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Mezentsev Y, Ershov P, Yablokov E, Kaluzhskiy L, Kupriyanov K, Gnedenko O, Ivanov A. Protein Interactome Profiling of Stable Molecular Complexes in Biomaterial Lysate. Int J Mol Sci 2022; 23:ijms232415697. [PMID: 36555337 PMCID: PMC9779103 DOI: 10.3390/ijms232415697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Most proteins function as part of various complexes, forming via stable and dynamic protein-protein interactions (PPIs). The profiling of PPIs expands the fundamental knowledge about the structures, functions, and regulation patterns of protein complexes and intracellular molecular machineries. Protein interactomics aims at solving three main tasks: (1) identification of protein partners and parts of complex intracellular structures; (2) analysis of PPIs parameters (affinity, molecular-recognition specificity, kinetic rate constants, and thermodynamic-parameters determination); (3) the study of the functional role of novel PPIs. The purpose of this work is to update the current state and prospects of multi-omics approaches to profiling of proteins involved in the formation of stable complexes. Methodological paradigm includes a development of protein-extraction and -separation techniques from tissues or cellular lysates and subsequent identification of proteins using mass-spectrometry analysis. In addition, some aspects of authors' experimental platforms, based on high-performance size-exclusion chromatography, procedures of molecular fishing, and protein identification, as well as the possibilities of interactomic taxonomy of each protein, are discussed.
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Park CG, Choi SH, Lee SY, Eun K, Park MG, Jang J, Jeong HJ, Kim SJ, Jeong S, Lee K, Kim H. Cytoplasmic LMO2-LDB1 Complex Activates STAT3 Signaling through Interaction with gp130-JAK in Glioma Stem Cells. Cells 2022; 11:cells11132031. [PMID: 35805116 PMCID: PMC9265747 DOI: 10.3390/cells11132031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/19/2022] [Accepted: 06/24/2022] [Indexed: 12/10/2022] Open
Abstract
The oncogenic role of nuclear LIM domain only 2 (LMO2) as a transcriptional regulator is well established, but its function in the cytoplasm is largely unknown. Here, we identified LMO2 as a cytoplasmic activator for signal transducer and activator of transcription 3 (STAT3) signaling in glioma stem cells (GSCs) through biochemical and bioinformatics analyses. LMO2 increases STAT3 phosphorylation by interacting with glycoprotein 130 (gp130) and Janus kinases (JAKs). LMO2-driven activation of STAT3 signaling requires the LDB1 protein and leads to increased expression of an inhibitor of differentiation 1 (ID1), a master regulator of cancer stemness. Our findings indicate that the cytoplasmic LMO2-LDB1 complex plays a crucial role in the activation of the GSC signaling cascade via interaction with gp130 and JAK1/2. Thus, LMO2-LDB1 is a bona fide oncogenic protein complex that activates either the JAK-STAT signaling cascade in the cytoplasm or direct transcriptional regulation in the nucleus.
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Affiliation(s)
- Cheol Gyu Park
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul 02841, Korea; (C.G.P.); (S.-H.C.); (S.Y.L.); (K.E.); (M.G.P.); (J.J.); (H.J.J.); (S.J.K.); (S.J.); (K.L.)
| | - Sang-Hun Choi
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul 02841, Korea; (C.G.P.); (S.-H.C.); (S.Y.L.); (K.E.); (M.G.P.); (J.J.); (H.J.J.); (S.J.K.); (S.J.); (K.L.)
| | - Seon Yong Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul 02841, Korea; (C.G.P.); (S.-H.C.); (S.Y.L.); (K.E.); (M.G.P.); (J.J.); (H.J.J.); (S.J.K.); (S.J.); (K.L.)
| | - Kiyoung Eun
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul 02841, Korea; (C.G.P.); (S.-H.C.); (S.Y.L.); (K.E.); (M.G.P.); (J.J.); (H.J.J.); (S.J.K.); (S.J.); (K.L.)
- Institute of Animal Molecular Biotechnology, Korea University, Seoul 02841, Korea
| | - Min Gi Park
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul 02841, Korea; (C.G.P.); (S.-H.C.); (S.Y.L.); (K.E.); (M.G.P.); (J.J.); (H.J.J.); (S.J.K.); (S.J.); (K.L.)
| | - Junseok Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul 02841, Korea; (C.G.P.); (S.-H.C.); (S.Y.L.); (K.E.); (M.G.P.); (J.J.); (H.J.J.); (S.J.K.); (S.J.); (K.L.)
| | - Hyeon Ju Jeong
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul 02841, Korea; (C.G.P.); (S.-H.C.); (S.Y.L.); (K.E.); (M.G.P.); (J.J.); (H.J.J.); (S.J.K.); (S.J.); (K.L.)
| | - Seong Jin Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul 02841, Korea; (C.G.P.); (S.-H.C.); (S.Y.L.); (K.E.); (M.G.P.); (J.J.); (H.J.J.); (S.J.K.); (S.J.); (K.L.)
| | - Sohee Jeong
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul 02841, Korea; (C.G.P.); (S.-H.C.); (S.Y.L.); (K.E.); (M.G.P.); (J.J.); (H.J.J.); (S.J.K.); (S.J.); (K.L.)
| | - Kanghun Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul 02841, Korea; (C.G.P.); (S.-H.C.); (S.Y.L.); (K.E.); (M.G.P.); (J.J.); (H.J.J.); (S.J.K.); (S.J.); (K.L.)
| | - Hyunggee Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul 02841, Korea; (C.G.P.); (S.-H.C.); (S.Y.L.); (K.E.); (M.G.P.); (J.J.); (H.J.J.); (S.J.K.); (S.J.); (K.L.)
