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Wilhelm E, Poirier M, Da Rocha M, Bédard M, McDonald PP, Lavigne P, Hunter CL, Bell B. Mitotic deacetylase complex (MiDAC) recognizes the HIV-1 core promoter to control activated viral gene expression. PLoS Pathog 2024; 20:e1011821. [PMID: 38781120 PMCID: PMC11115230 DOI: 10.1371/journal.ppat.1011821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/05/2024] [Indexed: 05/25/2024] Open
Abstract
The human immunodeficiency virus (HIV) integrates into the host genome forming latent cellular reservoirs that are an obstacle for cure or remission strategies. Viral transcription is the first step in the control of latency and depends upon the hijacking of the host cell RNA polymerase II (Pol II) machinery by the 5' HIV LTR. Consequently, "block and lock" or "shock and kill" strategies for an HIV cure depend upon a full understanding of HIV transcriptional control. The HIV trans-activating protein, Tat, controls HIV latency as part of a positive feed-forward loop that strongly activates HIV transcription. The recognition of the TATA box and adjacent sequences of HIV essential for Tat trans-activation (TASHET) of the core promoter by host cell pre-initiation complexes of HIV (PICH) has been shown to be necessary for Tat trans-activation, yet the protein composition of PICH has remained obscure. Here, DNA-affinity chromatography was employed to identify the mitotic deacetylase complex (MiDAC) as selectively recognizing TASHET. Using biophysical techniques, we show that the MiDAC subunit DNTTIP1 binds directly to TASHET, in part via its CTGC DNA motifs. Using co-immunoprecipitation assays, we show that DNTTIP1 interacts with MiDAC subunits MIDEAS and HDAC1/2. The Tat-interacting protein, NAT10, is also present in HIV-bound MiDAC. Gene silencing revealed a functional role for DNTTIP1, MIDEAS, and NAT10 in HIV expression in cellulo. Furthermore, point mutations in TASHET that prevent DNTTIP1 binding block the reactivation of HIV by latency reversing agents (LRA) that act via the P-TEFb/7SK axis. Our data reveal a key role for MiDAC subunits DNTTIP1, MIDEAS, as well as NAT10, in Tat-activated HIV transcription and latency. DNTTIP1, MIDEAS and NAT10 emerge as cell cycle-regulated host cell transcription factors that can control activated HIV gene expression, and as new drug targets for HIV cure strategies.
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Affiliation(s)
| | | | - Morgane Da Rocha
- Département de microbiologie et d’infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | - Mikaël Bédard
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | - Patrick P. McDonald
- Pulmonary Division, Medicine Faculty, Université de Sherbrooke; and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | - Pierre Lavigne
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | | | - Brendan Bell
- Département de microbiologie et d’infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, and Centre de recherche du CHUS, Sherbrooke, Québec, Canada
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2
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House IG, Derrick EB, Sek K, Chen AXY, Li J, Lai J, Todd KL, Munoz I, Michie J, Chan CW, Huang YK, Chan JD, Petley EV, Tong J, Nguyen D, Engel S, Savas P, Hogg SJ, Vervoort SJ, Kearney CJ, Burr ML, Lam EYN, Gilan O, Bedoui S, Johnstone RW, Dawson MA, Loi S, Darcy PK, Beavis PA. CRISPR-Cas9 screening identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and antitumor immunity. Cell Rep 2023; 42:113014. [PMID: 37605534 DOI: 10.1016/j.celrep.2023.113014] [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: 08/12/2022] [Revised: 06/13/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023] Open
Abstract
CXCL9 expression is a strong predictor of response to immune checkpoint blockade therapy. Accordingly, we sought to develop therapeutic strategies to enhance the expression of CXCL9 and augment antitumor immunity. To perform whole-genome CRISPR-Cas9 screening for regulators of CXCL9 expression, a CXCL9-GFP reporter line is generated using a CRISPR knockin strategy. This approach finds that IRF1 limits CXCL9 expression in both tumor cells and primary myeloid cells through induction of SOCS1, which subsequently limits STAT1 signaling. Thus, we identify a subset of STAT1-dependent genes that do not require IRF1 for their transcription, including CXCL9. Targeting of either IRF1 or SOCS1 potently enhances CXCL9 expression by intratumoral macrophages, which is further enhanced in the context of immune checkpoint blockade therapy. We hence show a non-canonical role for IRF1 in limiting the expression of a subset of STAT1-dependent genes through induction of SOCS1.
