1
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Park SJ, Nakai K. A computational approach for deciphering the interactions between proximal and distal gene regulators in GC B-cell response. NAR Genom Bioinform 2024; 6:lqae050. [PMID: 38711859 PMCID: PMC11071120 DOI: 10.1093/nargab/lqae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 04/15/2024] [Accepted: 04/27/2024] [Indexed: 05/08/2024] Open
Abstract
Delineating the intricate interplay between promoter-proximal and -distal regulators is crucial for understanding the function of transcriptional mediator complexes implicated in the regulation of gene expression. The present study aimed to develop a computational method for accurately modeling the spatial proximal and distal regulatory interactions. Our method combined regression-based models to identify key regulators through gene expression prediction and a graph-embedding approach to detect coregulated genes. This approach enabled a detailed investigation of the gene regulatory mechanisms for germinal center B cells, accompanied by dramatic rearrangements of the genome structure. We found that while the promoter-proximal regulatory elements were the principal regulators of gene expression, the distal regulators fine-tuned transcription. Moreover, our approach unveiled the presence of modular regulators, such as cofactors and proximal/distal transcription factors, which were co-expressed with their target genes. Some of these modules exhibited abnormal expression patterns in lymphoma. These findings suggest that the dysregulation of interactions between transcriptional and architectural factors is associated with chromatin reorganization failure, which may increase the risk of malignancy. Therefore, our computational approach helps decipher the transcriptional cis-regulatory code spatially interacting.
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Affiliation(s)
- Sung-Joon Park
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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2
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Zhang L, Toboso-Navasa A, Gunawan A, Camara A, Nakagawa R, Katja F, Chakravarty P, Newman R, Zhang Y, Eilers M, Wack A, Tolar P, Toellner KM, Calado DP. Regulation of BCR-mediated Ca 2+ mobilization by MIZ1-TMBIM4 safeguards IgG1 + GC B cell-positive selection. Sci Immunol 2024; 9:eadk0092. [PMID: 38579014 PMCID: PMC7615907 DOI: 10.1126/sciimmunol.adk0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/26/2024] [Indexed: 04/07/2024]
Abstract
The transition from immunoglobulin M (IgM) to affinity-matured IgG antibodies is vital for effective humoral immunity. This is facilitated by germinal centers (GCs) through affinity maturation and preferential maintenance of IgG+ B cells over IgM+ B cells. However, it is not known whether the positive selection of the different Ig isotypes within GCs is dependent on specific transcriptional mechanisms. Here, we explored IgG1+ GC B cell transcription factor dependency using a CRISPR-Cas9 screen and conditional mouse genetics. We found that MIZ1 was specifically required for IgG1+ GC B cell survival during positive selection, whereas IgM+ GC B cells were largely independent. Mechanistically, MIZ1 induced TMBIM4, an ancestral anti-apoptotic protein that regulated inositol trisphosphate receptor (IP3R)-mediated calcium (Ca2+) mobilization downstream of B cell receptor (BCR) signaling in IgG1+ B cells. The MIZ1-TMBIM4 axis prevented mitochondrial dysfunction-induced IgG1+ GC cell death caused by excessive Ca2+ accumulation. This study uncovers a unique Ig isotype-specific dependency on a hitherto unidentified mechanism in GC-positive selection.
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Affiliation(s)
- Lingling Zhang
- Immunity and Cancer, Francis Crick Institute, London, UK
| | | | - Arief Gunawan
- Immunity and Cancer, Francis Crick Institute, London, UK
| | | | | | | | | | - Rebecca Newman
- Immune Receptor Activation Laboratory, Francis Crick Institute, London, UK
| | - Yang Zhang
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Martin Eilers
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Pavel Tolar
- Immune Receptor Activation Laboratory, Francis Crick Institute, London, UK
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK
| | - Kai-Michael Toellner
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
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3
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Dabkowska A, Domka K, Firczuk M. Advancements in cancer immunotherapies targeting CD20: from pioneering monoclonal antibodies to chimeric antigen receptor-modified T cells. Front Immunol 2024; 15:1363102. [PMID: 38638442 PMCID: PMC11024268 DOI: 10.3389/fimmu.2024.1363102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/25/2024] [Indexed: 04/20/2024] Open
Abstract
CD20 located predominantly on the B cells plays a crucial role in their development, differentiation, and activation, and serves as a key therapeutic target for the treatment of B-cell malignancies. The breakthrough of monoclonal antibodies directed against CD20, notably exemplified by rituximab, revolutionized the prognosis of B-cell malignancies. Rituximab, approved across various hematological malignancies, marked a paradigm shift in cancer treatment. In the current landscape, immunotherapies targeting CD20 continue to evolve rapidly. Beyond traditional mAbs, advancements include antibody-drug conjugates (ADCs), bispecific antibodies (BsAbs), and chimeric antigen receptor-modified (CAR) T cells. ADCs combine the precision of antibodies with the cytotoxic potential of drugs, presenting a promising avenue for enhanced therapeutic efficacy. BsAbs, particularly CD20xCD3 constructs, redirect cytotoxic T cells to eliminate cancer cells, thereby enhancing both precision and potency in their therapeutic action. CAR-T cells stand as a promising strategy for combatting hematological malignancies, representing one of the truly personalized therapeutic interventions. Many new therapies are currently being evaluated in clinical trials. This review serves as a comprehensive summary of CD20-targeted therapies, highlighting the progress and challenges that persist. Despite significant advancements, adverse events associated with these therapies and the development of resistance remain critical issues. Understanding and mitigating these challenges is paramount for the continued success of CD20-targeted immunotherapies.
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Affiliation(s)
- Agnieszka Dabkowska
- Laboratory of Immunology, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Krzysztof Domka
- Laboratory of Immunology, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Malgorzata Firczuk
- Laboratory of Immunology, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
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4
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Diaz LR, Gil-Ranedo J, Jaworek KJ, Nsek N, Marques JP, Costa E, Hilton DA, Bieluczyk H, Warrington O, Hanemann CO, Futschik ME, Bossing T, Barros CS. Ribogenesis boosts controlled by HEATR1-MYC interplay promote transition into brain tumour growth. EMBO Rep 2024; 25:168-197. [PMID: 38225354 PMCID: PMC10897169 DOI: 10.1038/s44319-023-00017-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 01/17/2024] Open
Abstract
Cell commitment to tumourigenesis and the onset of uncontrolled growth are critical determinants in cancer development but the early events directing tumour initiating cell (TIC) fate remain unclear. We reveal a single-cell transcriptome profile of brain TICs transitioning into tumour growth using the brain tumour (brat) neural stem cell-based Drosophila model. Prominent changes in metabolic and proteostasis-associated processes including ribogenesis are identified. Increased ribogenesis is a known cell adaptation in established tumours. Here we propose that brain TICs boost ribogenesis prior to tumour growth. In brat-deficient TICs, we show that this dramatic change is mediated by upregulated HEAT-Repeat Containing 1 (HEATR1) to promote ribosomal RNA generation, TIC enlargement and onset of overgrowth. High HEATR1 expression correlates with poor glioma patient survival and patient-derived glioblastoma stem cells rely on HEATR1 for enhanced ribogenesis and tumourigenic potential. Finally, we show that HEATR1 binds the master growth regulator MYC, promotes its nucleolar localisation and appears required for MYC-driven ribogenesis, suggesting a mechanism co-opted in ribogenesis reprogramming during early brain TIC development.
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Affiliation(s)
- Laura R Diaz
- Peninsula Medical School, Faculty of Health, John Bull Building, University of Plymouth, PL6 8BU, Plymouth, UK
| | - Jon Gil-Ranedo
- Peninsula Medical School, Faculty of Health, John Bull Building, University of Plymouth, PL6 8BU, Plymouth, UK
| | - Karolina J Jaworek
- Peninsula Medical School, Faculty of Health, John Bull Building, University of Plymouth, PL6 8BU, Plymouth, UK
- School of Biological Sciences, Bangor University, LL57 2UW, Bangor, UK
| | - Nsikan Nsek
- Peninsula Medical School, Faculty of Health, John Bull Building, University of Plymouth, PL6 8BU, Plymouth, UK
| | - Joao Pinheiro Marques
- Peninsula Medical School, Faculty of Health, John Bull Building, University of Plymouth, PL6 8BU, Plymouth, UK
| | - Eleni Costa
- Peninsula Medical School, Faculty of Health, John Bull Building, University of Plymouth, PL6 8BU, Plymouth, UK
| | - David A Hilton
- Department of Cellular and Anatomical Pathology, University Hospitals Plymouth, PL6 8DH, Plymouth, UK
| | - Hubert Bieluczyk
- Peninsula Medical School, Faculty of Health, John Bull Building, University of Plymouth, PL6 8BU, Plymouth, UK
| | - Oliver Warrington
- Peninsula Medical School, Faculty of Health, John Bull Building, University of Plymouth, PL6 8BU, Plymouth, UK
- Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, University College London, WC1N 3AR, London, UK
| | - C Oliver Hanemann
- Peninsula Medical School, Faculty of Health, John Bull Building, University of Plymouth, PL6 8BU, Plymouth, UK
| | - Matthias E Futschik
- School of Biomedical Sciences, Faculty of Health, Derriford Research Facility, University of Plymouth, PL6 8BU, Plymouth, UK
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-504, Coimbra, Portugal
| | - Torsten Bossing
- Peninsula Medical School, Faculty of Health, John Bull Building, University of Plymouth, PL6 8BU, Plymouth, UK
| | - Claudia S Barros
- Peninsula Medical School, Faculty of Health, John Bull Building, University of Plymouth, PL6 8BU, Plymouth, UK.
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5
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Zhang Y, Zhang X, Zhang Y, Xu H, Wei Z, Wang X, Li Y, Guo J, Wu F, Fang X, Pang L, Deng B, Yu D. c-Myc inhibits LAPTM5 expression in B-cell lymphomas. Ann Hematol 2023; 102:3499-3513. [PMID: 37713124 DOI: 10.1007/s00277-023-05434-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023]
Abstract
Myc is a pivotal protooncogenic transcription factor that contributes to the development of almost all Burkitt's lymphomas and about one-third of diffuse large B-cell lymphomas. How B-cells sustain their uncontrolled proliferation due to high Myc is not yet well defined. Here, we found that Myc trans-represses the expression of murine LAPTM5, a gene coding a lysosome-associated protein, by binding to two E-boxes in the LAPTM5 promoter. While the product of intact mRNA (CDS+3'UTR) of LAPTM5 failed to suppress the growth of B-lymphomas, either the protein coded by coding sequence (CDS) itself or the non-coding 3'-untranslated region (3'UTR) mRNA was able to inhibit the growth of B-lymphomas. Moreover, Myc trans-activated miR-17-3p, which promoted tumor growth. Strikingly, LAPTM5 3'UTR contains 11 miR-17-3p-binding sites through which the LAPTM5 protein synthesis was inhibited. The functional interplay between low LAPTM5 mRNA and high miR-17-3p due to high Myc in B-lymphomas leads to further dampening of tumor-suppressive LAPTM5 protein, which promotes tumor progression. Our results indicate that Myc inhibits LAPTM5 expression in B-lymphoma cells by transcriptional and post-transcriptional modifications.
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Affiliation(s)
- Yanqing Zhang
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Xin Zhang
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
- Department of Pathology, Sir Run Run Shaw Hospital, Institute of Clinical Science, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Zhang
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Han Xu
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Zichen Wei
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Xin Wang
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Yan Li
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Junrong Guo
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Fan Wu
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Xiao Fang
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China
| | - Lei Pang
- Department of Gastroenterology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Bin Deng
- Department of Gastroenterology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Duonan Yu
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, China.
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University Medical College, 136 Jiangyang Road, Yangzhou, Jiangsu Province, 225009, China.
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6
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Kazimierska M, Podralska M, Żurawek M, Woźniak T, Kasprzyk ME, Sura W, Łosiewski W, Ziółkowska‐Suchanek I, Kluiver J, van den Berg A, Rozwadowska N, Dzikiewicz‐Krawczyk A. CRISPR/Cas9 screen for genome-wide interrogation of essential MYC-bound E-boxes in cancer cells. Mol Oncol 2023; 17:2295-2313. [PMID: 37519063 PMCID: PMC10620128 DOI: 10.1002/1878-0261.13493] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/28/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023] Open
Abstract
The transcription factor MYC is a proto-oncogene with a well-documented essential role in the pathogenesis and maintenance of several types of cancer. MYC binds to specific E-box sequences in the genome to regulate gene expression in a cell-type- and developmental-stage-specific manner. To date, a combined analysis of essential MYC-bound E-boxes and their downstream target genes important for growth of different types of cancer is missing. In this study, we designed a CRISPR/Cas9 library to destroy E-box sequences in a genome-wide fashion. In parallel, we used the Brunello library to knock out protein-coding genes. We performed high-throughput screens with these libraries in four MYC-dependent cancer cell lines-K562, ST486, HepG2, and MCF7-which revealed several essential E-boxes and genes. Among them, we pinpointed crucial common and cell-type-specific MYC-regulated genes involved in pathways associated with cancer development. Extensive validation of our approach confirmed that E-box disruption affects MYC binding, target-gene expression, and cell proliferation in vitro as well as tumor growth in vivo. Our unique, well-validated tool opens new possibilities to gain novel insights into MYC-dependent vulnerabilities in cancer cells.
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Affiliation(s)
- Marta Kazimierska
- Institute of Human GeneticsPolish Academy of SciencesPoznańPoland
- Institute of Bioorganic ChemistryPolish Academy of SciencesPoznańPoland
| | - Marta Podralska
- Institute of Human GeneticsPolish Academy of SciencesPoznańPoland
| | | | - Tomasz Woźniak
- Institute of Human GeneticsPolish Academy of SciencesPoznańPoland
| | | | - Weronika Sura
- Institute of Human GeneticsPolish Academy of SciencesPoznańPoland
| | | | | | - Joost Kluiver
- Department of Pathology and Medical BiologyUniversity of Groningen, University Medical Center GroningenThe Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical BiologyUniversity of Groningen, University Medical Center GroningenThe Netherlands
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7
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Purhonen J, Klefström J, Kallijärvi J. MYC-an emerging player in mitochondrial diseases. Front Cell Dev Biol 2023; 11:1257651. [PMID: 37731815 PMCID: PMC10507175 DOI: 10.3389/fcell.2023.1257651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023] Open
Abstract
The mitochondrion is a major hub of cellular metabolism and involved directly or indirectly in almost all biological processes of the cell. In mitochondrial diseases, compromised respiratory electron transfer and oxidative phosphorylation (OXPHOS) lead to compensatory rewiring of metabolism with resemblance to the Warburg-like metabolic state of cancer cells. The transcription factor MYC (or c-MYC) is a major regulator of metabolic rewiring in cancer, stimulating glycolysis, nucleotide biosynthesis, and glutamine utilization, which are known or predicted to be affected also in mitochondrial diseases. Albeit not widely acknowledged thus far, several cell and mouse models of mitochondrial disease show upregulation of MYC and/or its typical transcriptional signatures. Moreover, gene expression and metabolite-level changes associated with mitochondrial integrated stress response (mt-ISR) show remarkable overlap with those of MYC overexpression. In addition to being a metabolic regulator, MYC promotes cellular proliferation and modifies the cell cycle kinetics and, especially at high expression levels, promotes replication stress and genomic instability, and sensitizes cells to apoptosis. Because cell proliferation requires energy and doubling of the cellular biomass, replicating cells should be particularly sensitive to defective OXPHOS. On the other hand, OXPHOS-defective replicating cells are predicted to be especially vulnerable to high levels of MYC as it facilitates evasion of metabolic checkpoints and accelerates cell cycle progression. Indeed, a few recent studies demonstrate cell cycle defects and nuclear DNA damage in OXPHOS deficiency. Here, we give an overview of key mitochondria-dependent metabolic pathways known to be regulated by MYC, review the current literature on MYC expression in mitochondrial diseases, and speculate how its upregulation may be triggered by OXPHOS deficiency and what implications this has for the pathogenesis of these diseases.