- Institute of Animal Molecular Biotechnology, Korea University, Seoul 02841, Korea
- Correspondence: ; Tel.: +82-2-3290-3059; Fax: +82-2-3290-3040
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Homodimeric and Heterodimeric Interactions among Vertebrate Basic Helix-Loop-Helix Transcription Factors. Int J Mol Sci 2021; 22:ijms222312855. [PMID: 34884664 PMCID: PMC8657788 DOI: 10.3390/ijms222312855] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/11/2021] [Accepted: 11/17/2021] [Indexed: 01/01/2023] Open
Abstract
The basic helix–loop–helix transcription factor (bHLH TF) family is involved in tissue development, cell differentiation, and disease. These factors have transcriptionally positive, negative, and inactive functions by combining dimeric interactions among family members. The best known bHLH TFs are the E-protein homodimers and heterodimers with the tissue-specific TFs or ID proteins. These cooperative and dynamic interactions result in a complex transcriptional network that helps define the cell’s fate. Here, the reported dimeric interactions of 67 vertebrate bHLH TFs with other family members are summarized in tables, including specifications of the experimental techniques that defined the dimers. The compilation of these extensive data underscores homodimers of tissue-specific bHLH TFs as a central part of the bHLH regulatory network, with relevant positive and negative transcriptional regulatory roles. Furthermore, some sequence-specific TFs can also form transcriptionally inactive heterodimers with each other. The function, classification, and developmental role for all vertebrate bHLH TFs in four major classes are detailed.
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Milton-Harris L, Jeeves M, Walker SA, Ward SE, Mancini EJ. Small molecule inhibits T-cell acute lymphoblastic leukaemia oncogenic interaction through conformational modulation of LMO2. Oncotarget 2020; 11:1737-1748. [PMID: 32477463 PMCID: PMC7233811 DOI: 10.18632/oncotarget.27580] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/03/2020] [Indexed: 01/05/2023] Open
Abstract
Ectopic expression in T-cell precursors of LIM only protein 2 (LMO2), a key factor in hematopoietic development, has been linked to the onset of T-cell acute lymphoblastic leukaemia (T-ALL). In the T-ALL context, LMO2 drives oncogenic progression through binding to erythroid-specific transcription factor SCL/TAL1 and sequestration of E-protein transcription factors, normally required for T-cell differentiation. A key requirement for the formation of this oncogenic protein-protein interaction (PPI) is the conformational flexibility of LMO2. Here we identify a small molecule inhibitor of the SCL-LMO2 PPI, which hinders the interaction in vitro through direct binding to LMO2. Biophysical analysis demonstrates that this inhibitor acts through a mechanism of conformational modulation of LMO2. Importantly, this work has led to the identification of a small molecule inhibitor of the SCL-LMO2 PPI, which can provide a starting point for the development of new agents for the treatment of T-ALL. These results suggest that similar approaches, based on the modulation of protein conformation by small molecules, might be used for therapeutic targeting of other oncogenic PPIs.
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Affiliation(s)
- Leanne Milton-Harris
- School of Life Sciences, Biochemistry Department, University of Sussex, Falmer, Brighton, BN1 9QG, United Kingdom
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Sarah A Walker
- Sussex Drug Discovery Centre, University of Sussex, Brighton, BN1 9QJ, United Kingdom
| | - Simon E Ward
- Medicines Discovery Institute, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Erika J Mancini
- School of Life Sciences, Biochemistry Department, University of Sussex, Falmer, Brighton, BN1 9QG, United Kingdom
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Wu CC, Hsu TY, Chang JC, Ou CY, Kuo HC, Liu CA, Wang CL, Chuang H, Chen CP, Yang KD. Paternal Tobacco Smoke Correlated to Offspring Asthma and Prenatal Epigenetic Programming. Front Genet 2019; 10:471. [PMID: 31214241 PMCID: PMC6554446 DOI: 10.3389/fgene.2019.00471] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/01/2019] [Indexed: 12/15/2022] Open
Abstract
Rationale: Little is known about effects of paternal tobacco smoke (PTS) on the offspring's asthma and its prenatal epigenetic programming. Objective: To investigate whether PTS exposure was associated with the offspring's asthma and correlated to epigenetic CG methylation of potential tobacco-related immune genes: LMO2, GSTM1 or/and IL-10 genes. Measurements and Main Results: In a birth cohort of 1,629 newborns, we measured exposure rates of PTS (23%) and maternal tobacco smoke (MTS, 0.2%), cord blood DNA methylation, infant respiratory tract infection, childhood DNA methylation, and childhood allergic diseases. Infants with prenatal PTS exposure had a significantly higher risk of asthma by the age of 6 than those without (p = 0.026). The PTS exposure doses at 0, <20, and ≧20 cigarettes per day were significantly associated with the trend of childhood asthma and the increase of LMO2-E148 (p = 0.006), and IL10_P325 (p = 0.008) CG methylation. The combination of higher CG methylation levels of LMO2_E148, IL10_P325, and GSTM1_P266 corresponded to the highest risk of asthma by 43.48%, compared to other combinations (16.67-23.08%) in the 3-way multi-factor dimensionality reduction (MDR) analysis. The LMO2_P794 and GSTM1_P266 CG methylation levels at age 0 were significantly correlated to those at age of 6. Conclusions: Prenatal PTS exposure increases CG methylation contents of immune genes, such as LMO2 and IL-10, which significantly retained from newborn stage to 6 years of age and correlated to development of childhood asthma. Modulation of the LMO2 and IL-10 CG methylation and/or their gene expression may provide a regimen for early prevention of PTS-associated childhood asthma. Descriptor number: 1.10 Asthma Mediators. Scientific Knowledge on the Subject: It has been better known that maternal tobacco smoke (MTS) has an impact on the offspring's asthma via epigenetic modification. Little is known about effects of paternal tobacco smoke (PTS) on the offspring's asthma and its prenatal epigenetic programming. What This Study Adds to the Field: Prenatal tobacco smoke (PTS) can program epigenetic modifications in certain genes, such as LMO2 and IL-10, and that these modifications are correlated to childhood asthma development. The higher the PTS exposure dose the higher the CG methylation levels are found. The combination of higher CG methylation levels of LMO2_E148, IL10_P325 and GSTM1_P266 corresponded to the highest risk of asthma. Measuring the DNA methylation levels of certain genes might help to predict high-risk populations for childhood asthma and provide a potential target to prevent the development of childhood asthma.