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Affiliation(s)
- Imran G House
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Emily B Derrick
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kevin Sek
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Amanda X Y Chen
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jasmine Li
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Junyun Lai
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kirsten L Todd
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Isabelle Munoz
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jessica Michie
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Cheok Weng Chan
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Yu-Kuan Huang
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jack D Chan
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Emma V Petley
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Junming Tong
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - DatMinh Nguyen
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Sven Engel
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia; Institute of Experimental Immunology, University of Bonn, Bonn, Germany
| | - Peter Savas
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Simon J Hogg
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Stephin J Vervoort
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Conor J Kearney
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Marian L Burr
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia; Department of Anatomical Pathology, The Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - Enid Y N Lam
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Omer Gilan
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Sammy Bedoui
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia; Institute of Experimental Immunology, University of Bonn, Bonn, Germany
| | - Ricky W Johnstone
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Mark A Dawson
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia; Department of Haematology, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, VIC 3052, Australia; Centre for Cancer Research, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Sherene Loi
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Phillip K Darcy
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Immunology, Monash University, Clayton, VIC, Australia.
| | - Paul A Beavis
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia.
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3
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Liu Q, Xiong J, Xu D, Hao N, Zhang Y, Sang Y, Wang Z, Zheng X, Min J, Diao H, Raphael J, Vareki SM, Koropatnick J, Min W. TdIF1-LSD1 Axis Regulates Epithelial-Mesenchymal Transition and Metastasis via Histone Demethylation of E-Cadherin Promoter in Lung Cancer. Int J Mol Sci 2021; 23:250. [PMID: 35008676 PMCID: PMC8745707 DOI: 10.3390/ijms23010250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/27/2021] [Accepted: 12/23/2021] [Indexed: 12/26/2022] Open
Abstract
We have previously found that TdT-interacting factor 1 (TdIF1) is a potential oncogene expressed in non-small cell lung cancer (NSCLC) and is associated with poor prognosis. However, its exact mechanism is still unclear. The lysine-specific demethylase 1 (LSD1) is a crucial mediator of the epithelial-mesenchymal transition (EMT), an important process triggered during cancer metastasis. Here, we confirm that TdIF1 is highly expressed in NSCLC and related to lymph node metastasis through The Cancer Genome Atlas (TCGA) analysis of clinical samples. Silencing TdIF1 can regulate the expression of EMT-related factors and impair the migration and invasion ability of cancer cells in vitro. An analysis of tumor xenografts in nude mice confirmed that silencing TdIF1 inhibits tumor growth. Furthermore, we determined the interaction between TdIF1 and LSD1 using immunoprecipitation. Chromatin immunoprecipitation (ChIP) revealed that TdIF1 was enriched in the E-cadherin promoter region. The knockdown of TdIF1 repressed the enrichment of LSD1 at the E-cadherin promoter region, thereby regulating the level of promoter histone methylation and modulating E-cadherin transcription activity, ultimately leading to changes in EMT factors and cancer cell migration and invasion ability. The LSD1 inhibitor and TdIF1 knockdown combination showed a synergistic effect in inhibiting the growth, migration, and invasion of NSCLC cells. Taken together, this is the first demonstration that TdIF1 regulates E-cadherin transcription by recruiting LSD1 to the promoter region, thereby promoting EMT and tumor metastasis and highlighting the potential of TdIF1 as a therapeutic target for NSCLC.
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Affiliation(s)
- Qi Liu
- Institute of Immunotherapy, College of Basic Medicine, The First Affiliated Hospital of Nanchang University, Jiangxi Academy of Medical Sciences, Nanchang 330046, China; (Q.L.); (D.X.); (N.H.); (Y.Z.); (Y.S.); (Z.W.)