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Affiliation(s)
- Janne Purhonen
- Folkhälsan Research Center, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Juha Klefström
- Finnish Cancer Institute, FICAN South Helsinki University Hospital, Helsinki, Finland
- Translational Cancer Medicine, Medical Faculty, University of Helsinki, Helsinki, Finland
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, United States
| | - Jukka Kallijärvi
- Folkhälsan Research Center, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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8
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Khameneh HJ, Fonta N, Zenobi A, Niogret C, Ventura P, Guerra C, Kwee I, Rinaldi A, Pecoraro M, Geiger R, Cavalli A, Bertoni F, Vivier E, Trumpp A, Guarda G. Myc controls NK cell development, IL-15-driven expansion, and translational machinery. Life Sci Alliance 2023; 6:e202302069. [PMID: 37105715 PMCID: PMC10140547 DOI: 10.26508/lsa.202302069] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
MYC is a pleiotropic transcription factor involved in cancer, cell proliferation, and metabolism. Its regulation and function in NK cells, which are innate cytotoxic lymphocytes important to control viral infections and cancer, remain poorly defined. Here, we show that mice deficient for Myc in NK cells presented a severe reduction in these lymphocytes. Myc was required for NK cell development and expansion in response to the key cytokine IL-15, which induced Myc through transcriptional and posttranslational mechanisms. Mechanistically, Myc ablation in vivo largely impacted NK cells' ribosomagenesis, reducing their translation and expansion capacities. Similar results were obtained by inhibiting MYC in human NK cells. Impairing translation by pharmacological intervention phenocopied the consequences of deleting or blocking MYC in vitro. Notably, mice lacking Myc in NK cells exhibited defective anticancer immunity, which reflected their decreased numbers of mature NK cells exerting suboptimal cytotoxic functions. These results indicate that MYC is a central node in NK cells, connecting IL-15 to translational fitness, expansion, and anticancer immunity.
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Affiliation(s)
- Hanif J Khameneh
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Nicolas Fonta
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Alessandro Zenobi
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Charlène Niogret
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Pedro Ventura
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Concetta Guerra
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Ivo Kwee
- BigOmics Analytics SA, Lugano, Switzerland
| | - Andrea Rinaldi
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute of Oncology Research, Bellinzona, Switzerland
| | - Matteo Pecoraro
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Roger Geiger
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute of Oncology Research, Bellinzona, Switzerland
| | - Andrea Cavalli
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Francesco Bertoni
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute of Oncology Research, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Eric Vivier
- Aix-Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d'Immunologie de Marseille-Luminy, Marseille, France
- Innate Pharma Research Laboratories, Marseille, France
- APHM, Hôpital de la Timone, Marseille-Immunopôle, Marseille, France
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, DKFZ, Heidelberg, Germany
- HI-STEM: The Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany
| | - Greta Guarda
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
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9
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Tong Y, Lee Y, Liu X, Childs-Disney JL, Suresh BM, Benhamou RI, Yang C, Li W, Costales MG, Haniff HS, Sievers S, Abegg D, Wegner T, Paulisch TO, Lekah E, Grefe M, Crynen G, Van Meter M, Wang T, Gibaut QMR, Cleveland JL, Adibekian A, Glorius F, Waldmann H, Disney MD. Programming inactive RNA-binding small molecules into bioactive degraders. Nature 2023; 618:169-179. [PMID: 37225982 PMCID: PMC10232370 DOI: 10.1038/s41586-023-06091-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 04/17/2023] [Indexed: 05/26/2023]
Abstract
Target occupancy is often insufficient to elicit biological activity, particularly for RNA, compounded by the longstanding challenges surrounding the molecular recognition of RNA structures by small molecules. Here we studied molecular recognition patterns between a natural-product-inspired small-molecule collection and three-dimensionally folded RNA structures. Mapping these interaction landscapes across the human transcriptome defined structure-activity relationships. Although RNA-binding compounds that bind to functional sites were expected to elicit a biological response, most identified interactions were predicted to be biologically inert as they bind elsewhere. We reasoned that, for such cases, an alternative strategy to modulate RNA biology is to cleave the target through a ribonuclease-targeting chimera, where an RNA-binding molecule is appended to a heterocycle that binds to and locally activates RNase L1. Overlay of the substrate specificity for RNase L with the binding landscape of small molecules revealed many favourable candidate binders that might be bioactive when converted into degraders. We provide a proof of concept, designing selective degraders for the precursor to the disease-associated microRNA-155 (pre-miR-155), JUN mRNA and MYC mRNA. Thus, small-molecule RNA-targeted degradation can be leveraged to convert strong, yet inactive, binding interactions into potent and specific modulators of RNA function.
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Affiliation(s)
- Yuquan Tong
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Yeongju Lee
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Xiaohui Liu
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Blessy M Suresh
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Raphael I Benhamou
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Chunying Yang
- Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Weimin Li
- Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Matthew G Costales
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Hafeez S Haniff
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Sonja Sievers
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Compound Management and Screening Center, Dortmund, Germany
| | - Daniel Abegg
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Tristan Wegner
- Organisch-Chemisches Institut, University of Münster, Münster, Germany
| | | | - Elizabeth Lekah
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Maison Grefe
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Gogce Crynen
- Bioinformatics and Statistics Core, The Scripps Research Institute and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Montina Van Meter
- Histology Core, The Scripps Research Institute and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Tenghui Wang
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Quentin M R Gibaut
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - John L Cleveland
- Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Alexander Adibekian
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Frank Glorius
- Organisch-Chemisches Institut, University of Münster, Münster, Germany.
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology, Dortmund, Germany.
- Compound Management and Screening Center, Dortmund, Germany.
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany.
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA.
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10
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Winkle M, Tayari MM, Kok K, Duns G, Grot N, Kazimierska M, Seitz A, de Jong D, Koerts J, Diepstra A, Dzikiewicz-Krawczyk A, Steidl C, Kluiver J, van den Berg A. The lncRNA KTN1-AS1 co-regulates a variety of Myc-target genes and enhances proliferation of Burkitt lymphoma cells. Hum Mol Genet 2022; 31:4193-4206. [PMID: 35866590 DOI: 10.1093/hmg/ddac159] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/22/2022] [Accepted: 07/07/2022] [Indexed: 01/21/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in many normal and oncogenic pathways through a diverse repertoire of transcriptional and posttranscriptional regulatory mechanisms. LncRNAs that are under tight regulation of well-known oncogenic transcription factors such as c-Myc (Myc) are likely to be functionally involved in their disease-promoting mechanisms. Myc is a major driver of many subsets of B cell lymphoma and to date remains an undruggable target. We identified three Myc-induced and four Myc-repressed lncRNAs by use of multiple in vitro models of Myc-driven Burkitt lymphoma and detailed analysis of Myc binding profiles. We show that the top Myc-induced lncRNA KTN1-AS1 is strongly upregulated in different types of B cell lymphoma compared with their normal counterparts. We used CRISPR-mediated genome editing to confirm that the direct induction of KTN1-AS1 by Myc is dependent on the presence of a Myc E-box-binding motif. Knockdown of KTN1-AS1 revealed a strong negative effect on the growth of three BL cell lines. Global gene expression analysis upon KTN1-AS1 depletion shows a strong enrichment of key genes in the cholesterol biosynthesis pathway as well as co-regulation of many Myc-target genes, including a moderate negative effect on the levels of Myc itself. Our study suggests a critical role for KTN1-AS1 in supporting BL cell growth by mediating co-regulation of a variety of Myc-target genes and co-activating key genes involved in cholesterol biosynthesis. Therefore, KTN1-AS1 may represent a putative novel therapeutic target in lymphoma.
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Affiliation(s)
- Melanie Winkle
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands.,Department of Translational Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mina M Tayari
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands.,Department of Human Genetics, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Gerben Duns
- Department of Lymphoid Cancer Research, BC Cancer Center, Vancouver, BC, Canada
| | - Natalia Grot
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Marta Kazimierska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Annika Seitz
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Debora de Jong
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Jasper Koerts
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | | | - Christian Steidl
- Department of Lymphoid Cancer Research, BC Cancer Center, Vancouver, BC, Canada
| | - Joost Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
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11
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Losing CD45 and various B-cell markers in a case of MYC-driven pediatric high-grade B-cell lymphoma, not otherwise specified that transformed from Burkitt’s lymphoma during rituximab-containing treatments: a case report. Virchows Arch 2022:10.1007/s00428-022-03433-1. [DOI: 10.1007/s00428-022-03433-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/28/2022] [Accepted: 10/15/2022] [Indexed: 11/17/2022]
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12
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García R, Hussain A, Chen W, Wilson K, Koduru P. An artificial intelligence system applied to recurrent cytogenetic aberrations and genetic progression scores predicts MYC rearrangements in large B-cell lymphoma. EJHAEM 2022; 3:707-721. [PMID: 36051032 PMCID: PMC9421965 DOI: 10.1002/jha2.451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/05/2022] [Accepted: 04/09/2022] [Indexed: 11/20/2022]
Abstract
Diffuse large B-cell lymphoma (DLBCL), the most common type of non-Hodgkin lymphoma, is characterized by MYC rearrangements (MYC R) in up to 15% of cases, and these have unfavorable prognosis. Due to cryptic rearrangements and variations in MYC breakpoints, MYC R may be undetectable by conventional methods in up to 10%-15% of cases. In this study, a retrospective proof of concept study, we sought to identify recurrent cytogenetic aberrations (RCAs), generate genetic progression scores (GP) from RCAs and apply these to an artificial intelligence (AI) algorithm to predict MYC status in the karyotypes of published cases. The developed AI algorithm is validated for its performance on our institutional cases. In addition, cytogenetic evolution pattern and clinical impact of RCAs was performed. Chromosome losses were associated with MYC-, while partial gain of chromosome 1 was significant in MYC R tumors. MYC R was the sole driver alteration in MYC-rearranged tumors, and evolution patterns revealed RCAs associated with gene expression signatures. A higher GPS value was associated with MYC R tumors. A subsequent AI algorithm (composed of RCAs + GPS) obtained a sensitivity of 91.4 and specificity of 93.8 at predicting MYC R. Analysis of an additional 59 institutional cases with the AI algorithm showed a sensitivity and specificity of 100% and 87% each with positive predictive value of 92%, and a negative predictive value of 100%. Cases with a MYC R showed a shorter survival.
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Affiliation(s)
- Rolando García
- Department of PathologyUT Southwestern Medical CenterDallasTexasUSA
| | - Anas Hussain
- Deccan College of Medical SciencesHyderabadIndia
| | - Weina Chen
- Department of PathologyUT Southwestern Medical CenterDallasTexasUSA
| | - Kathleen Wilson
- Department of PathologyUT Southwestern Medical CenterDallasTexasUSA
| | - Prasad Koduru
- Department of PathologyUT Southwestern Medical CenterDallasTexasUSA
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13
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Tian Y, Wang X, Ai H, Lyu X, Wang Q, Wei X, Song Y, Yin Q. The different predictive effects of the intensity and proportion of CD20 expression on the prognosis of B-lineage acute lymphocyte leukemia. EJHAEM 2022; 3:443-452. [PMID: 35846053 PMCID: PMC9176059 DOI: 10.1002/jha2.414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 11/30/2022]
Abstract
The prognostic effects of the CD20 positivity have been studied extensively in B-lineage acute lymphocyte leukemia (B-ALL) patients, but the results remain controversial. The aim of this study is to investigate the different predictive effects of the intensity and proportion of CD20 expression on the prognosis for B-ALL patients by retrospective analysis. The mean fluorescence intensity (MFI) and percentage of CD20 on B-ALL cells from 206 patients with B-ALL were dynamically measured by flow cytometry, and their optimal cut-off values were determined using the receiver operating characteristic curve. Changes in MFI and percentage of CD20 at various time points and their relationship with prognosis were analyzed. We found that a low baseline CD20 MFI or high CD20 proportion was significantly associated with shorter 5-year overall survival and progression-free survival, and the combination of these two factors could more accurately predict worse survival for B-ALL patients. Furthermore, low CD20 MFI or a high CD20 proportion had different predictive effects for ALL patients with different clinical characteristics and could serve as an independent risk factor for adverse prognosis. There were significant decreases in both the intensity and proportion of CD20 after recurrence in the absence of rituximab treatment, particularly with CD20 intensity. Notably, the decrease of CD20 intensity after recurrence indicated a more shortened survival time. Finally, we conclude that a low intensity or high proportion of CD20 expression may be used as an indicator for inferior prognosis for B-ALL patients. CD20 intensity is more likely to be a more universal biomarker for worse prognosis.