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Affiliation(s)
- Chih-Chiang Wu
- Department of Pediatrics, Po-Zen Hospital, Kaohsiung, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Te-Yao Hsu
- Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Jen-Chieh Chang
- Genomic and Proteomic Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chia-Yu Ou
- Department of Obstetrics, Po-Zen Hospital, Kaohsiung, Taiwan
| | - Ho-Chang Kuo
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chieh-An Liu
- Department of Pediatrics, Po-Zen Hospital, Kaohsiung, Taiwan
| | - Chih-Lu Wang
- Department of Pediatrics, Po-Zen Hospital, Kaohsiung, Taiwan
| | - Hau Chuang
- Genomic and Proteomic Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chie-Pein Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Kuender D Yang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan.,Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan.,Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
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6
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Smith NC, Matthews JM. Mechanisms of DNA-binding specificity and functional gene regulation by transcription factors. Curr Opin Struct Biol 2016; 38:68-74. [PMID: 27295424 DOI: 10.1016/j.sbi.2016.05.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/14/2016] [Accepted: 05/17/2016] [Indexed: 10/21/2022]
Abstract
Eukaryotic transcription factors up-regulate and down-regulate the expression of genes in a very controlled manner. The DNA-binding domains of these proteins have quite well established mechanisms for binding to DNA, but a surprisingly poor intrinsic ability to discriminate target and variant non-target DNA sequences. Here, we summarise established mechanisms of protein-DNA recognition, as specified by both macromolecules. We also review recent advances in the fields of genome binding, molecular dynamics and biomolecular interaction studies that bring us close to a full understanding of how eukaryotic transcription factors find and target DNA in vivo to form functional centres of gene regulation through networks of protein-protein and protein-DNA interactions.
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Affiliation(s)
- Ngaio C Smith
- School of Life and Environmental Science, The University of Sydney, NSW 2006, Australia
| | - Jacqueline M Matthews
- School of Life and Environmental Science, The University of Sydney, NSW 2006, Australia.
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Banno K, Omori S, Hirata K, Nawa N, Nakagawa N, Nishimura K, Ohtaka M, Nakanishi M, Sakuma T, Yamamoto T, Toki T, Ito E, Yamamoto T, Kokubu C, Takeda J, Taniguchi H, Arahori H, Wada K, Kitabatake Y, Ozono K. Systematic Cellular Disease Models Reveal Synergistic Interaction of Trisomy 21 and GATA1 Mutations in Hematopoietic Abnormalities. Cell Rep 2016; 15:1228-41. [PMID: 27134169 DOI: 10.1016/j.celrep.2016.04.031] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 12/22/2015] [Accepted: 04/04/2016] [Indexed: 11/25/2022] Open
Abstract
Chromosomal aneuploidy and specific gene mutations are recognized early hallmarks of many oncogenic processes. However, the net effect of these abnormalities has generally not been explored. We focused on transient myeloproliferative disorder (TMD) in Down syndrome, which is characteristically associated with somatic mutations in GATA1. To better understand functional interplay between trisomy 21 and GATA1 mutations in hematopoiesis, we constructed cellular disease models using human induced pluripotent stem cells (iPSCs) and genome-editing technologies. Comparative analysis of these engineered iPSCs demonstrated that trisomy 21 perturbed hematopoietic development through the enhanced production of early hematopoietic progenitors and the upregulation of mutated GATA1, resulting in the accelerated production of aberrantly differentiated cells. These effects were mediated by dosage alterations of RUNX1, ETS2, and ERG, which are located in a critical 4-Mb region of chromosome 21. Our study provides insight into the genetic synergy that contributes to multi-step leukemogenesis.
