptosis. J Biol Chem 2019; 294:12957-12974. [PMID: 31296660 DOI: 10.1074/jbc.ra119.008100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 07/01/2019] [Indexed: 12/11/2022] Open
Abstract
Transcriptional regulator KAISO plays a critical role in cell cycle arrest and apoptosis through modulation of p53 acetylation by histone acetyltransferase p300. KAISO potently stimulates apoptosis in cells expressing WT p53, but not in p53-mutant or p53-null cells. Here, we investigated how KAISO transcription is regulated by p53, finding four potential p53-binding sites (p53-responsive DNA elements; p53REs) located in a distal 5'-upstream regulatory element, intron 1, exon 2 coding sequence, and a 3'-UTR region. Transient transcription assays of pG5-p53RE-Luc constructs with various p53REs revealed that p53 activates KAISO (ZBTB33) transcription by acting on p53RE1 (-4326 to -4227) of the 5'-upstream region and on p53RE3 (+2929 to +2959) of the exon 2 coding region during early DNA damage responses (DDRs). ChIP and oligonucleotide pulldown assays further disclosed that p53 binds to the p53RE1 and p53RE3 sites. Moreover, ataxia telangiectasia mutated (ATM) or ATM-Rad3-related (ATR) kinase-mediated p53 phosphorylation at Ser-15 or Ser-37 residues activated KAISO transcription by binding its p53RE1 or p53RE3 sites during early DDR. p53RE1 uniquely contained three p53-binding half-sites, a structural feature important for transcriptional activation by phosphorylated p53 Ser-15·Ser-37. During the later DDR phase, a KAISO-mediated acetylated p53 form (represented by a p53QRQ acetyl-mimic) robustly activated transcription by acting on p53RE1 in which this structural feature is not significant, but it provided sufficient KAISO levels to confer a p53 "apoptotic code." These results suggest that the critical apoptosis regulator KAISO is a p53 target gene that is differently regulated by phosphorylated p53 or acetylated p53, depending on DDR stage.
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Affiliation(s)
- Seo-Hyun Choi
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, 50-1 Yonsei-Ro, SeoDaeMoon-Ku, Seoul 03722, Korea
| | - Dong-In Koh
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, 50-1 Yonsei-Ro, SeoDaeMoon-Ku, Seoul 03722, Korea
| | - Su-Yeon Cho
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, 50-1 Yonsei-Ro, SeoDaeMoon-Ku, Seoul 03722, Korea
| | - Min-Kyeong Kim
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, 50-1 Yonsei-Ro, SeoDaeMoon-Ku, Seoul 03722, Korea
| | - Kyung-Sup Kim
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, 50-1 Yonsei-Ro, SeoDaeMoon-Ku, Seoul 03722, Korea
| | - Man-Wook Hur
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, 50-1 Yonsei-Ro, SeoDaeMoon-Ku, Seoul 03722, Korea.
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Koh DI, Han D, Ryu H, Choi WI, Jeon BN, Kim MK, Kim Y, Kim JY, Parry L, Clarke AR, Reynolds AB, Hur MW. KAISO, a critical regulator of p53-mediated transcription of CDKN1A and apoptotic genes. Proc Natl Acad Sci U S A 2014; 111:15078-83. [PMID: 25288747 PMCID: PMC4210320 DOI: 10.1073/pnas.1318780111] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
An unresolved issue in genotoxic stress response is identification of induced regulatory proteins and how these activate tumor suppressor p53 to determine appropriate cell responses. Transcription factor KAISO was previously described to repress transcription following binding to methylated DNA. In this study, we show that KAISO is induced by DNA damage in p53-expressing cells and then interacts with the p53-p300 complex to increase acetylation of p53 K320 and K382 residues, although decreasing K381 acetylation. Moreover, the p53 with this particular acetylation pattern shows increased DNA binding and potently induces cell cycle arrest and apoptosis by activating transcription of CDKN1A (cyclin-dependent kinase inhibitor 1) and various apoptotic genes. Analogously, in Kaiso KO mouse embryonic fibroblast cells, p53-to-promoter binding and up-regulation of p21 and apoptosis gene expression is significantly compromised. KAISO may therefore be a critical regulator of p53-mediated cell cycle arrest and apoptosis in response to various genotoxic stresses in mammalian cells.
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Affiliation(s)
- Dong-In Koh
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, SeoDaeMoon-Ku, Seoul 120-752, Korea
| | - Dohyun Han
- Department of Biomedical Sciences and Biomedical Engineering, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Hoon Ryu
- VA Boston Healthcare System and Department of Neurology, Boston University School of Medicine, Boston, MA 02130
| | - Won-Il Choi
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, SeoDaeMoon-Ku, Seoul 120-752, Korea
| | - Bu-Nam Jeon
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, SeoDaeMoon-Ku, Seoul 120-752, Korea
| | - Min-Kyeong Kim
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, SeoDaeMoon-Ku, Seoul 120-752, Korea
| | - Youngsoo Kim
- Department of Biomedical Sciences and Biomedical Engineering, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Jin Young Kim
- Mass Spectrometry Research Center, Korea Basic Science Institute, Ochang-eup, Cheongwon-gun, Chungbuk 363-883, Korea
| | - Lee Parry
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3XQ, United Kingdom; and
| | - Alan R Clarke
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3XQ, United Kingdom; and
| | - Albert B Reynolds
- Department of Cell Biology, Vanderbilt University, Nashville, TN 37232-2175
| | - Man-Wook Hur
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, SeoDaeMoon-Ku, Seoul 120-752, Korea;
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