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Affiliation(s)
- Yun Tian
- Department of Hematology, Henan Institute of HematologyAffiliated Cancer Hospital of Zhengzhou UniversityHenan Cancer HospitalZhengzhouHenanChina
| | - Xiaojiao Wang
- Department of Hematology, Henan Institute of HematologyAffiliated Cancer Hospital of Zhengzhou UniversityHenan Cancer HospitalZhengzhouHenanChina
| | - Hao Ai
- Department of Hematology, Henan Institute of HematologyAffiliated Cancer Hospital of Zhengzhou UniversityHenan Cancer HospitalZhengzhouHenanChina
| | - Xiaodong Lyu
- Department of Hematology, Henan Institute of HematologyAffiliated Cancer Hospital of Zhengzhou UniversityHenan Cancer HospitalZhengzhouHenanChina
| | - Qian Wang
- Department of Hematology, Henan Institute of HematologyAffiliated Cancer Hospital of Zhengzhou UniversityHenan Cancer HospitalZhengzhouHenanChina
| | - Xudong Wei
- Department of Hematology, Henan Institute of HematologyAffiliated Cancer Hospital of Zhengzhou UniversityHenan Cancer HospitalZhengzhouHenanChina
| | - Yongping Song
- Department of Hematology, Henan Institute of HematologyAffiliated Cancer Hospital of Zhengzhou UniversityHenan Cancer HospitalZhengzhouHenanChina
| | - Qingsong Yin
- Department of Hematology, Henan Institute of HematologyAffiliated Cancer Hospital of Zhengzhou UniversityHenan Cancer HospitalZhengzhouHenanChina
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14
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Szydłowski M, Garbicz F, Jabłońska E, Górniak P, Komar D, Pyrzyńska B, Bojarczuk K, Prochorec-Sobieszek M, Szumera-Ciećkiewicz A, Rymkiewicz G, Cybulska M, Statkiewicz M, Gajewska M, Mikula M, Gołas A, Domagała J, Winiarska M, Graczyk-Jarzynka A, Białopiotrowicz E, Polak A, Barankiewicz J, Puła B, Pawlak M, Nowis D, Golab J, Tomirotti AM, Brzózka K, Pacheco-Blanco M, Kupcova K, Green MR, Havranek O, Chapuy B, Juszczyński P. Inhibition of PIM Kinases in DLBCL Targets MYC Transcriptional Program and Augments the Efficacy of Anti-CD20 Antibodies. Cancer Res 2021; 81:6029-6043. [PMID: 34625423 DOI: 10.1158/0008-5472.can-21-1023] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/18/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022]
Abstract
The family of PIM serine/threonine kinases includes three highly conserved oncogenes, PIM1, PIM2, and PIM3, which regulate multiple pro-survival pathways and cooperate with other oncogenes such as MYC. Recent genomic CRISPR-Cas9 screens further highlighted oncogenic functions of PIMs in diffuse large B cell lymphoma (DLBCL) cells, justifying development of small molecule PIM inhibitors and therapeutic targeting of PIM kinases in lymphomas. However, detailed consequences of PIM inhibition in DLBCL remain undefined. Using chemical and genetic PIM blockade, we comprehensively characterized PIM kinase-associated pro-survival functions in DLBCL and the mechanisms of PIM inhibition-induced toxicity. Treatment of DLBCL cells with SEL24/MEN1703, a pan PIM inhibitor in clinical development, decreased BAD phosphorylation and cap-dependent protein translation, reduced MCL1 expression, and induced apoptosis. PIM kinases were tightly coexpressed with MYC in diagnostic DLBCL biopsies, and PIM inhibition in cell lines and patient-derived primary lymphoma cells decreased MYC levels as well as expression of multiple MYC-dependent genes, including PLK1. Chemical and genetic PIM inhibition upregulated surface CD20 levels in a MYC-dependent fashion. Consistently, MEN1703 and other clinically available pan-PIM inhibitors synergized with the anti-CD20 monoclonal antibody rituximab in vitro, increasing complement-dependent cytotoxicity and antibody-mediated phagocytosis. Combined treatment with PIM inhibitor and rituximab suppressed tumor growth in lymphoma xenografts more efficiently than either drug alone. Taken together, these results show that targeting PIM in DLBCL exhibits pleiotropic effects that combine direct cytotoxicity with potentiated susceptibility to anti-CD20 antibodies, justifying further clinical development of such combinatorial strategies.
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Affiliation(s)
- Maciej Szydłowski
- Dept. of Experimental Hematology, Institute of Hematology and Transfusion Medicine
| | - Filip Garbicz
- Dept. of Experimental Hematology, Institute of Hematology and Transfusion Medicine
| | - Ewa Jabłońska
- Department of Diagnostic Hematology, Institute of Hematology and Transfusion Medicine
| | - Patryk Górniak
- Dept. of Experimental Hematology, Institute of Hematology and Transfusion Medicine
| | - Dorota Komar
- Dept. of Experimental Hematology, Institute of Hematology and Transfusion Medicine
| | | | - Kamil Bojarczuk
- Department of Hematology and Medical Oncology, University Medical Center - Georg-August-Universität Göttingen
| | | | - Anna Szumera-Ciećkiewicz
- Department of Pathology and Laboratory Diagnostics, IMaria Sklodowska-Curie National Research Institute of Oncology
| | - Grzegorz Rymkiewicz
- Dept. of Pathology and Laboratory Diagnostics, National Research Institute of Oncology
| | | | | | - Marta Gajewska
- Dept. of Genetics, National Research Institute of Oncology
| | - Michal Mikula
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology
| | | | | | | | | | | | - Anna Polak
- Department of Diagnostic Hematology, Institute of Hematology and Transfusion Medicine
| | | | - Bartosz Puła
- Dept. of Hematology, Institute of Hematology and Transfusion Medicine
| | - Michał Pawlak
- Dept. of Experimental Hematology, Institute of Hematology and Transfusion Medicine
| | - Dominika Nowis
- Laboratory of Experimental Medicine, Medical University of Warsaw
| | - Jakub Golab
- Department of Immunology, Medical University of Warsaw
| | | | | | | | | | - Michael R Green
- Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center
| | | | - Bjoern Chapuy
- Department of Hematology and Medical Oncology, Universitätsmedizin Göttingen
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15
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Hashimoto A, Handa H, Hata S, Tsutaho A, Yoshida T, Hirano S, Hashimoto S, Sabe H. Inhibition of mutant KRAS-driven overexpression of ARF6 and MYC by an eIF4A inhibitor drug improves the effects of anti-PD-1 immunotherapy for pancreatic cancer. Cell Commun Signal 2021; 19:54. [PMID: 34001163 PMCID: PMC8127265 DOI: 10.1186/s12964-021-00733-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/16/2021] [Indexed: 01/05/2023] Open
Abstract
Many clinical trials are being conducted to clarify effective combinations of various drugs for immune checkpoint blockade (ICB) therapy. However, although extensive studies from multiple aspects have been conducted regarding treatments for pancreatic ductal adenocarcinoma (PDAC), there are still no effective ICB-based therapies or biomarkers for this cancer type. A series of our studies have identified that the small GTPase ARF6 and its downstream effector AMAP1 (also called ASAP1/DDEF1) are often overexpressed in different cancers, including PDAC, and closely correlate with poor patient survival. Mechanistically, the ARF6-AMAP1 pathway drives cancer cell invasion and immune evasion, via upregulating β1-integrins and PD-L1, and downregulating E-cadherin, upon ARF6 activation by external ligands. Moreover, the ARF6-AMAP1 pathway enhances the fibrosis caused by PDAC, which is another barrier for ICB therapies. KRAS mutations are prevalent in PDACs. We have shown previously that oncogenic KRAS mutations are the major cause of the aberrant overexpression of ARF6 and AMAP1, in which KRAS signaling enhances eukaryotic initiation factor 4A (eIF4A)-dependent ARF6 mRNA translation and eIF4E-dependent AMAP1 mRNA translation. MYC overexpression is also a key pathway in driving cancer malignancy. MYC mRNA is also known to be under the control of eIF4A, and the eIF4A inhibitor silvestrol suppresses MYC and ARF6 expression. Using a KPC mouse model of human PDAC (LSL-Kras(G12D/+); LSL-Trp53(R172H/+)); Pdx-1-Cre), we here demonstrate that inhibition of the ARF6-AMAP1 pathway by shRNAs in cancer cells results in therapeutic synergy with an anti-PD-1 antibody in vivo; and furthermore, that silvestrol improves the efficacy of anti-PD-1 therapy, whereas silvestrol on its own promotes tumor growth in vivo. ARF6 and MYC are both essential for normal cell functions. We demonstrate that silvestrol substantially mitigates the overexpression of ARF6 and MYC in KRAS-mutated cells, whereas the suppression is moderate in KRAS-intact cells. We propose that targeting eIF4A, as well as mutant KRAS, provides novel methods to improve the efficacy of anti-PD-1 and associated ICB therapies against PDACs, in which ARF6 and AMAP1 overexpression, as well as KRAS mutations of cancer cells are biomarkers to identify patients with drug-susceptible disease. The same may be applicable to other cancers with KRAS mutations. Video abstract.
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Affiliation(s)
- Ari Hashimoto
- Department of Molecular Biology, Hokkaido University Faculty of Medicine, N15W7 Kita-ku, Sapporo, Hokkaido 060-8638 Japan
| | - Haruka Handa
- Department of Molecular Biology, Hokkaido University Faculty of Medicine, N15W7 Kita-ku, Sapporo, Hokkaido 060-8638 Japan
| | - Soichiro Hata
- Department of Molecular Biology, Hokkaido University Faculty of Medicine, N15W7 Kita-ku, Sapporo, Hokkaido 060-8638 Japan
| | - Akio Tsutaho
- Department of Molecular Biology, Hokkaido University Faculty of Medicine, N15W7 Kita-ku, Sapporo, Hokkaido 060-8638 Japan
- Department of Gastroenterological Surgery II, Faculty of Medicine, Hokkaido University, N15W7 Kita-ku, Sapporo, Hokkaido 060-8638 Japan
| | - Takao Yoshida
- Research Center of Oncology, Ono Pharmaceutical Co., Ltd., 3-1-1 Sakurai, Shimaoto-cho, Mishima-gun, Osaka 618-8585 Japan
| | - Satoshi Hirano
- Department of Gastroenterological Surgery II, Faculty of Medicine, Hokkaido University, N15W7 Kita-ku, Sapporo, Hokkaido 060-8638 Japan
| | - Shigeru Hashimoto
- Department of Molecular Biology, Hokkaido University Faculty of Medicine, N15W7 Kita-ku, Sapporo, Hokkaido 060-8638 Japan
- Present Address: Laboratory of Immune Regulation, Immunology Frontier Research Center, Osaka University, Osaka, 565-0871 Japan
| | - Hisataka Sabe
- Department of Molecular Biology, Hokkaido University Faculty of Medicine, N15W7 Kita-ku, Sapporo, Hokkaido 060-8638 Japan
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16
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Pavlasova G, Mraz M. The regulation and function of CD20: an "enigma" of B-cell biology and targeted therapy. Haematologica 2021; 105:1494-1506. [PMID: 32482755 PMCID: PMC7271567 DOI: 10.3324/haematol.2019.243543] [Citation(s) in RCA: 182] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/15/2020] [Indexed: 12/26/2022] Open
Abstract
The introduction of anti-CD20 monoclonal antibodies such as rituximab, ofatumumab, or obinutuzumab improved the therapy of B-cell malignancies even though the precise physiological role and regulation of CD20 remains unclear. Furthermore, CD20 expression is highly variable between different B-cell malignancies, patients with the same malignancy, and even between intraclonal subpopulations in an individual patient. Several epigenetic (EZH2, HDAC1/2, HDAC1/4, HDAC6, complex Sin3A-HDAC1) and transcription factors (USF, OCT1/2, PU.1, PiP, ELK1, ETS1, SP1, NFκB, FOXO1, CREM, SMAD2/3) regulating CD20 expression (encoded by MS4A1) have been characterized. CD20 is induced in the context of microenvironmental interactions by CXCR4/SDF1 (CXCL12) chemokine signaling and the molecular function of CD20 has been linked to the signaling propensity of B-cell receptor (BCR). CD20 has also been shown to interact with multiple other surface proteins on B cells (such as CD40, MHCII, CD53, CD81, CD82, and CBP). Current efforts to combine anti-CD20 monoclonal antibodies with BCR signaling inhibitors targeting BTK or PI3K (ibrutinib, acalabrutinib, idelalisib, duvelisib) or BH3-mimetics (venetoclax) lead to the necessity to better understand both the mechanisms of regulation and the biological functions of CD20. This is underscored by the observation that CD20 is decreased in response to the "BCR inhibitor" ibrutinib which largely prevents its successful combination with rituximab. Several small molecules (such as histone deacetylase inhibitors, DNA methyl-transferase inhibitors, aurora kinase A/B inhibitors, farnesyltransferase inhibitors, FOXO1 inhibitors, and bryostatin-1) are being tested to upregulate cell-surface CD20 levels and increase the efficacy of anti-CD20 monoclonal antibodies. Herein, we review the current understanding of CD20 function, and the mechanisms of its regulation in normal and malignant B cells, highlighting the therapeutic implications.
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Affiliation(s)
- Gabriela Pavlasova
- Central European Institute of Technology, Masaryk University, Brno.,Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Central European Institute of Technology, Masaryk University, Brno .,Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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17
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Fairlie WD, Lee EF. Co-Operativity between MYC and BCL-2 Pro-Survival Proteins in Cancer. Int J Mol Sci 2021; 22:2841. [PMID: 33799592 PMCID: PMC8000576 DOI: 10.3390/ijms22062841] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/30/2022] Open
Abstract
B-Cell Lymphoma 2 (BCL-2), c-MYC and related proteins are arguably amongst the most widely studied in all of biology. Every year there are thousands of papers reporting on different aspects of their biochemistry, cellular and physiological mechanisms and functions. This plethora of literature can be attributed to both proteins playing essential roles in the normal functioning of a cell, and by extension a whole organism, but also due to their central role in disease, most notably, cancer. Many cancers arise due to genetic lesions resulting in deregulation of both proteins, and indeed the development and survival of tumours is often dependent on co-operativity between these protein families. In this review we will discuss the individual roles of both proteins in cancer, describe cancers where co-operativity between them has been well-characterised and finally, some strategies to target these proteins therapeutically.
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Affiliation(s)
- Walter Douglas Fairlie
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3084, Australia
| | - Erinna F. Lee
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3084, Australia
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18
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Ou M, Zhao M, Li C, Tang D, Xu Y, Dai W, Sui W, Zhang Y, Xiang Z, Mo C, Lin H, Dai Y. Single-cell sequencing reveals the potential oncogenic expression atlas of human iPSC-derived cardiomyocytes. Biol Open 2021; 10:10/2/bio053348. [PMID: 33589441 PMCID: PMC7903994 DOI: 10.1242/bio.053348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Human induced pluripotent stem cells (iPSCs) are important source for regenerative medicine. However, the links between pluripotency and oncogenic transformation raise safety issues. To understand the characteristics of iPSC-derived cells at single-cell resolution, we directly reprogrammed two human iPSC lines into cardiomyocytes and collected cells from four time points during cardiac differentiation for single-cell sequencing. We captured 32,365 cells and identified five molecularly distinct clusters that aligned well with our reconstructed differentiation trajectory. We discovered a set of dynamic expression events related to the upregulation of oncogenes and the decreasing expression of tumor suppressor genes during cardiac differentiation, which were similar to the gain-of-function and loss-of-function patterns during oncogenesis. In practice, we characterized the dynamic expression of the TP53 and Yamanaka factor genes (OCT4, SOX2, KLF4 and MYC), which were widely used for human iPSCs lines generation; and revealed the co-occurrence of MYC overexpression and TP53 silencing in some of human iPSC-derived TNNT2+ cardiomyocytes. In summary, our oncogenic expression atlas is valuable for human iPSCs application and the single-cell resolution highlights the clues potentially associated with the carcinogenic risk of human iPSC-derived cells. Summary: The single-cell expression atlas in the cardiomyocytes generated from human iPSCs provide potential carcinogenic information for the clinical application of human iPSC-derived cells.