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Affiliation(s)
- Kimihiko Banno
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Sayaka Omori
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Katsuya Hirata
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Nobutoshi Nawa
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Natsuki Nakagawa
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ken Nishimura
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Manami Ohtaka
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8562, Japan
| | - Mahito Nakanishi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8562, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Tsutomu Toki
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori 036-8562, Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori 036-8562, Japan
| | - Toshiyuki Yamamoto
- Institute for Integrated Medical Sciences, Tokyo Women's Medical University, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Chikara Kokubu
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Junji Takeda
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hidetoshi Taniguchi
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hitomi Arahori
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuko Wada
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasuji Kitabatake
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan.
| | - Keiichi Ozono
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
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8
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Editing the genome to introduce a beneficial naturally occurring mutation associated with increased fetal globin. Nat Commun 2015; 6:7085. [PMID: 25971621 DOI: 10.1038/ncomms8085] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 03/31/2015] [Indexed: 12/15/2022] Open
Abstract
Genetic disorders resulting from defects in the adult globin genes are among the most common inherited diseases. Symptoms worsen from birth as fetal γ-globin expression is silenced. Genome editing could permit the introduction of beneficial single-nucleotide variants to ameliorate symptoms. Here, as proof of concept, we introduce the naturally occurring Hereditary Persistance of Fetal Haemoglobin (HPFH) -175T>C point mutation associated with elevated fetal γ-globin into erythroid cell lines. We show that this mutation increases fetal globin expression through de novo recruitment of the activator TAL1 to promote chromatin looping of distal enhancers to the modified γ-globin promoter.
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Kim SH, Kim EJ, Hitomi M, Oh SY, Jin X, Jeon HM, Beck S, Jin X, Kim JK, Park CG, Chang SY, Yin J, Kim T, Jeon YJ, Song J, Lim YC, Lathia JD, Nakano I, Kim H. The LIM-only transcription factor LMO2 determines tumorigenic and angiogenic traits in glioma stem cells. Cell Death Differ 2015; 22:1517-25. [PMID: 25721045 DOI: 10.1038/cdd.2015.7] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 12/30/2014] [Accepted: 01/14/2015] [Indexed: 01/23/2023] Open
Abstract
Glioblastomas (GBMs) maintain their cellular heterogeneity with glioma stem cells (GSCs) producing a variety of tumor cell types. Here we interrogated the oncogenic roles of Lim domain only 2 (LMO2) in GBM and GSCs in mice and human. High expression of LMO2 was found in human patient-derived GSCs compared with the differentiated progeny cells. LMO2 is required for GSC proliferation both in vitro and in vivo, as shRNA-mediated LMO2 silencing attenuated tumor growth derived from human GSCs. Further, LMO2 is sufficient to induce stem cell characteristics (stemness) in mouse premalignant astrocytes, as forced LMO2 expression facilitated in vitro and in vivo growth of astrocytes derived from Ink4a/Arf null mice and acquisition of GSC phenotypes. A subset of mouse and human GSCs converted into vascular endothelial-like tumor cells both in vitro and in vivo, which phenotype was attenuated by LMO2 silencing and promoted by LMO2 overexpression. Mechanistically, the action of LMO2 for induction of glioma stemness is mediated by transcriptional regulation of Jagged1 resulting in activation of the Notch pathway, whereas LMO2 directly occupies the promoter regions of the VE-cadherin gene for a gain of endothelial cellular phenotype. Subsequently, selective ablation of human GSC-derived VE-cadherin-expressing cells attenuated vascular formation in mouse intracranial tumors, thereby significantly prolonging mouse survival. Clinically, LMO2 expression was elevated in GBM tissues and inversely correlated with prognosis of GBM patients. Taken together, our findings describe novel dual roles of LMO2 to induce tumorigenesis and angiogenesis, and provide potential therapeutic targets in GBMs.
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Affiliation(s)
- S-H Kim
- 1] School of Life Sciences and Biotechnology and Institute of Life Science and Natural Resources, Korea University, Seoul 136-713, Republic of Korea [2] Department of Neurological Surgery, The Ohio State University, Columbus, OH 43210, USA
| | - E-J Kim
- School of Life Sciences and Biotechnology and Institute of Life Science and Natural Resources, Korea University, Seoul 136-713, Republic of Korea
| | - M Hitomi
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - S-Y Oh
- School of Life Sciences and Biotechnology and Institute of Life Science and Natural Resources, Korea University, Seoul 136-713, Republic of Korea
| | - X Jin
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - H-M Jeon
- School of Life Sciences and Biotechnology and Institute of Life Science and Natural Resources, Korea University, Seoul 136-713, Republic of Korea
| | - S Beck
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - X Jin
- School of Life Sciences and Biotechnology and Institute of Life Science and Natural Resources, Korea University, Seoul 136-713, Republic of Korea
| | - J-K Kim
- School of Life Sciences and Biotechnology and Institute of Life Science and Natural Resources, Korea University, Seoul 136-713, Republic of Korea
| | - C G Park
- School of Life Sciences and Biotechnology and Institute of Life Science and Natural Resources, Korea University, Seoul 136-713, Republic of Korea
| | - S-Y Chang
- School of Life Sciences and Biotechnology and Institute of Life Science and Natural Resources, Korea University, Seoul 136-713, Republic of Korea
| | - J Yin
- Specific Organs Cancer Branch, Research Institute and Hospital, National Cancer Center, Goyang 410-769, Republic of Korea
| | - T Kim
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Y-J Jeon