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5A5, Canada; (X.Z.); (S.M.V.); (J.K.)
| | - Juan Xiong
- Department of Preventive Medicine, School of Medicine, Shenzhen University, Shenzhen 518054, China;
| | - Derong Xu
- Institute of Immunotherapy, College of Basic Medicine, The First Affiliated Hospital of Nanchang University, Jiangxi Academy of Medical Sciences, Nanchang 330046, China; (Q.L.); (D.X.); (N.H.); (Y.Z.); (Y.S.); (Z.W.)
| | - Nan Hao
- Institute of Immunotherapy, College of Basic Medicine, The First Affiliated Hospital of Nanchang University, Jiangxi Academy of Medical Sciences, Nanchang 330046, China; (Q.L.); (D.X.); (N.H.); (Y.Z.); (Y.S.); (Z.W.)
| | - Yujuan Zhang
- Institute of Immunotherapy, College of Basic Medicine, The First Affiliated Hospital of Nanchang University, Jiangxi Academy of Medical Sciences, Nanchang 330046, China; (Q.L.); (D.X.); (N.H.); (Y.Z.); (Y.S.); (Z.W.)
| | - Yi Sang
- Institute of Immunotherapy, College of Basic Medicine, The First Affiliated Hospital of Nanchang University, Jiangxi Academy of Medical Sciences, Nanchang 330046, China; (Q.L.); (D.X.); (N.H.); (Y.Z.); (Y.S.); (Z.W.)
| | - Zhigang Wang
- Institute of Immunotherapy, College of Basic Medicine, The First Affiliated Hospital of Nanchang University, Jiangxi Academy of Medical Sciences, Nanchang 330046, China; (Q.L.); (D.X.); (N.H.); (Y.Z.); (Y.S.); (Z.W.)
| | - Xiufen Zheng
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5A5, Canada; (X.Z.); (S.M.V.); (J.K.)
- Department of Surgery, University of Western Ontario, London, ON N6A 5A5, Canada
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5A5, Canada
- Department of Oncology, University of Western Ontario, London, ON N6A 5A5, Canada;
| | - Jeffrey Min
- London Regional Cancer Program, Matthew Mailing Centre for Translational Transplantation Studies, Lawson Health Research Institute, London, ON N6A 5A5, Canada; (J.M.); (H.D.)
| | - Hong Diao
- London Regional Cancer Program, Matthew Mailing Centre for Translational Transplantation Studies, Lawson Health Research Institute, London, ON N6A 5A5, Canada; (J.M.); (H.D.)
| | - Jacques Raphael
- Department of Oncology, University of Western Ontario, London, ON N6A 5A5, Canada;
- London Regional Cancer Program, Matthew Mailing Centre for Translational Transplantation Studies, Lawson Health Research Institute, London, ON N6A 5A5, Canada; (J.M.); (H.D.)
| | - Saman Maleki Vareki
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5A5, Canada; (X.Z.); (S.M.V.); (J.K.)
- Department of Oncology, University of Western Ontario, London, ON N6A 5A5, Canada;
- London Regional Cancer Program, Matthew Mailing Centre for Translational Transplantation Studies, Lawson Health Research Institute, London, ON N6A 5A5, Canada; (J.M.); (H.D.)
| | - James Koropatnick
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5A5, Canada; (X.Z.); (S.M.V.); (J.K.)
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5A5, Canada
- Department of Oncology, University of Western Ontario, London, ON N6A 5A5, Canada;
- London Regional Cancer Program, Matthew Mailing Centre for Translational Transplantation Studies, Lawson Health Research Institute, London, ON N6A 5A5, Canada; (J.M.); (H.D.)
| | - Weiping Min
- Institute of Immunotherapy, College of Basic Medicine, The First Affiliated Hospital of Nanchang University, Jiangxi Academy of Medical Sciences, Nanchang 330046, China; (Q.L.); (D.X.); (N.H.); (Y.Z.); (Y.S.); (Z.W.)
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5A5, Canada; (X.Z.); (S.M.V.); (J.K.)