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Affiliation(s)
- Minglin Ou
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin 541000, China.,Clinical Medical Research Center, The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Min Zhao
- GeneCology Research Centre/Seaweed Research Group, School of Science and Engineering, University of the Sunshine Coast, Queensland 4556, Australia
| | - Chunhong Li
- Guangxi Key laboratory of Metabolic Diseases Research, Central Laboratory of Guilin No. 181 Hospital, Guilin 541002, China.,College of Life Science, Guangxi Normal University, Guilin 541006, China
| | - Donge Tang
- Clinical Medical Research Center, The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Yong Xu
- Clinical Medical Research Center, The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin 78712, Texas, USA
| | - Weiguo Sui
- Guangxi Key laboratory of Metabolic Diseases Research, Central Laboratory of Guilin No. 181 Hospital, Guilin 541002, China
| | - Yue Zhang
- Guangxi Key laboratory of Metabolic Diseases Research, Central Laboratory of Guilin No. 181 Hospital, Guilin 541002, China
| | - Zhen Xiang
- Guangxi Key laboratory of Metabolic Diseases Research, Central Laboratory of Guilin No. 181 Hospital, Guilin 541002, China
| | - Chune Mo
- Guangxi Key laboratory of Metabolic Diseases Research, Central Laboratory of Guilin No. 181 Hospital, Guilin 541002, China
| | - Hua Lin
- Guangxi Key laboratory of Metabolic Diseases Research, Central Laboratory of Guilin No. 181 Hospital, Guilin 541002, China
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China .,Guangxi Key laboratory of Metabolic Diseases Research, Central Laboratory of Guilin No. 181 Hospital, Guilin 541002, China
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19
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Luinenburg DG, Dinitzen AB, Flohr Svendsen A, Cengiz R, Ausema A, Weersing E, Bystrykh L, de Haan G. Persistent expression of microRNA-125a targets is required to induce murine hematopoietic stem cell repopulating activity. Exp Hematol 2021; 94:47-59.e5. [PMID: 33333212 DOI: 10.1016/j.exphem.2020.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 01/17/2023]
Abstract
MicroRNAs (miRs) are small noncoding RNAs that regulate gene expression posttranscriptionally by binding to the 3' untranslated regions of their target mRNAs. The evolutionarily conserved microRNA-125a (miR-125a) is highly expressed in both murine and human hematopoietic stem cells (HSCs), and previous studies have found that miR-125 strongly enhances self-renewal of HSCs and progenitors. In this study we explored whether temporary overexpression of miR-125a would be sufficient to permanently increase HSC self-renewal or, rather, whether persistent overexpression of miR-125a is required. We used three complementary in vivo approaches to reversibly enforce expression of miR-125a in murine HSCs. Additionally, we interrogated the underlying molecular mechanisms responsible for the functional changes that occur in HSCs on overexpression of miR-125a. Our data indicate that continuous expression of miR-125a is required to enhance HSC activity. Our molecular analysis confirms changes in pathways that explain the characteristics of miR-125a overexpressing HSCs. Moreover, it provides several novel putative miR-125a targets, but also highlights the complex molecular changes that collectively lead to enhanced HSC function.
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Affiliation(s)
- Daniëlle G Luinenburg
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander Bak Dinitzen
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Arthur Flohr Svendsen
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Roza Cengiz
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Albertina Ausema
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ellen Weersing
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Leonid Bystrykh
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gerald de Haan
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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20
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Kuo MT, Chen HHW, Feun LG, Savaraj N. Targeting the Proline-Glutamine-Asparagine-Arginine Metabolic Axis in Amino Acid Starvation Cancer Therapy. Pharmaceuticals (Basel) 2021; 14:ph14010072. [PMID: 33477430 PMCID: PMC7830038 DOI: 10.3390/ph14010072] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022] Open
Abstract
Proline, glutamine, asparagine, and arginine are conditionally non-essential amino acids that can be produced in our body. However, they are essential for the growth of highly proliferative cells such as cancers. Many cancers express reduced levels of these amino acids and thus require import from the environment. Meanwhile, the biosynthesis of these amino acids is inter-connected but can be intervened individually through the inhibition of key enzymes of the biosynthesis of these amino acids, resulting in amino acid starvation and cell death. Amino acid starvation strategies have been in various stages of clinical applications. Targeting asparagine using asparaginase has been approved for treating acute lymphoblastic leukemia. Targeting glutamine and arginine starvations are in various stages of clinical trials, and targeting proline starvation is in preclinical development. The most important obstacle of these therapies is drug resistance, which is mostly due to reactivation of the key enzymes involved in biosynthesis of the targeted amino acids and reprogramming of compensatory survival pathways via transcriptional, epigenetic, and post-translational mechanisms. Here, we review the interactive regulatory mechanisms that control cellular levels of these amino acids for amino acid starvation therapy and how drug resistance is evolved underlying treatment failure.
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Affiliation(s)
- Macus Tien Kuo
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence:
| | - Helen H. W. Chen
- Department of Radiation Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70428, Taiwan;
| | - Lynn G. Feun
- Department of Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA;
| | - Niramol Savaraj
- Division of Hematology and Oncology, Miami Veterans Affairs Heaithcare System, Miami, FL 33136, USA;
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21
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Single-Cell Analysis of Different Stages of Oral Cancer Carcinogenesis in a Mouse Model. Int J Mol Sci 2020; 21:ijms21218171. [PMID: 33142921 PMCID: PMC7662772 DOI: 10.3390/ijms21218171] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022] Open
Abstract
Oral carcinogenesis involves the progression of the normal mucosa into potentially malignant disorders and finally into cancer. Tumors are heterogeneous, with different clusters of cells expressing different genes and exhibiting different behaviors. 4-nitroquinoline 1-oxide (4-NQO) and arecoline were used to induce oral cancer in mice, and the main factors for gene expression influencing carcinogenesis were identified through single-cell RNA sequencing analysis. Male C57BL/6J mice were divided into two groups: a control group (receiving normal drinking water) and treatment group (receiving drinking water containing 4-NQO (200 mg/L) and arecoline (500 mg/L)) to induce the malignant development of oral cancer. Mice were sacrificed at 8, 16, 20, and 29 weeks. Except for mice sacrificed at 8 weeks, all mice were treated for 16 weeks and then either sacrificed or given normal drinking water for the remaining weeks. Tongue lesions were excised, and all cells obtained from mice in the 29- and 16-week treatment groups were clustered into 17 groups by using the Louvain algorithm. Cells in subtypes 7 (stem cells) and 9 (keratinocytes) were analyzed through gene set enrichment analysis. Results indicated that their genes were associated with the MYC_targets_v1 pathway, and this finding was confirmed by the presence of cisplatin-resistant nasopharyngeal carcinoma cell lines. These cell subtype biomarkers can be applied for the detection of patients with precancerous lesions, the identification of high-risk populations, and as a treatment target.
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22
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Senigl F, Maman Y, Dinesh RK, Alinikula J, Seth RB, Pecnova L, Omer AD, Rao SSP, Weisz D, Buerstedde JM, Aiden EL, Casellas R, Hejnar J, Schatz DG. Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation. Cell Rep 2020; 29:3902-3915.e8. [PMID: 31851922 PMCID: PMC6980758 DOI: 10.1016/j.celrep.2019.11.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/26/2019] [Accepted: 11/08/2019] [Indexed: 12/26/2022] Open
Abstract
Somatic hypermutation (SHM) introduces point mutations into immunoglobulin (Ig) genes but also causes mutations in other parts of the genome. We have used lentiviral SHM reporter vectors to identify regions of the genome that are susceptible (“hot”) and resistant (“cold”) to SHM, revealing that SHM susceptibility and resistance are often properties of entire topologically associated domains (TADs). Comparison of hot and cold TADs reveals that while levels of transcription are equivalent, hot TADs are enriched for the cohesin loader NIPBL, super-enhancers, markers of paused/stalled RNA polymerase 2, and multiple important B cell transcription factors. We demonstrate that at least some hot TADs contain enhancers that possess SHM targeting activity and that insertion of a strong Ig SHM-targeting element into a cold TAD renders it hot. Our findings lead to a model for SHM susceptibility involving the cooperative action of cis-acting SHM targeting elements and the dynamic and architectural properties of TADs. Senigl et al. show that genome susceptibility to somatic hypermutation (SHM) is confined within topologically associated domains (TADs) and is linked to markers of strong enhancers and stalled transcription and high levels of the cohesin loader NIPBL. Insertion of an ectopic SHM targeting element renders an entire TAD susceptible to SHM.
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Affiliation(s)
- Filip Senigl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic.
| | - Yaakov Maman
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ravi K Dinesh
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Jukka Alinikula
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Rashu B Seth
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Lubomira Pecnova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Arina D Omer
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Erez Lieberman Aiden
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Jiri Hejnar
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic
| | - David G Schatz
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA.
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23
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Toboso-Navasa A, Gunawan A, Morlino G, Nakagawa R, Taddei A, Damry D, Patel Y, Chakravarty P, Janz M, Kassiotis G, Brink R, Eilers M, Calado DP. Restriction of memory B cell differentiation at the germinal center B cell positive selection stage. J Exp Med 2020; 217:e20191933. [PMID: 32407433 PMCID: PMC7336312 DOI: 10.1084/jem.20191933] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 02/24/2020] [Accepted: 04/03/2020] [Indexed: 12/15/2022] Open
Abstract
Memory B cells (MBCs) are key for protection from reinfection. However, it is mechanistically unclear how germinal center (GC) B cells differentiate into MBCs. MYC is transiently induced in cells fated for GC expansion and plasma cell (PC) formation, so-called positively selected GC B cells. We found that these cells coexpressed MYC and MIZ1 (MYC-interacting zinc-finger protein 1 [ZBTB17]). MYC and MIZ1 are transcriptional activators; however, they form a transcriptional repressor complex that represses MIZ1 target genes. Mice lacking MYC-MIZ1 complexes displayed impaired cell cycle entry of positively selected GC B cells and reduced GC B cell expansion and PC formation. Notably, absence of MYC-MIZ1 complexes in positively selected GC B cells led to a gene expression profile alike that of MBCs and increased MBC differentiation. Thus, at the GC positive selection stage, MYC-MIZ1 complexes are required for effective GC expansion and PC formation and to restrict MBC differentiation. We propose that MYC and MIZ1 form a module that regulates GC B cell fate.
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Affiliation(s)
| | - Arief Gunawan
- Immunity and Cancer, Francis Crick Institute, London, UK
| | - Giulia Morlino
- Immunity and Cancer, Francis Crick Institute, London, UK
| | | | - Andrea Taddei
- Immunity and Cancer, Francis Crick Institute, London, UK
| | - Djamil Damry
- Immunity and Cancer, Francis Crick Institute, London, UK
| | - Yash Patel
- Retroviral Immunology, Francis Crick Institute, London, UK
| | | | - Martin Janz
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité – Universitätsmedizin Berlin, Berlin, Germany
| | | | - Robert Brink
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Martin Eilers
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Würzburg, Germany
| | - Dinis Pedro Calado
- Immunity and Cancer, Francis Crick Institute, London, UK
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London, UK
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24
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Liu M, Yao B, Gui T, Guo C, Wu X, Li J, Ma L, Deng Y, Xu P, Wang Y, Yang D, Li Q, Zeng X, Li X, Hu R, Ge J, Yu Z, Chen Y, Chen B, Ju J, Zhao Q. PRMT5-dependent transcriptional repression of c-Myc target genes promotes gastric cancer progression. Theranostics 2020; 10:4437-4452. [PMID: 32292506 PMCID: PMC7150477 DOI: 10.7150/thno.42047] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/25/2020] [Indexed: 12/17/2022] Open
Abstract
The proto-oncogene c-Myc regulates multiple biological processes mainly through selectively activating gene expression. However, the mechanisms underlying c-Myc-mediated gene repression in the context of cancer remain less clear. This study aimed to clarify the role of PRMT5 in the transcriptional repression of c-Myc target genes in gastric cancer. Methods: Immunohistochemistry was used to evaluate the expression of PRMT5, c-Myc and target genes in gastric cancer patients. PRMT5 and c-Myc interaction was assessed by immunofluorescence, co-immunoprecipitation and GST pull-down assays. Bioinformatics analysis, immunoblotting, real-time PCR, chromatin immunoprecipitation, and rescue experiments were used to evaluate the mechanism. Results: We found that c-Myc directly interacts with protein arginine methyltransferase 5 (PRMT5) to transcriptionally repress the expression of a cohort of genes, including PTEN, CDKN2C (p18INK4C), CDKN1A (p21CIP1/WAF1), CDKN1C (p57KIP2) and p63, to promote gastric cancer cell growth. Specifically, we found that PRMT5 was required to promote gastric cancer cell growth in vitro and in vivo, and for transcriptional repression of this cohort of genes, which was dependent on its methyltransferase activity. Consistently, the promoters of this gene cohort were enriched for both PRMT5-mediated symmetric di-methylation of histone H4 on Arg 3 (H4R3me2s) and c-Myc, and c-Myc depletion also upregulated their expression. H4R3me2s also colocalized with the c-Myc-binding E-box motif (CANNTG) on these genes. We show that PRMT5 directly binds to c-Myc, and this binding is required for transcriptional repression of the target genes. Both c-Myc and PRMT5 expression levels were upregulated in primary human gastric cancer tissues, and their expression levels inversely correlated with clinical outcomes. Conclusions: Taken together, our study reveals a novel mechanism by which PRMT5-dependent transcriptional repression of c-Myc target genes is required for gastric cancer progression, and provides a potential new strategy for therapeutic targeting of gastric cancer.
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25
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de Barrios O, Meler A, Parra M. MYC's Fine Line Between B Cell Development and Malignancy. Cells 2020; 9:E523. [PMID: 32102485 PMCID: PMC7072781 DOI: 10.3390/cells9020523] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022] Open
Abstract
The transcription factor MYC is transiently expressed during B lymphocyte development, and its correct modulation is essential in defined developmental transitions. Although temporary downregulation of MYC is essential at specific points, basal levels of expression are maintained, and its protein levels are not completely silenced until the B cell becomes fully differentiated into a plasma cell or a memory B cell. MYC has been described as a proto-oncogene that is closely involved in many cancers, including leukemia and lymphoma. Aberrant expression of MYC protein in these hematological malignancies results in an uncontrolled rate of proliferation and, thereby, a blockade of the differentiation process. MYC is not activated by mutations in the coding sequence, and, as reviewed here, its overexpression in leukemia and lymphoma is mainly caused by gene amplification, chromosomal translocations, and aberrant regulation of its transcription. This review provides a thorough overview of the role of MYC in the developmental steps of B cells, and of how it performs its essential function in an oncogenic context, highlighting the importance of appropriate MYC regulation circuitry.
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Affiliation(s)
| | | | - Maribel Parra
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute, IJC Building, Campus ICO-Germans Trias i Pujol, Ctra de Can Ruti, 08916 Barcelona, Spain (A.M.)