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - J Song
- Department of Neurological Surgery, The Ohio State University, Columbus, OH 43210, USA
| | - Y C Lim
- Department of Otorhinolaryngology-Head and Neck Surgery, Research Institute of Medical Science, Konkuk University School of Medicine, Seoul 143-752, Republic of Korea
| | - J D Lathia
- 1] Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA [2] Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Cleveland, OH 44195, USA [3] Case Comprehensive Cancer Center, Cleveland, OH 44195, USA
| | - I Nakano
- 1] Department of Neurological Surgery, The Ohio State University, Columbus, OH 43210, USA [2] James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - H Kim
- School of Life Sciences and Biotechnology and Institute of Life Science and Natural Resources, Korea University, Seoul 136-713, Republic of Korea
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10
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Yun WJ, Kim YW, Kang Y, Lee J, Dean A, Kim A. The hematopoietic regulator TAL1 is required for chromatin looping between the β-globin LCR and human γ-globin genes to activate transcription. Nucleic Acids Res 2014; 42:4283-93. [PMID: 24470145 PMCID: PMC3985645 DOI: 10.1093/nar/gku072] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
TAL1 is a key hematopoietic transcription factor that binds to regulatory regions of a large cohort of erythroid genes as part of a complex with GATA-1, LMO2 and Ldb1. The complex mediates long-range interaction between the β-globin locus control region (LCR) and active globin genes, and although TAL1 is one of the two DNA-binding complex members, its role is unclear. To explore the role of TAL1 in transcription activation of the human γ-globin genes, we reduced the expression of TAL1 in erythroid K562 cells using lentiviral short hairpin RNA, compromising its association in the β-globin locus. In the TAL1 knockdown cells, the γ-globin transcription was reduced to 35% and chromatin looping of the Gγ-globin gene with the LCR was disrupted with decreased occupancy of the complex member Ldb1 and LMO2 in the locus. However, GATA-1 binding, DNase I hypersensitive site formation and several histone modifications were largely maintained across the β-globin locus. In addition, overexpression of TAL1 increased the γ-globin transcription and increased interaction frequency between the Gγ-globin gene and LCR. These results indicate that TAL1 plays a critical role in chromatin loop formation between the γ-globin genes and LCR, which is a critical step for the transcription of the γ-globin genes.
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Affiliation(s)
- Won Ju Yun
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Pusan 609-735, Korea and Laboratory of Cellular and Developmental Biology, NIDDK, NIH, Bethesda, MD 20892, USA
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11
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Love PE, Warzecha C, Li L. Ldb1 complexes: the new master regulators of erythroid gene transcription. Trends Genet 2013; 30:1-9. [PMID: 24290192 DOI: 10.1016/j.tig.2013.10.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/17/2013] [Accepted: 10/18/2013] [Indexed: 10/26/2022]
Abstract
Elucidation of the genetic pathways that control red blood cell development has been a central goal of erythropoiesis research over the past decade. Notably, data from several recent studies have provided new insights into the regulation of erythroid gene transcription. Transcription profiling demonstrates that erythropoiesis is mainly controlled by a small group of lineage-restricted transcription factors [Gata binding protein 1 (Gata1), T cell acute lymphocytic leukemia 1 protein (Tal1), and Erythroid Kruppel-like factor (EKLF; henceforth referred to as Klf1)]. Binding-site mapping using ChIP-Seq indicates that most DNA-bound Gata1 and Tal1 proteins are contained within higher order complexes (Ldb1 complexes) that include the nuclear adapters Ldb1 and Lmo2. Ldb1 complexes regulate Klf1, and Ldb1 complex-binding sites frequently colocalize with Klf1 at erythroid genes and cis-regulatory elements, indicating strong functional synergy between Gata1, Tal1, and Klf1. Together with new data demonstrating that Ldb1 can mediate long-range promoter-enhancer interactions, these findings provide a foundation for the first comprehensive models of the global regulation of erythroid gene transcription.
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Affiliation(s)
- Paul E Love
- Eunice Kennedy Shriver, National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Claude Warzecha
- Eunice Kennedy Shriver, National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - LiQi Li
- Eunice Kennedy Shriver, National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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12
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El Omari K, Hoosdally SJ, Tuladhar K, Karia D, Hall-Ponselé E, Platonova O, Vyas P, Patient R, Porcher C, Mancini EJ. Structural basis for LMO2-driven recruitment of the SCL:E47bHLH heterodimer to hematopoietic-specific transcriptional targets. Cell Rep 2013; 4:135-47. [PMID: 23831025 PMCID: PMC3714592 DOI: 10.1016/j.celrep.2013.06.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/23/2013] [Accepted: 06/06/2013] [Indexed: 01/25/2023] Open
Abstract
Cell fate is governed by combinatorial actions of transcriptional regulators assembling into multiprotein complexes. However, the molecular details of how these complexes form are poorly understood. One such complex, which contains the basic-helix-loop-helix heterodimer SCL:E47 and bridging proteins LMO2:LDB1, critically regulates hematopoiesis and induces T cell leukemia. Here, we report the crystal structure of (SCL:E47)bHLH:LMO2:LDB1LID bound to DNA, providing a molecular account of the network of interactions assembling this complex. This reveals an unexpected role for LMO2. Upon binding to SCL, LMO2 induces new hydrogen bonds in SCL:E47, thereby strengthening heterodimer formation. This imposes a rotation movement onto E47 that weakens the heterodimer:DNA interaction, shifting the main DNA-binding activity onto additional protein partners. Along with biochemical analyses, this illustrates, at an atomic level, how hematopoietic-specific SCL sequesters ubiquitous E47 and associated cofactors and supports SCL's reported DNA-binding-independent functions. Importantly, this work will drive the design of small molecules inhibiting leukemogenic processes.