- Department of Surgery, University of Western Ontario, London, ON N6A 5A5, Canada
- Department of Oncology, University of Western Ontario, London, ON N6A 5A5, Canada;
- London Regional Cancer Program, Matthew Mailing Centre for Translational Transplantation Studies, Lawson Health Research Institute, London, ON N6A 5A5, Canada; (J.M.); (H.D.)
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4
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Mondal B, Jin H, Kallappagoudar S, Sedkov Y, Martinez T, Sentmanat MF, Poet GJ, Li C, Fan Y, Pruett-Miller SM, Herz HM. The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression program to control neurite outgrowth. eLife 2020; 9:57519. [PMID: 32297854 PMCID: PMC7192582 DOI: 10.7554/elife.57519] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
The mitotic deacetylase complex (MiDAC) is a recently identified histone deacetylase (HDAC) complex. While other HDAC complexes have been implicated in neurogenesis, the physiological role of MiDAC remains unknown. Here, we show that MiDAC constitutes an important regulator of neural differentiation. We demonstrate that MiDAC functions as a modulator of a neurodevelopmental gene expression program and binds to important regulators of neurite outgrowth. MiDAC upregulates gene expression of pro-neural genes such as those encoding the secreted ligands SLIT3 and NETRIN1 (NTN1) by a mechanism suggestive of H4K20ac removal on promoters and enhancers. Conversely, MiDAC inhibits gene expression by reducing H3K27ac on promoter-proximal and -distal elements of negative regulators of neurogenesis. Furthermore, loss of MiDAC results in neurite outgrowth defects that can be rescued by supplementation with SLIT3 and/or NTN1. These findings indicate a crucial role for MiDAC in regulating the ligands of the SLIT3 and NTN1 signaling axes to ensure the proper integrity of neurite development.
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Affiliation(s)
- Baisakhi Mondal
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Hongjian Jin
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Satish Kallappagoudar
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Yurii Sedkov
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Tanner Martinez
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Monica F Sentmanat
- Genome Engineering & iPS Center, Department of Genetics, Washington University, St. Louis, United States
| | - Greg J Poet
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Shondra M Pruett-Miller
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Hans-Martin Herz
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
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5
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Wong KC, Lin J, Li X, Lin Q, Liang C, Song YQ. Heterodimeric DNA motif synthesis and validations. Nucleic Acids Res 2019; 47:1628-1636. [PMID: 30590725 PMCID: PMC6393289 DOI: 10.1093/nar/gky1297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/04/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023] Open
Abstract
Bound by transcription factors, DNA motifs (i.e. transcription factor binding sites) are prevalent and important for gene regulation in different tissues at different developmental stages of eukaryotes. Although considerable efforts have been made on elucidating monomeric DNA motif patterns, our knowledge on heterodimeric DNA motifs are still far from complete. Therefore, we propose to develop a computational approach to synthesize a heterodimeric DNA motif from two monomeric DNA motifs. The approach is sequentially divided into two components (Phases A and B). In Phase A, we propose to develop the inference models on how two DNA monomeric motifs can be oriented and overlapped with each other at nucleotide level. In Phase B, given the two monomeric DNA motifs oriented, we further propose to develop DNA-binding family-specific input-output hidden Markov models (IOHMMs) to synthesize a heterodimeric DNA motif. To validate the approach, we execute and cross-validate it with the experimentally verified 618 heterodimeric DNA motifs across 49 DNA-binding family combinations. We observe that our approach can even "rescue" the existing heterodimeric DNA motif pattern (i.e. HOXB2_EOMES) previously published on Nature. Lastly, we apply the proposed approach to infer previously uncharacterized heterodimeric motifs. Their motif instances are supported by DNase accessibility, gene ontology, protein-protein interactions, in vivo ChIP-seq peaks, and even structural data from PDB. A public web-server is built for open accessibility and scientific impact. Its address is listed as follows: http://motif.cs.cityu.edu.hk/custom/MotifKirin.