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26
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Srikanth S, Ramachandran S, Mohan S S. Construction of the gene regulatory network identifies MYC as a transcriptional regulator of SWI/SNF complex. Sci Rep 2020; 10:158. [PMID: 31932624 PMCID: PMC6957478 DOI: 10.1038/s41598-019-56844-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022] Open
Abstract
Precise positioning of nucleosomes at the gene regulatory elements mediated by the SWI/SNF family of remodelling complex is important for the transcriptional regulation of genes. A wide set of genes are either positively or negatively regulated by SWI/SNF. In higher eukaryotes, around thirty genes were found to code for SWI/SNF subunits. The construction of a gene regulatory network of SWI/SNF subunits identifies MYC as a common regulator for many of the SWI/SNF subunit genes. A meta-analysis study was conducted to investigate the MYC dependent regulation of SWI/SNF remodelling complex. Subunit information and the promoter sequences of the subunit genes were used to find the canonical E-box motif and its variants. Detailed analysis of mouse and human ChIP-Seq at the SWI/SNF subunit loci indicates the presence of MYC binding peaks overlapping with E-boxes. The co-expression correlation and the differential expression analysis of wt vs. MYC perturbed MEFs indicate the MYC dependent regulation of some of the SWI/SNF subunits. The extension of the analysis was done on MYC proficient and MYC deficient embryonic fibroblast cell lines, TGR1 and HO15, and in one of the MYC amplified cancer types, Medulloblastoma. A transcriptional regulatory feedback loop between MYC and SWI/SNF could be a major factor contributing to the aggressiveness of MYC dependent cancers.
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Affiliation(s)
- Srimari Srikanth
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, India
| | - Srimathy Ramachandran
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, India
| | - Suma Mohan S
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, India.
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27
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Filip D, Mraz M. The role of MYC in the transformation and aggressiveness of ‘indolent’ B-cell malignancies. Leuk Lymphoma 2019; 61:510-524. [DOI: 10.1080/10428194.2019.1675877] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Daniel Filip
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Haematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Haematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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28
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Jiménez-González V, Ogalla-García E, García-Quintanilla M, García-Quintanilla A. Deciphering GRINA/Lifeguard1: Nuclear Location, Ca 2+ Homeostasis and Vesicle Transport. Int J Mol Sci 2019; 20:ijms20164005. [PMID: 31426446 PMCID: PMC6719933 DOI: 10.3390/ijms20164005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/31/2019] [Accepted: 08/12/2019] [Indexed: 01/31/2023] Open
Abstract
The Glutamate Receptor Ionotropic NMDA-Associated Protein 1 (GRINA) belongs to the Lifeguard family and is involved in calcium homeostasis, which governs key processes, such as cell survival or the release of neurotransmitters. GRINA is mainly associated with membranes of the endoplasmic reticulum, Golgi, endosome, and the cell surface, but its presence in the nucleus has not been explained yet. Here we dissect, with the help of different software tools, the potential roles of GRINA in the cell and how they may be altered in diseases, such as schizophrenia or celiac disease. We describe for the first time that the cytoplasmic N-terminal half of GRINA (which spans a Proline-rich domain) contains a potential DNA-binding sequence, in addition to cleavage target sites and probable PY-nuclear localization sequences, that may enable it to be released from the rest of the protein and enter the nucleus under suitable conditions, where it could participate in the transcription, alternative splicing, and mRNA export of a subset of genes likely involved in lipid and sterol synthesis, ribosome biogenesis, or cell cycle progression. To support these findings, we include additional evidence based on an exhaustive review of the literature and our preliminary data of the protein–protein interaction network of GRINA.
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Affiliation(s)
| | - Elena Ogalla-García
- Department of Pharmacology, School of Pharmacy, University of Seville, 41012 Seville, Spain
| | - Meritxell García-Quintanilla
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
| | - Albert García-Quintanilla
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Seville, 41012 Seville, Spain.
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29
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Zirin J, Ni X, Sack LM, Yang-Zhou D, Hu Y, Brathwaite R, Bulyk ML, Elledge SJ, Perrimon N. Interspecies analysis of MYC targets identifies tRNA synthetases as mediators of growth and survival in MYC-overexpressing cells. Proc Natl Acad Sci U S A 2019; 116:14614-14619. [PMID: 31262815 PMCID: PMC6642371 DOI: 10.1073/pnas.1821863116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aberrant MYC oncogene activation is one of the most prevalent characteristics of cancer. By overlapping datasets of Drosophila genes that are insulin-responsive and also regulate nucleolus size, we enriched for Myc target genes required for cellular biosynthesis. Among these, we identified the aminoacyl tRNA synthetases (aaRSs) as essential mediators of Myc growth control in Drosophila and found that their pharmacologic inhibition is sufficient to kill MYC-overexpressing human cells, indicating that aaRS inhibitors might be used to selectively target MYC-driven cancers. We suggest a general principle in which oncogenic increases in cellular biosynthesis sensitize cells to disruption of protein homeostasis.
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Affiliation(s)
- Jonathan Zirin
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Xiaochun Ni
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Laura M Sack
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | | | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | | | - Martha L Bulyk
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
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30
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Kleo K, Dimitrova L, Oker E, Tomaszewski N, Berg E, Taruttis F, Engelmann JC, Schwarzfischer P, Reinders J, Spang R, Gronwald W, Oefner PJ, Hummel M. Identification of ADGRE5 as discriminating MYC target between Burkitt lymphoma and diffuse large B-cell lymphoma. BMC Cancer 2019; 19:322. [PMID: 30953469 PMCID: PMC6451309 DOI: 10.1186/s12885-019-5537-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 03/27/2019] [Indexed: 12/27/2022] Open
Abstract
Background MYC is a heterogeneously expressed transcription factor that plays a multifunctional role in many biological processes such as cell proliferation and differentiation. It is also associated with many types of cancer including the malignant lymphomas. There are two types of aggressive B-cell lymphoma, namely Burkitt lymphoma (BL) and a subgroup of diffuse large cell lymphoma (DLBCL), which both carry MYC translocations and overexpress MYC but both differ significantly in their clinical outcome. In DLBCL, MYC translocations are associated with an aggressive behavior and poor outcome, whereas MYC-positive BL show a superior outcome. Methods To shed light on this phenomenon, we investigated the different modes of actions of MYC in aggressive B-cell lymphoma cell lines subdivided into three groups: (i) MYC-positive BL, (ii) DLBCL with MYC translocation (DLBCLpos) and (iii) DLBCL without MYC translocation (DLBCLneg) for control. In order to identify genome-wide MYC-DNA binding sites a chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) was performed. In addition, ChIP-Seq for H3K4me3 was used for determination of genomic regions accessible for transcriptional activity. These data were supplemented with gene expression data derived from RNA-Seq. Results Bioinformatics integration of all data sets revealed different MYC-binding patterns and transcriptional profiles in MYC-positive BL and DLBCL cell lines indicating different functional roles of MYC for gene regulation in aggressive B-cell lymphomas. Based on this multi-omics analysis we identified ADGRE5 (alias CD97) - a member of the EGF-TM7 subfamily of adhesion G protein-coupled receptors - as a MYC target gene, which is specifically expressed in BL but not in DLBCL regardless of MYC translocation. Conclusion Our study describes a diverse genome-wide MYC-DNA binding pattern in BL and DLBCL cell lines with and without MYC translocations. Furthermore, we identified ADREG5 as a MYC target gene able to discriminate between BL and DLBCL irrespectively of the presence of MYC breaks in DLBCL. Since ADGRE5 plays an important role in tumor cell formation, metastasis and invasion, it might also be instrumental to better understand the different pathobiology of BL and DLBCL and help to explain discrepant clinical characteristics of BL and DLBCL. Electronic supplementary material The online version of this article (10.1186/s12885-019-5537-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karsten Kleo
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, D-10117, Berlin, Germany.
| | - Lora Dimitrova
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, D-10117, Berlin, Germany
| | - Elisabeth Oker
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, D-10117, Berlin, Germany
| | - Nancy Tomaszewski
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, D-10117, Berlin, Germany
| | - Erika Berg
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, D-10117, Berlin, Germany
| | - Franziska Taruttis
- Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, D-93053, Regensburg, Germany
| | - Julia C Engelmann
- Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, D-93053, Regensburg, Germany.,Present address: Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1790, AB, Den Burg, The Netherlands
| | - Philipp Schwarzfischer
- Functional Genomics, Institute of Functional Genomics, University of Regensburg, D-93053, Regensburg, Germany
| | - Jörg Reinders
- Functional Genomics, Institute of Functional Genomics, University of Regensburg, D-93053, Regensburg, Germany
| | - Rainer Spang
- Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, D-93053, Regensburg, Germany
| | - Wolfram Gronwald
- Functional Genomics, Institute of Functional Genomics, University of Regensburg, D-93053, Regensburg, Germany
| | - Peter J Oefner
- Functional Genomics, Institute of Functional Genomics, University of Regensburg, D-93053, Regensburg, Germany
| | - Michael Hummel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, D-10117, Berlin, Germany
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31
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Chen LL, Lin HP, Zhou WJ, He CX, Zhang ZY, Cheng ZL, Song JB, Liu P, Chen XY, Xia YK, Chen XF, Sun RQ, Zhang JY, Sun YP, Song L, Liu BJ, Du RK, Ding C, Lan F, Huang SL, Zhou F, Liu S, Xiong Y, Ye D, Guan KL. SNIP1 Recruits TET2 to Regulate c-MYC Target Genes and Cellular DNA Damage Response. Cell Rep 2018; 25:1485-1500.e4. [PMID: 30404004 PMCID: PMC6317994 DOI: 10.1016/j.celrep.2018.10.028] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 09/21/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022] Open
Abstract
The TET2 DNA dioxygenase regulates gene expression by catalyzing demethylation of 5-methylcytosine, thus epigenetically modulating the genome. TET2 does not contain a sequence-specific DNA-binding domain, and how it is recruited to specific genomic sites is not fully understood. Here we carried out a mammalian two-hybrid screen and identified multiple transcriptional regulators potentially interacting with TET2. The SMAD nuclear interacting protein 1 (SNIP1) physically interacts with TET2 and bridges TET2 to bind several transcription factors, including c-MYC. SNIP1 recruits TET2 to the promoters of c-MYC target genes, including those involved in DNA damage response and cell viability. TET2 protects cells from DNA damage-induced apoptosis dependending on SNIP1. Our observations uncover a mechanism for targeting TET2 to specific promoters through a ternary interaction with a co-activator and many sequence-specific DNA-binding factors. This study also reveals a TET2-SNIP1-c-MYC pathway in mediating DNA damage response, thereby connecting epigenetic control to maintenance of genome stability.
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Affiliation(s)
- Lei-Lei Chen
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Huai-Peng Lin
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Medical College of Xiamen University, Xiamen 361102, China
| | - Wen-Jie Zhou
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chen-Xi He
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhi-Yong Zhang
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhou-Li Cheng
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jun-Bin Song
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Peng Liu
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xin-Yu Chen
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yu-Kun Xia
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xiu-Fei Chen
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ren-Qiang Sun
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jing-Ye Zhang
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yi-Ping Sun
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for National Center for Protein Science (The PHOENIX Center), Beijing, China
| | - Bing-Jie Liu
- Fudan University Shanghai Cancer Center, Key Laboratory of Breast Cancer in Shanghai, Innovation Center for Cell Signaling Network, Cancer Institutes, Fudan University, Shanghai, China
| | - Rui-Kai Du
- Fudan University Shanghai Cancer Center, Key Laboratory of Breast Cancer in Shanghai, Innovation Center for Cell Signaling Network, Cancer Institutes, Fudan University, Shanghai, China
| | - Chen Ding
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for National Center for Protein Science (The PHOENIX Center), Beijing, China
| | - Fei Lan
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Sheng-Lin Huang
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Feng Zhou
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Suling Liu
- Fudan University Shanghai Cancer Center, Key Laboratory of Breast Cancer in Shanghai, Innovation Center for Cell Signaling Network, Cancer Institutes, Fudan University, Shanghai, China
| | - Yue Xiong
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Dan Ye
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Kun-Liang Guan
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
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32
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Zhao M, Joy J, Zhou W, De S, Wood WH, Becker KG, Ji H, Sen R. Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation. PLoS Biol 2018; 16:e2006347. [PMID: 30199532 PMCID: PMC6147668 DOI: 10.1371/journal.pbio.2006347] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 09/20/2018] [Accepted: 08/23/2018] [Indexed: 11/26/2022] Open
Abstract
Transcription factor nuclear factor kappa B (NF-κB) regulates cellular responses to environmental cues. Many stimuli induce NF-κB transiently, making time-dependent transcriptional outputs a fundamental feature of NF-κB activation. Here we show that NF-κB target genes have distinct kinetic patterns in activated B lymphoma cells. By combining RELA binding, RNA polymerase II (Pol II) recruitment, and perturbation of NF-κB activation, we demonstrate that kinetic differences amongst early- and late-activated RELA target genes can be understood based on chromatin configuration prior to cell activation and RELA-dependent priming, respectively. We also identified genes that were repressed by RELA activation and others that responded to RELA-activated transcription factors. Cumulatively, our studies define an NF-κB-responsive inducible gene cascade in activated B cells. The nuclear factor kappa B (NF-κB) family of transcription factors regulates cellular responses to a wide variety of environmental cues. These could be extracellular stimuli that activate cell surface receptors, such as pathogens, or intracellular stress signals such as DNA damage or oxidative stress. In response to these triggers, NF-κB proteins accumulate in the cell nucleus, bind to specific DNA sequences in the genome, and thereby modulate gene transcription. Because of the diversity of signals that activate NF-κB and the ubiquity of this pathway in most cell types, cellular outcomes via NF-κB activation must be finely tuned to respond to the initiating stimulus. One mechanism by which NF-κB-dependent gene expression is regulated is by varying the duration of nuclear NF-κB; some signals lead to persistent nuclear NF-κB, while others lead to transient nuclear NF-κB. Consequently, time dependency of transcriptional responses is a unique signature of the initiating stimulus. Here we probed mechanisms that generate kinetic patterns of NF-κB-dependent gene expression in B lymphoma cells responding to a transient NF-κB-activating stimulus. By genetically manipulating NF-κB induction, we identified direct targets of RELA, a member of the NF-κB family, and provide evidence that kinetic patterns are established by a combination of factors that include the chromatin state of genes prior to cell activation and cofactors that work with RELA.