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Affiliation(s)
- Kamel El Omari
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
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13
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Abstract
LIM-domain proteins are a large family of proteins that are emerging as key molecules in a wide variety of human cancers. In particular, all members of the human LIM-domain-only (LMO) proteins, LMO1-4, which are required for many developmental processes, are implicated in the onset or the progression of several cancers, including T cell leukaemia, breast cancer and neuroblastoma. These small proteins contain two protein-interacting LIM domains but little additional sequence, and they seem to function by nucleating the formation of new transcriptional complexes and/or by disrupting existing transcriptional complexes to modulate gene expression programmes. Through these activities, the LMO proteins have important cellular roles in processes that are relevant to cancer such as self-renewal, cell cycle regulation and metastasis. These functions highlight the therapeutic potential of targeting these proteins in cancer.
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Affiliation(s)
- Jacqueline M Matthews
- School of Molecular Bioscience, The University of Sydney, New South Wales 2006, Australia. jacqui.matthews@ sydney.edu.au
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14
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Transcriptional activation of prostate specific homeobox gene NKX3-1 in subsets of T-cell lymphoblastic leukemia (T-ALL). PLoS One 2012; 7:e40747. [PMID: 22848398 PMCID: PMC3407137 DOI: 10.1371/journal.pone.0040747] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 06/12/2012] [Indexed: 01/26/2023] Open
Abstract
Homeobox genes encode transcription factors impacting key developmental processes including embryogenesis, organogenesis, and cell differentiation. Reflecting their tight transcriptional control, homeobox genes are often embedded in large non-coding, cis-regulatory regions, containing tissue specific elements. In T-cell acute lymphoblastic leukemia (T-ALL) homeobox genes are frequently deregulated by chromosomal aberrations, notably translocations adding T-cell specific activatory elements. NKX3-1 is a prostate specific homeobox gene activated in T-ALL patients expressing oncogenic TAL1 or displaying immature T-cell characteristics. After investigating regulation of NKX3-1 in primary cells and cell lines, we report its ectopic expression in T-ALL cells independent of chromosomal rearrangements. Using siRNAs and expression profiling, we exploited NKX3-1 positive T-ALL cell lines as tools to investigate aberrant activatory mechanisms. Our data confirmed NKX3-1 activation by TAL1/GATA3/LMO and identified LYL1 as an alternative activator in immature T-ALL cells devoid of GATA3. Moreover, we showed that NKX3-1 is directly activated by early T-cell homeodomain factor MSX2. These activators were regulated by MLL and/or by IL7-, BMP4- and IGF2-signalling. Finally, we demonstrated homeobox gene SIX6 as a direct leukemic target of NKX3-1 in T-ALL. In conclusion, we identified three major mechanisms of NKX3-1 regulation in T-ALL cell lines which are represented by activators TAL1, LYL1 and MSX2, corresponding to particular T-ALL subtypes described in patients. These results may contribute to the understanding of leukemic transcriptional networks underlying disturbed T-cell differentiation in T-ALL.
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15
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The detection and quantitation of protein oligomerization. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 747:19-41. [PMID: 22949109 DOI: 10.1007/978-1-4614-3229-6_2] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There are many different techniques available to biologists and biochemists that can be used to detect and characterize the self-association of proteins. Each technique has strengths and weaknesses and it is often useful to combine several approaches to maximize the former and minimize the latter. Here we review a range of methodologies that identify protein self-association and/or allow the stoichiometry and affinity of the interaction to be determined, placing an emphasis on what type of information can be obtained and outlining the advantages and disadvantages involved. In general, in vitro biophysical techniques, such as size exclusion chromatography, analytical ultracentrifugation, scattering techniques, NMR spectroscopy, isothermal titration calorimetry, fluorescence anisotropy and mass spectrometry, provide information on stoichiometry and/or binding affinities. Other approaches such as cross-linking, fluorescence methods (e.g., fluorescence correlation spectroscopy, FCS; Förster resonance energy transfer, FRET; fluorescence recovery after photobleaching, FRAP; and proximity imaging, PRIM) and complementation approaches (e.g., yeast two hybrid assays and bimolecular fluorescence complementation, BiFC) can be used to detect protein self-association in a cellular context.
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16
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Structural basis of simultaneous recruitment of the transcriptional regulators LMO2 and FOG1/ZFPM1 by the transcription factor GATA1. Proc Natl Acad Sci U S A 2011; 108:14443-8. [PMID: 21844373 DOI: 10.1073/pnas.1105898108] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The control of red blood cell and megakaryocyte development by the regulatory protein GATA1 is a paradigm for transcriptional regulation of gene expression in cell lineage differentiation and maturation. Most GATA1-regulated events require GATA1 to bind FOG1, and essentially all GATA1-activated genes are cooccupied by a TAL1/E2A/LMO2/LDB1 complex; however, it is not known whether FOG1 and TAL1/E2A/LMO2/LDB1 are simultaneously recruited by GATA1. Our structural data reveal that the FOG1-binding domain of GATA1, the N finger, can also directly contact LMO2 and show that, despite the small size (< 50 residues) of the GATA1 N finger, both FOG1 and LMO2 can simultaneously bind this domain. LMO2 in turn can simultaneously contact both GATA1 and the DNA-binding protein TAL1/E2A at bipartite E-box/WGATAR sites. Taken together, our data provide the first structural snapshot of multiprotein complex formation at GATA1-dependent genes and support a model in which FOG1 and TAL1/E2A/LMO2/LDB1 can cooccupy E-box/WGATAR sites to facilitate GATA1-mediated activation of gene activation.
