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Chen H, Pi C, Chen M, Du X, Cui Y, Zhang D, Guo Q, Xie J, Zhou X. Runx1 alleviates osteoarthritis progression in aging mice. J Histotechnol 2024; 47:57-67. [PMID: 37966852 DOI: 10.1080/01478885.2023.2281790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/06/2023] [Indexed: 11/16/2023]
Abstract
With rates growing quickly with age, osteoarthritis (OA) is the most common cause of chronic disability in aging persons. The discomfort and reduced motion associated with osteoarthritis have a significant impact on quality of life, and there is no known solution. Runt-related transcription factor 1(Runx1) has been shown to play a protective role in the development of osteoarthritis by promoting chondrogenesis. We had created models of ageing mice with osteoarthritis by anterior cruciate ligament transection (ACLT) and analyzed the effects of intra-articular injection of adeno-associated virus/Runx1 (AAV/Runx1) on the models. The results showed that the AAV/Runx1-group maintained better articular cartilage integrity and retained more proteoglycan than the OA group after injection of AAV-Runx1. The markers related to pathological changes in cartilage were downregulated, while the markers related to physiological changes in cartilage were upregulated. This suggests that Runx1 may impede OA progression on the knee joint of ageing mice, potentially playing a protective role in OA and becoming a probable treatment target for osteoarthritis among ageing patients in the future.
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Affiliation(s)
- Haoran Chen
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Caixia Pi
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mingyang Chen
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xinmei Du
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yujia Cui
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Demao Zhang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qiang Guo
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jing Xie
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Zhou J, Toh SHM, Tan TK, Balan K, Lim JQ, Tan TZ, Xiong S, Jia Y, Ng SB, Peng Y, Jeyasekharan AD, Fan S, Lim ST, Ong CAJ, Ong CK, Sanda T, Chng WJ. Super-enhancer-driven TOX2 mediates oncogenesis in Natural Killer/T Cell Lymphoma. Mol Cancer 2023; 22:69. [PMID: 37032358 PMCID: PMC10084643 DOI: 10.1186/s12943-023-01767-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 03/24/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Extranodal natural killer/T-cell lymphoma (NKTL) is an aggressive type of non-Hodgkin lymphoma with dismal outcome. A better understanding of disease biology and key oncogenic process is necessary for the development of targeted therapy. Super-enhancers (SEs) have been shown to drive pivotal oncogenes in various malignancies. However, the landscape of SEs and SE-associated oncogenes remain elusive in NKTL. METHODS We used Nano-ChIP-seq of the active enhancer marker histone H3 lysine 27 acetylation (H3K27ac) to profile unique SEs NKTL primary tumor samples. Integrative analysis of RNA-seq and survival data further pinned down high value, novel SE oncogenes. We utilized shRNA knockdown, CRISPR-dCas9, luciferase reporter assay, ChIP-PCR to investigate the regulation of transcription factor (TF) on SE oncogenes. Multi-color immunofluorescence (mIF) staining was performed on an independent cohort of clinical samples. Various function experiments were performed to evaluate the effects of TOX2 on the malignancy of NKTL in vitro and in vivo. RESULTS SE landscape was substantially different in NKTL samples in comparison with normal tonsils. Several SEs at key transcriptional factor (TF) genes, including TOX2, TBX21(T-bet), EOMES, RUNX2, and ID2, were identified. We confirmed that TOX2 was aberrantly overexpressed in NKTL relative to normal NK cells and high expression of TOX2 was associated with worse survival. Modulation of TOX2 expression by shRNA, CRISPR-dCas9 interference of SE function impacted on cell proliferation, survival and colony formation ability of NKTL cells. Mechanistically, we found that RUNX3 regulates TOX2 transcription by binding to the active elements of its SE. Silencing TOX2 also impaired tumor formation of NKTL cells in vivo. Metastasis-associated phosphatase PRL-3 has been identified and validated as a key downstream effector of TOX2-mediated oncogenesis. CONCLUSIONS Our integrative SE profiling strategy revealed the landscape of SEs, novel targets and insights into molecular pathogenesis of NKTL. The RUNX3-TOX2-SE-TOX2-PRL-3 regulatory pathway may represent a hallmark of NKTL biology. Targeting TOX2 could be a valuable therapeutic intervene for NKTL patients and warrants further study in clinic.