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Affiliation(s)
- Mingming Zhao
- Gene Regulation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, Maryland, United States of America
| | - Jaimy Joy
- Gene Regulation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, Maryland, United States of America
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Supriyo De
- Gene Expression and Genomics Unit, Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, Maryland, United States of America
| | - William H. Wood
- Gene Expression and Genomics Unit, Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, Maryland, United States of America
| | - Kevin G. Becker
- Gene Expression and Genomics Unit, Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, Maryland, United States of America
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Ranjan Sen
- Gene Regulation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, Maryland, United States of America
- * E-mail:
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33
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Weniger MA, Tiacci E, Schneider S, Arnolds J, Rüschenbaum S, Duppach J, Seifert M, Döring C, Hansmann ML, Küppers R. Human CD30+ B cells represent a unique subset related to Hodgkin lymphoma cells. J Clin Invest 2018; 128:2996-3007. [PMID: 29889102 DOI: 10.1172/jci95993] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 04/17/2018] [Indexed: 01/05/2023] Open
Abstract
Very few B cells in germinal centers (GCs) and extrafollicular (EF) regions of lymph nodes express CD30. Their specific features and relationship to CD30-expressing Hodgkin and Reed/Sternberg (HRS) cells of Hodgkin lymphoma are unclear but highly relevant, because numerous patients with lymphoma are currently treated with an anti-CD30 immunotoxin. We performed a comprehensive analysis of human CD30+ B cells. Phenotypic and IgV gene analyses indicated that CD30+ GC B lymphocytes represent typical GC B cells, and that CD30+ EF B cells are mostly post-GC B cells. The transcriptomes of CD30+ GC and EF B cells largely overlapped, sharing a strong MYC signature, but were strikingly different from conventional GC B cells and memory B and plasma cells, respectively. CD30+ GC B cells represent MYC+ centrocytes redifferentiating into centroblasts; CD30+ EF B cells represent active, proliferating memory B cells. HRS cells shared typical transcriptome patterns with CD30+ B cells, suggesting that they originate from these lymphocytes or acquire their characteristic features during lymphomagenesis. By comparing HRS to normal CD30+ B cells we redefined aberrant and disease-specific features of HRS cells. A remarkable downregulation of genes regulating genomic stability and cytokinesis in HRS cells may explain their genomic instability and multinuclearity.
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Affiliation(s)
| | | | | | - Judith Arnolds
- Department of Otorhinolaryngology, University of Duisburg-Essen, Essen, Germany
| | | | | | - Marc Seifert
- Institute of Cell Biology (Cancer Research), and
| | - Claudia Döring
- Dr. Senckenberg Institute of Pathology, University of Frankfurt/Main, Medical School, Frankfurt, Germany
| | - Martin-Leo Hansmann
- Dr. Senckenberg Institute of Pathology, University of Frankfurt/Main, Medical School, Frankfurt, Germany.,Frankfurt Institute for Advanced Studies, Frankfurt, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), and
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34
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Barros-Silva D, Costa-Pinheiro P, Duarte H, Sousa EJ, Evangelista AF, Graça I, Carneiro I, Martins AT, Oliveira J, Carvalho AL, Marques MM, Henrique R, Jerónimo C. MicroRNA-27a-5p regulation by promoter methylation and MYC signaling in prostate carcinogenesis. Cell Death Dis 2018; 9:167. [PMID: 29415999 PMCID: PMC5833437 DOI: 10.1038/s41419-017-0241-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 12/10/2017] [Accepted: 12/18/2017] [Indexed: 12/14/2022]
Abstract
Upregulation of MYC and miRNAs deregulation are common in prostate cancer (PCa). Overactive MYC may cause miRNAs’ expression deregulation through transcriptional and post-transcriptional mechanisms and epigenetic alterations are also involved in miRNAs dysregulation. Herein, we aimed to elucidate the role of regulatory network between MYC and miRNAs in prostate carcinogenesis. MYC expression was found upregulated in PCa cases and matched precursor lesions. MicroRNA’s microarray analysis of PCa samples with opposed MYC levels identified miRNAs significantly overexpressed in high-MYC PCa. However, validation of miR-27a-5p in primary prostate tissues disclosed downregulation in PCa, instead, correlating with aberrant promoter methylation. In a series of castration-resistant PCa (CRPC) cases, miR-27a-5p was upregulated, along with promoter hypomethylation. MYC and miR-27a-5p expression levels in LNCaP and PC3 cells mirrored those observed in hormone-naíve PCa and CRPC, respectively. ChIP analysis showed that miR-27a-5p expression is only regulated by c-Myc in the absence of aberrant promoter methylation. MiR-27a-5p knockdown in PC3 cells promoted cell growth, whereas miRNA forced expression in LNCaP and stable MYC-knockdown PC3 cells attenuated the malignant phenotype, suggesting a tumor suppressive role for miR-27a-5p. Furthermore, miR-27a-5p upregulation decreased EGFR/Akt1/mTOR signaling. We concluded that miR-27a-5p is positively regulated by MYC, and its silencing due to aberrant promoter methylation occurs early in prostate carcinogenesis, concomitantly with loss of MYC regulatory activity. Our results further suggest that along PCa progression, miR-27a-5p promoter becomes hypomethylated, allowing for MYC to resume its regulatory activity. However, the altered cellular context averts miR-27a-5p from successfully accomplishing its tumor suppressive function at this stage of disease.
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Affiliation(s)
- Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
| | - Pedro Costa-Pinheiro
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Henrique Duarte
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Elsa Joana Sousa
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | | | - Inês Graça
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Isa Carneiro
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
| | - Ana Teresa Martins
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
| | - Jorge Oliveira
- Department of Urology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - André L Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Márcia M Marques
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Barretos School of Health Sciences, Barretos, São Paulo, Brazil
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS)-University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal. .,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS)-University of Porto, Porto, Portugal.
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35
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Schrader A, Meyer K, Walther N, Stolz A, Feist M, Hand E, von Bonin F, Evers M, Kohler C, Shirneshan K, Vockerodt M, Klapper W, Szczepanowski M, Murray PG, Bastians H, Trümper L, Spang R, Kube D. Identification of a new gene regulatory circuit involving B cell receptor activated signaling using a combined analysis of experimental, clinical and global gene expression data. Oncotarget 2018; 7:47061-47081. [PMID: 27166259 PMCID: PMC5216924 DOI: 10.18632/oncotarget.9219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 03/31/2016] [Indexed: 12/12/2022] Open
Abstract
To discover new regulatory pathways in B lymphoma cells, we performed a combined analysis of experimental, clinical and global gene expression data. We identified a specific cluster of genes that was coherently expressed in primary lymphoma samples and suppressed by activation of the B cell receptor (BCR) through αIgM treatment of lymphoma cells in vitro. This gene cluster, which we called BCR.1, includes numerous cell cycle regulators. A reduced expression of BCR.1 genes after BCR activation was observed in different cell lines and also in CD10+ germinal center B cells. We found that BCR activation led to a delayed entry to and progression of mitosis and defects in metaphase. Cytogenetic changes were detected upon long-term αIgM treatment. Furthermore, an inverse correlation of BCR.1 genes with c-Myc co-regulated genes in distinct groups of lymphoma patients was observed. Finally, we showed that the BCR.1 index discriminates activated B cell-like and germinal centre B cell-like diffuse large B cell lymphoma supporting the functional relevance of this new regulatory circuit and the power of guided clustering for biomarker discovery.
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Affiliation(s)
- Alexandra Schrader
- Department of Haematology and Medical Oncology, University Medical Centre of the Georg-August University Göttingen, Göttingen, Germany.,GRK1034 of the Deutsche Forschungsgemeinschaft, Georg-August University Göttingen, Göttingen, Germany.,Department of Anatomy, University Medical Centre of the Georg-August University Göttingen, Göttingen, Germany.,Present address: Laboratory of Lymphocyte Signaling and Oncoproteome, Department I of Internal Medicine, University Hospital Cologne, Center for Integrated Oncology (CIO) Köln-Bonn, Cologne, Germany
| | - Katharina Meyer
- Department of Statistical Bioinformatics, Institute for Functional Genomics, University of Regensburg, Regensburg, Germany.,BMBF-Network HämatoSys, Germany
| | - Neele Walther
- Department of Haematology and Medical Oncology, University Medical Centre of the Georg-August University Göttingen, Göttingen, Germany
| | - Ailine Stolz
- Goettingen Center for Molecular Biosciences (GZMB) and University Medical Center, Institute of Molecular Oncology, Section for Cellular Oncology, Göttingen, Germany
| | - Maren Feist
- Department of Haematology and Medical Oncology, University Medical Centre of the Georg-August University Göttingen, Göttingen, Germany.,BMBF-Network Myc-Sys, Germany
| | - Elisabeth Hand
- Department of Haematology and Medical Oncology, University Medical Centre of the Georg-August University Göttingen, Göttingen, Germany.,BMBF-Network HämatoSys, Germany
| | - Frederike von Bonin
- Department of Haematology and Medical Oncology, University Medical Centre of the Georg-August University Göttingen, Göttingen, Germany
| | - Maurits Evers
- Department of Statistical Bioinformatics, Institute for Functional Genomics, University of Regensburg, Regensburg, Germany.,BMBF-Network HämatoSys, Germany.,Current address: The John Curtin School of Medical Research the Australian National University Canberra, Australia
| | - Christian Kohler
- Department of Statistical Bioinformatics, Institute for Functional Genomics, University of Regensburg, Regensburg, Germany.,BMBF-Network HämatoSys, Germany
| | - Katayoon Shirneshan
- Department of Haematology and Medical Oncology, University Medical Centre of the Georg-August University Göttingen, Göttingen, Germany
| | - Martina Vockerodt
- Network Molecular Mechanism of Malignant Lymphoma (MMML) of the Deutsche Krebshilfe, Germany.,School of Cancer Sciences, University of Birmingham, Birmingham, UK.,Department of Anatomy, University Medical Centre of the Georg-August University Göttingen, Göttingen, Germany.,Present address: Department of Anatomy, University Medical Centre of the Georg-August University Göttingen, Göttingen, Germany
| | - Wolfram Klapper
- Network Molecular Mechanism of Malignant Lymphoma (MMML) of the Deutsche Krebshilfe, Germany.,BMBF-Network HämatoSys, Germany.,BMBF-Network Myc-Sys, Germany.,University-Hospital Schleswig-Holstein, Hematopathology Section and Lymph Node Registry Kiel, Kiel, Germany
| | - Monika Szczepanowski
- Network Molecular Mechanism of Malignant Lymphoma (MMML) of the Deutsche Krebshilfe, Germany.,BMBF-Network HämatoSys, Germany.,BMBF-Network Myc-Sys, Germany.,University-Hospital Schleswig-Holstein, Hematopathology Section and Lymph Node Registry Kiel, Kiel, Germany
| | - Paul G Murray
- School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | - Holger Bastians
- Goettingen Center for Molecular Biosciences (GZMB) and University Medical Center, Institute of Molecular Oncology, Section for Cellular Oncology, Göttingen, Germany
| | - Lorenz Trümper
- Department of Haematology and Medical Oncology, University Medical Centre of the Georg-August University Göttingen, Göttingen, Germany.,GRK1034 of the Deutsche Forschungsgemeinschaft, Georg-August University Göttingen, Göttingen, Germany.,Network Molecular Mechanism of Malignant Lymphoma (MMML) of the Deutsche Krebshilfe, Germany.,BMBF-Network Myc-Sys, Germany
| | - Rainer Spang
- Department of Statistical Bioinformatics, Institute for Functional Genomics, University of Regensburg, Regensburg, Germany.,Network Molecular Mechanism of Malignant Lymphoma (MMML) of the Deutsche Krebshilfe, Germany.,BMBF-Network HämatoSys, Germany.,BMBF-Network Myc-Sys, Germany
| | - Dieter Kube
- Department of Haematology and Medical Oncology, University Medical Centre of the Georg-August University Göttingen, Göttingen, Germany.,GRK1034 of the Deutsche Forschungsgemeinschaft, Georg-August University Göttingen, Göttingen, Germany.,Network Molecular Mechanism of Malignant Lymphoma (MMML) of the Deutsche Krebshilfe, Germany.,BMBF-Network HämatoSys, Germany.,BMBF-Network Myc-Sys, Germany
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36
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Kühl I, Miranda M, Atanassov I, Kuznetsova I, Hinze Y, Mourier A, Filipovska A, Larsson NG. Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals. eLife 2017; 6:30952. [PMID: 29132502 PMCID: PMC5703644 DOI: 10.7554/elife.30952] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/06/2017] [Indexed: 12/28/2022] Open
Abstract
Dysfunction of the oxidative phosphorylation (OXPHOS) system is a major cause of human disease and the cellular consequences are highly complex. Here, we present comparative analyses of mitochondrial proteomes, cellular transcriptomes and targeted metabolomics of five knockout mouse strains deficient in essential factors required for mitochondrial DNA gene expression, leading to OXPHOS dysfunction. Moreover, we describe sequential protein changes during post-natal development and progressive OXPHOS dysfunction in time course analyses in control mice and a middle lifespan knockout, respectively. Very unexpectedly, we identify a new response pathway to OXPHOS dysfunction in which the intra-mitochondrial synthesis of coenzyme Q (ubiquinone, Q) and Q levels are profoundly decreased, pointing towards novel possibilities for therapy. Our extensive omics analyses provide a high-quality resource of altered gene expression patterns under severe OXPHOS deficiency comparing several mouse models, that will deepen our understanding, open avenues for research and provide an important reference for diagnosis and treatment.
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Affiliation(s)
- Inge Kühl
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Department of Cell Biology, Institute of Integrative Biology of the Cell (I2BC) UMR9198, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Maria Miranda
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Ilian Atanassov
- Proteomics Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Irina Kuznetsova
- Harry Perkins Institute of Medical Research, The University of Western Australia, Nedlands, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, Australia
| | - Yvonne Hinze
- Proteomics Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Arnaud Mourier
- The Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, Bordeaux, France
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, The University of Western Australia, Nedlands, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, Australia
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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37
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LMO2-negative Expression Predicts the Presence of MYC Translocations in Aggressive B-Cell Lymphomas. Am J Surg Pathol 2017; 41:877-886. [PMID: 28288039 DOI: 10.1097/pas.0000000000000839] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
MYC translocation is a defining feature of Burkitt lymphoma (BL), and the new category of high-grade B-cell lymphomas with MYC and BCL2 and/or BCL6 translocations, and occurs in 6% to 15% of diffuse large B-cell lymphomas (DLBCLs). The low incidence of MYC translocations in DLBCL makes the genetic study of all these lymphomas cumbersome. Strategies based on an initial immunophenotypic screening to select cases with a high probability of carrying the translocation may be useful. LMO2 is a germinal center marker expressed in most lymphomas originated in these cells. Mining gene expression profiling studies, we observed LMO2 downregulation in BL and large B-cell lymphoma (LBCL) with MYC translocations, and postulated that LMO2 protein expression could assist to identify such cases. We analyzed LMO2 protein expression in 46 BLs and 284 LBCL. LMO2 was expressed in 1/46 (2%) BL cases, 146/268 (54.5%) DLBCL cases, and 2/16 (12.5%) high-grade B-cell lymphoma cases with MYC and BCL2 and/or BCL6 translocations. All BLs carried MYC translocation (P<0.001), whereas LMO2 was only positive in 6/42 (14%) LBCL with MYC translocation (P<0.001). The relationship between LMO2 negativity and MYC translocation was further analyzed in different subsets of tumors according to CD10 expression and cell of origin. Lack of LMO2 expression was associated with the detection of MYC translocations with high sensitivity (87%), specificity (87%), positive predictive value and negative predictive value (74% and 94%, respectively), and accuracy (87%) in CD10 LBCL. Comparing LMO2 and MYC protein expression, all statistic measures of performance of LMO2 surpassed MYC in CD10 LBCL. These findings suggest that LMO2 loss may be a good predictor for the presence of MYC translocation in CD10 LBCL.