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17
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Tanaka T, Sewell H, Waters S, Phillips SEV, Rabbitts TH. Single domain intracellular antibodies from diverse libraries: emphasizing dual functions of LMO2 protein interactions using a single VH domain. J Biol Chem 2011; 286:3707-16. [PMID: 20980262 PMCID: PMC3030373 DOI: 10.1074/jbc.m110.188193] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Indexed: 11/06/2022] Open
Abstract
Interfering intracellular antibodies are valuable for biological studies as drug surrogates and as potential macromolecular drugs per se. Their application is still limited because of the difficulty of acquisition of functional intracellular antibodies. We describe the use of the new intracellular antibody capture procedure (IAC(3)) to facilitate direct isolation of functional single domain antibody fragments using four independent target molecules (LMO2, TP53, CRAF1, and Hoxa9) from a set of diverse libraries. Initially, these have variability in only one of the three antigen-binding CDR regions of VH or VL and first round single domains are affinity matured by iterative randomization of the two other CDRs and reselection. We highlight the approach using a single domain binding to LMO2 protein. Our results show that interfering with LMO2 protein function demonstrates a role specifically in erythroid differentiation, confirm a necessary and sufficient function for LMO2 as a cancer therapy target in T-cell neoplasia and allowed for the first time production of soluble recombinant LMO2 protein by co-expression with intracellular domain antibodies. Co-crystallization of LMO2 and the anti-LMO2 VH protein was successful. These results demonstrate that this third generation IAC(3) offers a robust toolbox for various biomedical applications and consolidates functional features of the LMO2 protein complex, which includes the importance of Lmo2-Ldb1 protein interaction.
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Affiliation(s)
- Tomoyuki Tanaka
- From the Leeds Institute of Molecular Medicine, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, United Kingdom and
| | - Helen Sewell
- From the Leeds Institute of Molecular Medicine, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, United Kingdom and
| | - Simon Waters
- From the Leeds Institute of Molecular Medicine, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, United Kingdom and
| | - Simon E. V. Phillips
- Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0FA, United Kingdom
| | - Terence H. Rabbitts
- From the Leeds Institute of Molecular Medicine, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, United Kingdom and
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Abstract
The most common translocation in childhood T-cell acute lymphoblastic leukemia (T-ALL) involves the LMO2 locus, resulting in ectopic expression of the LMO2 gene in human thymocytes. The LMO2 gene was also activated in patients with X-linked Severe Combined Immune Deficiency treated with gene therapy because of retroviral insertion in the LMO2 locus. The LMO2 insertions predisposed these children to T-ALL, yet how LMO2 contributes to T cell transformation remains unclear. The LIM (Lin 11, Isl-1, Mec-3) domain containing LMO2 protein regulates erythropoiesis as part of a large transcriptional complex consisting of LMO2, TAL1, E47, GATA1 and LDB1 that recognizes bipartite E-box-GATA1 sites on target genes. Similarly, a TAL1/E47/LMO2/LDB1 complex is observed in human T-ALL and Tal1 and Lmo2 expression in mice results in disease acceleration. To address the mechanism(s) of Tal1/Lmo2 synergy in leukemia, we generated Lmo2 transgenic mice and mated them with mice that express wild-type Tal1 or a DNA-binding mutant of TAL1. Tal1/Lmo2 and MutTAL1/Lmo2 bitransgenic mice exhibit perturbations in thymocyte development due to reduced E47/HEB transcriptional activity and develop leukemia with identical kinetics. These data demonstrate that the DNA-binding activity of Tal1 is not required to cooperate with Lmo2 to cause leukemia in mice and suggest that Lmo2 may cooperate with Tal1 to interfere with E47/HEB function(s).
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19
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Appert A, Nam CH, Lobato N, Priego E, Miguel RN, Blundell T, Drynan L, Sewell H, Tanaka T, Rabbitts T. Targeting LMO2 with a peptide aptamer establishes a necessary function in overt T-cell neoplasia. Cancer Res 2009; 69:4784-90. [PMID: 19487290 DOI: 10.1158/0008-5472.can-08-4774] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
LMO2 is a transcription regulator involved in human T-cell leukemia, including some occurring in X-SCID gene therapy trials, and in B-cell lymphomas and prostate cancer. LMO2 functions in transcription complexes via protein-protein interactions involving two LIM domains and causes a preleukemic T-cell development blockade followed by clonal tumors. Therefore, LMO2 is necessary but not sufficient for overt neoplasias, which must undergo additional mutations before frank malignancy. An open question is the importance of LMO2 in tumor development as opposed to sustaining cancer. We have addressed this using a peptide aptamer that binds to the second LIM domain of the LMO2 protein and disrupts its function. This specificity is mediated by a conserved Cys-Cys motif, which is similar to the zinc-binding LIM domains. The peptide inhibits Lmo2 function in a mouse T-cell tumor transplantation assay by preventing Lmo2-dependent T-cell neoplasia. Lmo2 is, therefore, required for sustained T-cell tumor growth, in addition to its preleukemic effect. Interference with LMO2 complexes is a strategy for controlling LMO2-mediated cancers, and the finger structure of LMO2 is an explicit focus for drug development.