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Affiliation(s)
- Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- NUS Centre for Cancer Research (N2CR), 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Sabrina Hui-Min Toh
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Kalpnaa Balan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Jing Quan Lim
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore
- Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Tuan Zea Tan
- Genomics and Data Analytics Core (GeDaC), Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Sinan Xiong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Yunlu Jia
- Department of Medical Oncology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Siok-Bian Ng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
| | - Yanfen Peng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- NUS Centre for Cancer Research (N2CR), 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Shuangyi Fan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
| | - Soon Thye Lim
- Director's office, National Cancer Centre, Singapore, 168583, Singapore
- Office of Education, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Chin-Ann Johnny Ong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre, Singapore, 168583, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, 168583, Singapore
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre, Singapore, 168583, Singapore
- SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- SingHealth Duke-NUS Surgery Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, 138673, Singapore
| | - Choon Kiat Ong
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore.
- Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- NUS Centre for Cancer Research (N2CR), 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore.
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Health System (NUHS), 1E, Kent Ridge Road, Singapore, 119228, Singapore.
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Menezes AC, Dixon C, Scholz A, Nicholson R, Leckenby A, Azevedo A, Baker S, Gilkes AF, Davies S, Darley RL, Tonks A. RUNX3 overexpression inhibits normal human erythroid development. Sci Rep 2022; 12:1243. [PMID: 35075235 PMCID: PMC8786893 DOI: 10.1038/s41598-022-05371-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
RUNX proteins belong to a family of transcription factors essential for cellular proliferation, differentiation, and apoptosis with emerging data implicating RUNX3 in haematopoiesis and haematological malignancies. Here we show that RUNX3 plays an important regulatory role in normal human erythropoiesis. The impact of altering RUNX3 expression on erythropoiesis was determined by transducing human CD34+ cells with RUNX3 overexpression or shRNA knockdown vectors. Analysis of RUNX3 mRNA expression showed that RUNX3 levels decreased during erythropoiesis. Functionally, RUNX3 overexpression had a modest impact on early erythroid growth and development. However, in late-stage erythroid development, RUNX3 promoted growth and inhibited terminal differentiation with RUNX3 overexpressing cells exhibiting lower expression of glycophorin A, greater cell size and less differentiated morphology. These results suggest that suppression of RUNX3 is required for normal erythropoiesis. Overexpression of RUNX3 increased colony formation in liquid culture whilst, corresponding RUNX3 knockdown suppressed colony formation but otherwise had little impact. This study demonstrates that the downregulation of RUNX3 observed in normal human erythropoiesis is important in promoting the terminal stages of erythroid development and may further our understanding of the role of this transcription factor in haematological malignancies.
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Affiliation(s)
- Ana Catarina Menezes
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Christabel Dixon
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Anna Scholz
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Rachael Nicholson
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Adam Leckenby
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Aleksandra Azevedo
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Sarah Baker
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK.,Cardiff Experimental Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Amanda F Gilkes
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK.,Cardiff Experimental Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Sara Davies
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Richard L Darley
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Alex Tonks
- Division of Cancer & Genetics, Department of Haematology, School of Medicine, Cardiff University, Cardiff, Wales, CF14 4XN, UK.
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Szczepińska T, Mollah AF, Plewczynski D. Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows. Int J Mol Sci 2021; 22:ijms222111591. [PMID: 34769020 PMCID: PMC8584073 DOI: 10.3390/ijms222111591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/28/2022] Open
Abstract
The nature of genome organization into two basic structural compartments is as yet undiscovered. However, it has been indicated to be a mechanism of gene expression regulation. Using the classification approach, we ranked genomic marks that hint at compartmentalization. We considered a broad range of marks, including GC content, histone modifications, DNA binding proteins, open chromatin, transcription and genome regulatory segmentation in GM12878 cells. Genomic marks were defined over CTCF or RNAPII loops, which are basic elements of genome 3D structure, and over 100 kb genomic windows. Experiments were carried out to empirically assess the whole set of features, as well as the individual features in classification of loops/windows, into compartment A or B. Using Monte Carlo Feature Selection and Analysis of Variance, we constructed a ranking of feature importance for classification. The best simple indicator of compartmentalization is DNase-seq open chromatin measurement for CTCF loops, H3K4me1 for RNAPII loops and H3K79me2 for genomic windows. Among DNA binding proteins, this is RUNX3 transcription factor for loops and RNAPII for genomic windows. Chromatin state prediction methods that indicate active elements like promoters, enhancers or heterochromatin enhance the prediction of loop segregation into compartments. However, H3K9me3, H4K20me1, H3K27me3 histone modifications and GC content poorly indicate compartments.
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Affiliation(s)
- Teresa Szczepińska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; (T.S.); (A.F.M.)
- CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
| | - Ayatullah Faruk Mollah
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; (T.S.); (A.F.M.)
- Department of Computer Science and Engineering, Aliah University, Kolkata 700160, India
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; (T.S.); (A.F.M.)
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland
- Correspondence: ; Tel.: +48-22-554-3654; Fax: +48-22-554-0801
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