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38
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Vergara D, Stanca E, Guerra F, Priore P, Gaballo A, Franck J, Simeone P, Trerotola M, De Domenico S, Fournier I, Bucci C, Salzet M, Giudetti AM, Maffia M. β-Catenin Knockdown Affects Mitochondrial Biogenesis and Lipid Metabolism in Breast Cancer Cells. Front Physiol 2017; 8:544. [PMID: 28798698 PMCID: PMC5529387 DOI: 10.3389/fphys.2017.00544] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/12/2017] [Indexed: 12/27/2022] Open
Abstract
β-catenin plays an important role as regulatory hub in several cellular processes including cell adhesion, metabolism, and epithelial mesenchymal transition. This is mainly achieved by its dual role as structural component of cadherin-based adherens junctions, and as a key nuclear effector of the Wnt pathway. For this dual role, different classes of proteins are differentially regulated via β-catenin dependent mechanisms. Here, we applied a liquid chromatography-mass spectrometry (LC-MS/MS) approach to identify proteins modulated after β-catenin knockdown in the breast cancer cell line MCF-7. We used a label free analysis to compare trypsin-digested proteins from CTR (shCTR) and β-catenin knockout cells (shβcat). This led to the identification of 98 differentially expressed proteins, 53 of them were up-regulated and 45 down-regulated. Loss of β-catenin induced morphological changes and a significant modulation of the expression levels of proteins associated with primary metabolic processes. In detail, proteins involved in carbohydrate metabolism and tricarboxylic acid cycle were found to be down-regulated, whereas proteins associated to lipid metabolism were found up-regulated in shβcat compared to shCTR. A loss of mitochondrial mass and membrane potential was also assessed by fluorescent probes in shβcat cells with respect to the controls. These data are consistent with the reduced expression of transcriptional factors regulating mitochondrial biogenesis detected in shβcat cells. β-catenin driven metabolic reprogramming resulted also in a significant modulation of lipogenic enzyme expression and activity. Compared to controls, β-catenin knockout cells showed increased incorporation of [1-14C]acetate and decreased utilization of [U-14C]glucose for fatty acid synthesis. Our data highlight a role of β-catenin in the regulation of metabolism and energy homeostasis in breast cancer cells.
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Affiliation(s)
- Daniele Vergara
- Department of Biological and Environmental Sciences and Technologies, University of SalentoLecce, Italy.,Laboratory of Clinical Proteomic, "Giovanni Paolo II" HospitalLecce, Italy
| | - Eleonora Stanca
- Department of Biological and Environmental Sciences and Technologies, University of SalentoLecce, Italy.,Laboratory of Clinical Proteomic, "Giovanni Paolo II" HospitalLecce, Italy
| | - Flora Guerra
- Department of Biological and Environmental Sciences and Technologies, University of SalentoLecce, Italy
| | - Paola Priore
- CNR NANOTEC - Institute of NanotechnologyLecce, Italy
| | | | - Julien Franck
- University of Lille, Institut national de la santé et de la recherche médicale, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISMLille, France
| | - Pasquale Simeone
- Unit of Cytomorphology, CeSI-MeT and Department of Medicine and Aging Sciences, School of Medicine and Health Sciences, University "G. d'Annunzio"Chieti, Italy
| | - Marco Trerotola
- Unit of Cancer Pathology, CeSI-MeT and Department of Medical, Oral and Biotechnological Sciences, University "G. d'Annunzio"Chieti, Italy
| | | | - Isabelle Fournier
- University of Lille, Institut national de la santé et de la recherche médicale, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISMLille, France
| | - Cecilia Bucci
- Department of Biological and Environmental Sciences and Technologies, University of SalentoLecce, Italy
| | - Michel Salzet
- University of Lille, Institut national de la santé et de la recherche médicale, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISMLille, France
| | - Anna M Giudetti
- Department of Biological and Environmental Sciences and Technologies, University of SalentoLecce, Italy
| | - Michele Maffia
- Department of Biological and Environmental Sciences and Technologies, University of SalentoLecce, Italy.,Laboratory of Clinical Proteomic, "Giovanni Paolo II" HospitalLecce, Italy
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39
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Lollies A, Hartmann S, Schneider M, Bracht T, Weiß AL, Arnolds J, Klein-Hitpass L, Sitek B, Hansmann ML, Küppers R, Weniger MA. An oncogenic axis of STAT-mediated BATF3 upregulation causing MYC activity in classical Hodgkin lymphoma and anaplastic large cell lymphoma. Leukemia 2017; 32:92-101. [PMID: 28659618 DOI: 10.1038/leu.2017.203] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 06/13/2017] [Accepted: 06/16/2017] [Indexed: 02/07/2023]
Abstract
Classical Hodgkin lymphoma (cHL) and anaplastic large cell lymphoma (ALCL) feature high expression of activator protein-1 (AP-1) transcription factors, which regulate various physiological processes but also promote lymphomagenesis. The AP-1 factor basic leucine zipper transcription factor, ATF-like 3 (BATF3), is highly transcribed in cHL and ALCL; however, its functional importance in lymphomagenesis is unknown. Here we show that proto-typical CD30+ lymphomas, namely cHL (21/30) and primary mediastinal B-cell lymphoma (8/9), but also CD30+ diffuse large B-cell lymphoma (15/20) frequently express BATF3 protein. Mass spectrometry and co-immunoprecipitation established interactions of BATF3 with JUN and JUNB in cHL and ALCL lines. BATF3 knockdown using short hairpin RNAs was toxic for cHL and ALCL lines, reducing their proliferation and survival. We identified MYC as a critical BATF3 target and confirmed binding of BATF3 to the MYC promoter. JAK/STAT signaling regulated BATF3 expression, as chemical JAK2 inhibition reduced and interleukin 13 stimulation induced BATF3 expression in cHL lines. Chromatin immunoprecipitation substantiated a direct regulation of BATF3 by STAT proteins in cHL and ALCL lines. In conclusion, we identified STAT-mediated BATF3 expression that is essential for lymphoma cell survival and promoted MYC activity in cHL and ALCL, hence we recognized a new oncogenic axis in these lymphomas.
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Affiliation(s)
- A Lollies
- Institute of Cell Biology (Cancer Research), Faculty of Medicine, University of Duisburg-Essen, Essen, Germany
| | - S Hartmann
- Dr Senckenberg Institute of Pathology, Goethe-University of Frankfurt, Medical School, Frankfurt, Germany
| | - M Schneider
- Institute of Cell Biology (Cancer Research), Faculty of Medicine, University of Duisburg-Essen, Essen, Germany.,Dr Senckenberg Institute of Pathology, Goethe-University of Frankfurt, Medical School, Frankfurt, Germany
| | - T Bracht
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
| | - A L Weiß
- Institute of Cell Biology (Cancer Research), Faculty of Medicine, University of Duisburg-Essen, Essen, Germany
| | - J Arnolds
- Department of Otorhinolaryngology, Faculty of Medicine, University of Duisburg-Essen, Essen, Germany
| | - L Klein-Hitpass
- Institute of Cell Biology (Cancer Research), Faculty of Medicine, University of Duisburg-Essen, Essen, Germany
| | - B Sitek
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
| | - M-L Hansmann
- Dr Senckenberg Institute of Pathology, Goethe-University of Frankfurt, Medical School, Frankfurt, Germany
| | - R Küppers
- Institute of Cell Biology (Cancer Research), Faculty of Medicine, University of Duisburg-Essen, Essen, Germany
| | - M A Weniger
- Institute of Cell Biology (Cancer Research), Faculty of Medicine, University of Duisburg-Essen, Essen, Germany
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40
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Xiong X, Zhang Y, Yan J, Jain S, Chee S, Ren B, Zhao H. A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis. ACS Synth Biol 2017; 6:1034-1042. [PMID: 28215080 DOI: 10.1021/acssynbio.6b00358] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Eukaryotic transcriptional factors (TFs) typically recognize short genomic sequences alone or together with other proteins to modulate gene expression. Mapping of TF-DNA interactions in the genome is crucial for understanding the gene regulatory programs in cells. While chromatin immunoprecipitation followed by sequencing (ChIP-Seq) is commonly used for this purpose, its application is severely limited by the availability of suitable antibodies for TFs. To overcome this limitation, we developed an efficient and scalable strategy named cmChIP-Seq that combines the clustered regularly interspaced short palindromic repeats (CRISPR) technology with microhomology mediated end joining (MMEJ) to genetically engineer a TF with an epitope tag. We demonstrated the utility of this tool by applying it to four TFs in a human colorectal cancer cell line. The highly scalable procedure makes this strategy ideal for ChIP-Seq analysis of TFs in diverse species and cell types.
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Affiliation(s)
- Xiong Xiong
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jian Yan
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Surbhi Jain
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Sora Chee
- Department
of Cellular and Molecular Medicine, Institute of Genome Medicine,
Moores Cancer Center, University of California San Diego, School of Medicine, San Diego, California 92093, United States
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Cellular and Molecular Medicine, Institute of Genome Medicine,
Moores Cancer Center, University of California San Diego, School of Medicine, San Diego, California 92093, United States
| | - Huimin Zhao
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Departments
of Chemistry and Bioengineering, Carl R. Woese Institute for Genomic
Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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41
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Wang T, Lu Y, Polk A, Chowdhury P, Murga-Zamalloa C, Fujiwara H, Suemori K, Beyersdorf N, Hristov AC, Lim MS, Bailey NG, Wilcox RA. T-cell Receptor Signaling Activates an ITK/NF-κB/GATA-3 axis in T-cell Lymphomas Facilitating Resistance to Chemotherapy. Clin Cancer Res 2016; 23:2506-2515. [PMID: 27780854 DOI: 10.1158/1078-0432.ccr-16-1996] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/16/2016] [Accepted: 10/11/2016] [Indexed: 12/11/2022]
Abstract
Purpose: T-cell lymphomas are a molecularly heterogeneous group of non-Hodgkin lymphomas (NHL) that account for a disproportionate number of NHL disease-related deaths due to their inherent and acquired resistance to standard multiagent chemotherapy regimens. Despite their molecular heterogeneity and frequent loss of various T cell-specific receptors, the T-cell antigen receptor is retained in the majority of these lymphomas. As T-cell receptor (TCR) engagement activates a number of signaling pathways and transcription factors that regulate T-cell growth and survival, we examined the TCR's role in mediating resistance to chemotherapy.Experimental Design: Genetic and pharmacologic strategies were utilized to determine the contribution of tyrosine kinases and transcription factors activated in conventional T cells following TCR engagement in acquired chemotherapy resistance in primary T-cell lymphoma cells and patient-derived cell lines.Results: Here, we report that TCR signaling activates a signaling axis that includes ITK, NF-κB, and GATA-3 and promotes chemotherapy resistance.Conclusions: These observations have significant therapeutic implications, as pharmacologic inhibition of ITK prevented the activation of this signaling axis and overcame chemotherapy resistance. Clin Cancer Res; 23(10); 2506-15. ©2016 AACR.
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MESH Headings
- Adenine/analogs & derivatives
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/immunology
- GATA3 Transcription Factor/genetics
- GATA3 Transcription Factor/immunology
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Lymphoma, Non-Hodgkin/drug therapy
- Lymphoma, Non-Hodgkin/genetics
- Lymphoma, Non-Hodgkin/immunology
- Lymphoma, T-Cell/drug therapy
- Lymphoma, T-Cell/genetics
- Lymphoma, T-Cell/immunology
- NF-kappa B/genetics
- NF-kappa B/immunology
- Piperidines
- Primary Cell Culture
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Protein-Tyrosine Kinases/immunology
- Pyrazoles/administration & dosage
- Pyrimidines/administration & dosage
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Signal Transduction/drug effects
- T-Lymphocytes/immunology
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Affiliation(s)
- Tianjiao Wang
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Ye Lu
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Avery Polk
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Pinki Chowdhury
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Carlos Murga-Zamalloa
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Hiroshi Fujiwara
- Department of Hematology, Clinical Immunology and Infectious Disease, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Koichiro Suemori
- Department of Hematology, Clinical Immunology and Infectious Disease, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Niklas Beyersdorf
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Alexandra C Hristov
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan
| | - Megan S Lim
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nathanael G Bailey
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ryan A Wilcox
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan.
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42
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Compensatory RNA polymerase 2 loading determines the efficacy and transcriptional selectivity of JQ1 in Myc-driven tumors. Leukemia 2016; 31:479-490. [PMID: 27443262 PMCID: PMC5310924 DOI: 10.1038/leu.2016.182] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/18/2016] [Accepted: 06/10/2016] [Indexed: 12/15/2022]
Abstract
Inhibition of bromodomain and extraterminal motif (BET) proteins such as BRD4 bears great promise for cancer treatment and its efficacy has been frequently attributed to Myc downregulation. Here, we use B-cell tumors as a model to address the mechanism of action of JQ1, a widely used BET inhibitor. Although JQ1 led to widespread eviction of BRD4 from chromatin, its effect on gene transcription was limited to a restricted set of genes. This was unlinked to Myc downregulation or its chromatin association. Yet, JQ1-sensitive genes were enriched for Myc and E2F targets, were expressed at high levels, and showed high promoter occupancy by RNAPol2, BRD4, Myc and E2F. Their marked decrease in transcriptional elongation upon JQ1 treatment, indicated that BRD4-dependent promoter clearance was rate limiting for transcription. At JQ1-insensitive genes the drop in transcriptional elongation still occurred, but was compensated by enhanced RNAPol2 recruitment. Similar results were obtained with other inhibitors of transcriptional elongation. Thus, the selective transcriptional effects following JQ1 treatment are linked to the inability of JQ1-sensitive genes to sustain compensatory RNAPol2 recruitment to promoters. These observations highlight the role of BET proteins in supporting transcriptional elongation and rationalize how a general suppression of elongation may selectively affects transcription.
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43
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Hartl M. The Quest for Targets Executing MYC-Dependent Cell Transformation. Front Oncol 2016; 6:132. [PMID: 27313991 PMCID: PMC4889588 DOI: 10.3389/fonc.2016.00132] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/20/2016] [Indexed: 12/26/2022] Open
Abstract
MYC represents a transcription factor with oncogenic potential converting multiple cellular signals into a broad transcriptional response, thereby controlling the expression of numerous protein-coding and non-coding RNAs important for cell proliferation, metabolism, differentiation, and apoptosis. Constitutive activation of MYC leads to neoplastic cell transformation, and deregulated MYC alleles are frequently observed in many human cancer cell types. Multiple approaches have been performed to isolate genes differentially expressed in cells containing aberrantly activated MYC proteins leading to the identification of thousands of putative targets. Functional analyses of genes differentially expressed in MYC-transformed cells had revealed that so far more than 40 upregulated or downregulated MYC targets are actively involved in cell transformation or tumorigenesis. However, further systematic and selective approaches are required for determination of the known or yet unidentified targets responsible for processing the oncogenic MYC program. The search for critical targets in MYC-dependent tumor cells is exacerbated by the fact that during tumor development, cancer cells progressively evolve in a multistep process, thereby acquiring their characteristic features in an additive manner. Functional expression cloning, combinatorial gene expression, and appropriate in vivo tests could represent adequate tools for dissecting the complex scenario of MYC-specified cell transformation. In this context, the central goal is to identify a minimal set of targets that suffices to phenocopy oncogenic MYC. Recently developed genomic editing tools could be employed to confirm the requirement of crucial transformation-associated targets. Knowledge about essential MYC-regulated genes is beneficial to expedite the development of specific inhibitors to interfere with growth and viability of human tumor cells in which MYC is aberrantly activated. Approaches based on the principle of synthetic lethality using MYC-overexpressing cancer cells and chemical or RNAi libraries have been employed to search for novel anticancer drugs, also leading to the identification of several druggable targets. Targeting oncogenic MYC effector genes instead of MYC may lead to compounds with higher specificities and less side effects. This class of drugs could also display a wider pharmaceutical window because physiological functions of MYC, which are important for normal cell growth, proliferation, and differentiation would be less impaired.