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Affiliation(s)
- Alex Appert
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
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20
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Martinez Barrio A, Eriksson O, Badhai J, Fröjmark AS, Bongcam-Rudloff E, Dahl N, Schuster J. Targeted resequencing and analysis of the Diamond-Blackfan anemia disease locus RPS19. PLoS One 2009; 4:e6172. [PMID: 19587786 PMCID: PMC2703794 DOI: 10.1371/journal.pone.0006172] [Citation(s) in RCA: 10] [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: 03/16/2009] [Accepted: 05/27/2009] [Indexed: 11/19/2022] Open
Abstract
Background The Ribosomal protein S19 gene locus (RPS19) has been linked to two kinds of red cell aplasia, Diamond-Blackfan Anemia (DBA) and Transient Erythroblastopenia in Childhood (TEC). Mutations in RPS19 coding sequences have been found in 25% of DBA patients, but not in TEC patients. It has been suggested that non-coding RPS19 sequence variants contribute to the considerable clinical variability in red cell aplasia. We therefore aimed at identifying non-coding variations associated with DBA or TEC phenotypes. Methodology/Principal Findings We targeted a region of 19'980 bp encompassing the RPS19 gene in a cohort of 89 DBA and TEC patients for resequencing. We provide here a catalog of the considerable, previously unrecognized degree of variation in this region. We identified 73 variations (65 SNPs, 8 indels) that all are located outside of the RPS19 open reading frame, and of which 67.1% are classified as novel. We hypothesize that specific alleles in non-coding regions of RPS19 could alter the binding of regulatory proteins or transcription factors. Therefore, we carried out an extensive analysis to identify transcription factor binding sites (TFBS). A series of putative interaction sites coincide with detected variants. Sixteen of the corresponding transcription factors are of particular interest, as they are housekeeping genes or show a direct link to hematopoiesis, tumorigenesis or leukemia (e.g. GATA-1/2, PU.1, MZF-1). Conclusions Specific alleles at predicted TFBSs may alter the expression of RPS19, modify an important interaction between transcription factors with overlapping TFBS or remove an important stimulus for hematopoiesis. We suggest that the detected interactions are of importance for hematopoiesis and could provide new insights into individual response to treatment.
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Affiliation(s)
- Alvaro Martinez Barrio
- The Linnaeus Centre for Bioinformatics Uppsala University/Swedish University of Agricultural Sciences, Uppsala University, Uppsala, Sweden
| | - Oskar Eriksson
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Jitendra Badhai
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Anne-Sophie Fröjmark
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Erik Bongcam-Rudloff
- The Linnaeus Centre for Bioinformatics Uppsala University/Swedish University of Agricultural Sciences, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Uppsala University, Uppsala, Sweden
| | - Niklas Dahl
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Jens Schuster
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail:
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Abstract
LMO (LIM-only) and LIM-HD (LIM-homeodomain) proteins form a family of proteins that is required for myriad developmental processes and which can contribute to diseases such as T-cell leukaemia and breast cancer. The four LMO and 12 LIM-HD proteins in mammals are expressed in a combinatorial manner in many cell types, forming a transcriptional ‘LIM code’. The proteins all contain a pair of closely spaced LIM domains near their N-termini that mediate protein–protein interactions, including binding to the ∼30-residue LID (LIM interaction domain) of the essential co-factor protein Ldb1 (LIM domain-binding protein 1). In an attempt to understand the molecular mechanisms behind the LIM code, we have determined the molecular basis of binding of LMO and LIM-HD proteins for Ldb1LID through a series of structural, mutagenic and biophysical studies. These studies provide an explanation for why Ldb1 binds the LIM domains of the LMO/LIM-HD family, but not LIM domains from other proteins. The LMO/LIM-HD family exhibit a range of affinities for Ldb1, which influences the formation of specific functional complexes within cells. We have also identified an additional LIM interaction domain in one of the LIM-HD proteins, Isl1. Despite low sequence similarity to Ldb1LID, this domain binds another LIM-HD protein, Lhx3, in an identical manner to Ldb1LID. Through our and other studies, it is emerging that the multiple layers of competitive binding involving LMO and LIM-HD proteins and their partner proteins contribute significantly to cell fate specification and development.
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Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes. EMBO J 2008; 27:2018-29. [PMID: 18583962 DOI: 10.1038/emboj.2008.123] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2008] [Accepted: 06/02/2008] [Indexed: 01/15/2023] Open
Abstract
LIM-homeodomain (LIM-HD) transcription factors form a combinatorial 'LIM code' that contributes to the specification of cell types. In the ventral spinal cord, the binary LIM homeobox protein 3 (Lhx3)/LIM domain-binding protein 1 (Ldb1) complex specifies the formation of V2 interneurons. The additional expression of islet-1 (Isl1) in adjacent cells instead specifies the formation of motor neurons through assembly of a ternary complex in which Isl1 contacts both Lhx3 and Ldb1, displacing Lhx3 as the binding partner of Ldb1. However, little is known about how this molecular switch occurs. Here, we have identified the 30-residue Lhx3-binding domain on Isl1 (Isl1(LBD)). Although the LIM interaction domain of Ldb1 (Ldb1(LID)) and Isl1(LBD) share low levels of sequence homology, X-ray and NMR structures reveal that they bind Lhx3 in an identical manner, that is, Isl1(LBD) mimics Ldb1(LID). These data provide a structural basis for the formation of cell type-specific protein-protein interactions in which unstructured linear motifs with diverse sequences compete to bind protein partners. The resulting alternate protein complexes can target different genes to regulate key biological events.
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