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Affiliation(s)
- Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Jiecong Lin
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Xiangtao Li
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Qiuzhen Lin
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Cheng Liang
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
| | - You-Qiang Song
- School of Biomedical Sciences, University of Hong Kong, Pokfulam, Hong Kong SAR
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6
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Zhang Y, Wang Z, Huang Y, Ying M, Wang Y, Xiong J, Liu Q, Cao F, Joshi R, Liu Y, Xu D, Zhang M, Yuan K, Zhou N, Koropatnick J, Min W. TdIF1: a putative oncogene in NSCLC tumor progression. Signal Transduct Target Ther 2018; 3:28. [PMID: 30345081 PMCID: PMC6194072 DOI: 10.1038/s41392-018-0030-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/04/2018] [Accepted: 09/05/2018] [Indexed: 12/17/2022] Open
Abstract
TdT-interacting factor 1 (TdIF1) is a ubiquitously expressed DNA- and protein-binding protein that directly binds to terminal deoxynucleotidyl transferase (TdT) polymerase. Little is known about the functional role of TdIF1 in cancer cellular signaling, nor has it previously been identified as aberrant in any type of cancer. We report here for the first time that TdIF1 is abundantly expressed in clinical lung cancer patients and that high expression of TdIF1 is associated with poor patient prognosis. We further established that TdIF1 is highly expressed in human non-small cell lung cancer (NSCLC) cell lines compared to a normal lung cell line. shRNA-mediated gene silencing of TdIF1 resulted in the suppression of proliferation and anchorage-independent colony formation of the A549 adenocarcinoma cell line. Moreover, when these TdIF1-silenced cells were used to establish a mouse xenograft model of human NSCLC, tumor size was greatly reduced. These data suggest that TdIF1 is a potent regulator of lung tumor development. Several cell cycle-related and tumor growth signaling pathways, including the p53 and HDAC1/2 pathways, were identified as participating in the TdIF1 signaling network by in silico analysis. Microarray, transcriptome and protein-level analyses validated p53 and HDAC1/2 modulation upon TdIF1 downregulation in an NSCLC cellular model. Moreover, several other cell cycle regulators were affected at the transcript level by TdIF1 silencing, including an increase in CDKN1A/p21 transcripts. Taken together, these results indicate that TdIF1 is a bona fide tumor-promoting factor in NSCLC and a potential target for therapy. A protein involved in the immune system also plays a role in the most common type of lung cancer. Weiping Min, of the University of Western Ontario in Canada, and international colleagues found, for the first time, that the protein TdIF1 is significantly upregulated in non-small cell lung cancer (NSCLC) tissues in patients. High expression levels of this protein were correlated with poor prognosis. NSCLC tumor tissues grown in mice where TdIF1 expression was ‘knocked down’ were significantly smaller than in those without TdIF1 knockdown. Further analyses showed the protein was involved in known cell signaling pathways with roles in NSCLC progression. The findings indicate TdIF1 should be further investigated as a biomarker of NSCLC or as a molecular target for its treatment.
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Affiliation(s)
- Yujuan Zhang
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China.,3Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
| | - Zhigang Wang
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Yanqing Huang
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Muying Ying
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Yifan Wang
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China.,4Department of Surgery, Pathology and Oncology, University of Western Ontario, London, Canada
| | - Juan Xiong
- 5Department of Preventive Medicine, School of Medicine, Shenzhen University, Shenzhen, China
| | - Qi Liu
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Fan Cao
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Rakesh Joshi
- 4Department of Surgery, Pathology and Oncology, University of Western Ontario, London, Canada
| | - Yanling Liu
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Derong Xu
- 6Institute of Translational Medicine, Nanchang University, Nanchang, China
| | - Meng Zhang
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China.,4Department of Surgery, Pathology and Oncology, University of Western Ontario, London, Canada
| | - Keng Yuan
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Nanjin Zhou
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - James Koropatnick
- 4Department of Surgery, Pathology and Oncology, University of Western Ontario, London, Canada
| | - Weiping Min
- 1Institute of Immunotherapy and College of Basic Medicine of Nanchang University, and Jiangxi Academy of Medical Sciences, Nanchang, China.,Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China.,4Department of Surgery, Pathology and Oncology, University of Western Ontario, London, Canada
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