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Affiliation(s)
- Markus Hartl
- Institute of Biochemistry and Center of Molecular Biosciences (CMBI), University of Innsbruck , Innsbruck , Austria
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44
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Xu-Monette ZY, Deng Q, Manyam GC, Tzankov A, Li L, Xia Y, Wang XX, Zou D, Visco C, Dybkær K, Li J, Zhang L, Liang H, Montes-Moreno S, Chiu A, Orazi A, Zu Y, Bhagat G, Richards KL, Hsi ED, Choi WWL, van Krieken JH, Huh J, Ponzoni M, Ferreri AJM, Parsons BM, Møller MB, Wang SA, Miranda RN, Piris MA, Winter JN, Medeiros LJ, Li Y, Young KH. Clinical and Biologic Significance of MYC Genetic Mutations in De Novo Diffuse Large B-cell Lymphoma. Clin Cancer Res 2016; 22:3593-605. [PMID: 26927665 DOI: 10.1158/1078-0432.ccr-15-2296] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/09/2016] [Indexed: 12/21/2022]
Abstract
PURPOSE MYC is a critical driver oncogene in many cancers, and its deregulation in the forms of translocation and overexpression has been implicated in lymphomagenesis and progression of diffuse large B-cell lymphoma (DLBCL). The MYC mutational profile and its roles in DLBCL are unknown. This study aims to determine the spectrum of MYC mutations in a large group of patients with DLBCL, and to evaluate the clinical significance of MYC mutations in patients with DLBCL treated with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) immunochemotherapy. EXPERIMENTAL DESIGN We identified MYC mutations in 750 patients with DLBCL using Sanger sequencing and evaluated the prognostic significance in 602 R-CHOP-treated patients. RESULTS The frequency of MYC mutations was 33.3% at the DNA level (mutations in either the coding sequence or the untranslated regions) and 16.1% at the protein level (nonsynonymous mutations). Most of the nonsynonymous mutations correlated with better survival outcomes; in contrast, T58 and F138 mutations (which were associated with MYC rearrangements), as well as several mutations occurred at the 3' untranslated region, correlated with significantly worse survival outcomes. However, these mutations occurred infrequently (only in approximately 2% of DLBCL). A germline SNP encoding the Myc-N11S variant (observed in 6.5% of the study cohort) was associated with significantly better patient survival, and resulted in reduced tumorigenecity in mouse xenografts. CONCLUSIONS Various types of MYC gene mutations are present in DLBCL and show different impact on Myc function and clinical outcomes. Unlike MYC gene translocations and overexpression, most MYC gene mutations may not have a role in driving lymphomagenesis. Clin Cancer Res; 22(14); 3593-605. ©2016 AACR.
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Affiliation(s)
- Zijun Y Xu-Monette
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qipan Deng
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio
| | - Ganiraju C Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Ling Li
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yi Xia
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiao-Xiao Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dehui Zou
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Jun Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Li Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - April Chiu
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Attilio Orazi
- Weill Medical College of Cornell University, New York, New York
| | - Youli Zu
- The Methodist Hospital, Houston, Texas
| | - Govind Bhagat
- Columbia University Medical Center and New York Presbyterian Hospital, New York, New York
| | - Kristy L Richards
- University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | | | - William W L Choi
- University of Hong Kong Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - J Han van Krieken
- Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Jooryung Huh
- Asan Medical Center, Ulsan University College of Medicine, Seoul, Korea
| | | | | | - Ben M Parsons
- Gundersen Lutheran Health System, La Crosse, Wisconsin
| | | | - Sa A Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roberto N Miranda
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Miguel A Piris
- Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Jane N Winter
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yong Li
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio.
| | - Ken H Young
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas. The University of Texas School of Medicine, Graduate School of Biomedical Sciences, Houston, Texas.
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Aughey GN, Grice SJ, Liu JL. The Interplay between Myc and CTP Synthase in Drosophila. PLoS Genet 2016; 12:e1005867. [PMID: 26889675 PMCID: PMC4759343 DOI: 10.1371/journal.pgen.1005867] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/23/2016] [Indexed: 01/24/2023] Open
Abstract
CTP synthase (CTPsyn) is essential for the biosynthesis of pyrimidine nucleotides. It has been shown that CTPsyn is incorporated into a novel cytoplasmic structure which has been termed the cytoophidium. Here, we report that Myc regulates cytoophidium formation during Drosophila oogenesis. We have found that Myc protein levels correlate with cytoophidium abundance in follicle epithelia. Reducing Myc levels results in cytoophidium loss and small nuclear size in follicle cells, while overexpression of Myc increases the length of cytoophidia and the nuclear size of follicle cells. Ectopic expression of Myc induces cytoophidium formation in late stage follicle cells. Furthermore, knock-down of CTPsyn is sufficient to suppress the overgrowth phenotype induced by Myc overexpression, suggesting CTPsyn acts downstream of Myc and is required for Myc-mediated cell size control. Taken together, our data suggest a functional link between Myc, a renowned oncogene, and the essential nucleotide biosynthetic enzyme CTPsyn. The coordination of metabolism with cell growth is critical for regulation of organismal development. Therefore there is significant interplay between metabolic enzymes and key developmental regulators such as transcription factors. The enzyme CTP synthase (CTPsyn) is essential for metabolic homeostasis as well as growth and development, due to its role in synthesising precursors for many fundamental cellular macromolecules such as RNA and lipids. However, the mechanisms by which CTPsyn is regulated during development are little understood. Here we have shown that Myc, an oncogene and a key developmental regulator, is necessary and sufficient for the assembly of CTPsyn-containing macrostructures termed cytoophidia. We show that the presence of CTPsyn is required for Myc to mediate its effect on cell growth during Drosophila oogenesis. Roles for CTPsyn and Myc in tumourigenesis have been well established and both proteins have been considered promising therapeutic targets. By better understanding the relationship between these two proteins, we can gain important insights, not only into tumour pathology and aetiology, but also metazoan developmental processes.
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Affiliation(s)
- Gabriel N. Aughey
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Stuart J. Grice
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Ji-Long Liu
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Functional transcription factor target discovery via compendia of binding and expression profiles. Sci Rep 2016; 6:20649. [PMID: 26857150 PMCID: PMC4746627 DOI: 10.1038/srep20649] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/07/2016] [Indexed: 12/21/2022] Open
Abstract
Genome-wide experiments to map the DNA-binding locations of transcription-associated factors (TFs) have shown that the number of genes bound by a TF far exceeds the number of possible direct target genes. Distinguishing functional from non-functional binding is therefore a major challenge in the study of transcriptional regulation. We hypothesized that functional targets can be discovered by correlating binding and expression profiles across multiple experimental conditions. To test this hypothesis, we obtained ChIP-seq and RNA-seq data from matching cell types from the human ENCODE resource, considered promoter-proximal and distal cumulative regulatory models to map binding sites to genes, and used a combination of linear and non-linear measures to correlate binding and expression data. We found that a high degree of correlation between a gene’s TF-binding and expression profiles was significantly more predictive of the gene being differentially expressed upon knockdown of that TF, compared to using binding sites in the cell type of interest only. Remarkably, TF targets predicted from correlation across a compendium of cell types were also predictive of functional targets in other cell types. Finally, correlation across a time course of ChIP-seq and RNA-seq experiments was also predictive of functional TF targets in that tissue.
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Kin K, Chen X, Gonzalez-Garay M, Fakhouri WD. The effect of non-coding DNA variations on P53 and cMYC competitive inhibition at cis-overlapping motifs. Hum Mol Genet 2016; 25:1517-27. [PMID: 26908612 DOI: 10.1093/hmg/ddw030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/01/2016] [Indexed: 01/22/2023] Open
Abstract
Non-coding DNA variations play a critical role in increasing the risk for development of common complex diseases, and account for the majority of SNPs highly associated with cancer. However, it remains a challenge to identify etiologic variants and to predict their pathological effects on target gene expression for clinical purposes. Cis-overlapping motifs (COMs) are elements of enhancer regions that impact gene expression by enabling competitive binding and switching between transcription factors. Mutations within COMs are especially important when the involved transcription factors have opposing effects on gene regulation, like P53 tumor suppressor and cMYC proto-oncogene. In this study, genome-wide analysis of ChIP-seq data from human cancer and mouse embryonic cells identified a significant number of putative regulatory elements with signals for both P53 and cMYC. Each co-occupied element contains, on average, two COMs, and one common SNP every two COMs. Gene ontology of predicted target genes for COMs showed that the majority are involved in DNA damage, apoptosis, cell cycle regulation, and RNA processing. EMSA results showed that both cMYC and P53 bind to cis-overlapping motifs within a ChIP-seq co-occupied region in Chr12. In vitro functional analysis of selected co-occupied elements verified enhancer activity, and also showed that the occurrence of SNPs within three COMs significantly altered enhancer activity. We identified a list of COM-associated functional SNPs that are in close proximity to SNPs associated with common diseases in large population studies. These results suggest a potential molecular mechanism to identify etiologic regulatory mutations associated with common diseases.
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Affiliation(s)
- Katherine Kin
- Department of Diagnostic and Biomedical Sciences, Center for Craniofacial Research, University of Texas Health Science Center at Houston School of Dentistry, Houston, TX 77054, USA and
| | - Xi Chen
- Department of Diagnostic and Biomedical Sciences, Center for Craniofacial Research, University of Texas Health Science Center at Houston School of Dentistry, Houston, TX 77054, USA and
| | - Manuel Gonzalez-Garay
- Center for Molecular Imaging, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Walid D Fakhouri
- Department of Diagnostic and Biomedical Sciences, Center for Craniofacial Research, University of Texas Health Science Center at Houston School of Dentistry, Houston, TX 77054, USA and
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48
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BPTF is required for c-MYC transcriptional activity and in vivo tumorigenesis. Nat Commun 2016; 7:10153. [PMID: 26729287 PMCID: PMC4728380 DOI: 10.1038/ncomms10153] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 11/06/2015] [Indexed: 01/06/2023] Open
Abstract
c-MYC oncogene is deregulated in most human tumours. Histone marks associated with transcriptionally active genes define high-affinity c-MYC targets. The mechanisms involved in their recognition by c-MYC are unknown. Here we report that c-MYC interacts with BPTF, a core subunit of the NURF chromatin-remodelling complex. BPTF is required for the activation of the full c-MYC transcriptional programme in fibroblasts. BPTF knockdown leads to decreased c-MYC recruitment to DNA and changes in chromatin accessibility. In Bptf-null MEFs, BPTF is necessary for c-MYC-driven proliferation, G1–S progression and replication stress, but not for c-MYC-driven apoptosis. Bioinformatics analyses unveil that BPTF levels correlate positively with c-MYC-driven transcriptional signatures. In vivo, Bptf inactivation in pre-neoplastic pancreatic acinar cells significantly delays tumour development and extends survival. Our findings uncover BPTF as a crucial c-MYC co-factor required for its biological activity and suggest that the BPTF-c-MYC axis is a potential therapeutic target in cancer. c-MYC genomic distribution is dictated by the epigenetic context but the mechanisms are unknown. Here, the authors show that c-MYC requires the chromatin reader BPTF to activate its transcriptional program and promote tumour development in vivo, suggesting that BPTF is a potential target for cancer therapy.
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Kreuz S, Holmes KB, Tooze RM, Lefevre PF. Loss of PIM2 enhances the anti-proliferative effect of the pan-PIM kinase inhibitor AZD1208 in non-Hodgkin lymphomas. Mol Cancer 2015; 14:205. [PMID: 26643319 PMCID: PMC4672512 DOI: 10.1186/s12943-015-0477-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/02/2015] [Indexed: 12/25/2022] Open
Abstract
Background A promising therapeutic approach for aggressive B-cell Non-Hodgkin lymphoma (NHL), including diffuse large B-cell lymphoma (DLBCL), and Burkitt lymphoma (BL) is to target kinases involved in signal transduction and gene regulation. PIM1/2 serine/threonine kinases are highly expressed in activated B-cell-like DLBCL (ABC-DLBCL) with poor prognosis. In addition, both PIM kinases have a reported synergistic effect with c-MYC in mediating tumour development in several cancers, c-MYC gene being translocated to one of the immunoglobulin loci in nearly all BLs. Methods For these reasons, we tested the efficiency of several PIM kinase inhibitors (AZD1208, SMI4a, PIM1/2 inhibitor VI and Quercetagetin) in preventing proliferation of aggressive NHL-derived cell lines and compared their efficiency with PIM1 and/or PIM2 knockdown. Results We observed that most of the anti-proliferative potential of these inhibitors in NHL was due to an off-target effect. Interestingly, we present evidence of a kinase-independent function of PIM2 in regulating cell cycle. Moreover, combining AZD1208 treatment and PIM2 knockdown additively repressed cell proliferation. Conclusion Taken together, this study suggests that at least a part of PIM1/2 oncogenic potential could be independent of their kinase activity, justifying the limited anti-tumorigenic outcome of PIM-kinase inhibitors in NHL. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0477-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- S Kreuz
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, The Wellcome Trust Brenner Building, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - K B Holmes
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, The Wellcome Trust Brenner Building, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - R M Tooze
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, The Wellcome Trust Brenner Building, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - P F Lefevre
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, The Wellcome Trust Brenner Building, St. James's University Hospital, Leeds, LS9 7TF, UK.
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50
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Cai Q, Medeiros LJ, Xu X, Young KH. MYC-driven aggressive B-cell lymphomas: biology, entity, differential diagnosis and clinical management. Oncotarget 2015; 6:38591-616. [PMID: 26416427 PMCID: PMC4770723 DOI: 10.18632/oncotarget.5774] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 09/04/2015] [Indexed: 01/09/2023] Open
Abstract
MYC, a potent oncogene located at chromosome locus 8q24.21, was identified initially by its involvement in Burkitt lymphoma with t(8;14)(q24;q32). MYC encodes a helix-loop-helix transcription factor that accentuates many cellular functions including proliferation, growth and apoptosis. MYC alterations also have been identified in other mature B-cell neoplasms and are associated with aggressive clinical behavior. There are several regulatory factors and dysregulated signaling that lead to MYC up-regulation in B-cell lymphomas. One typical example is the failure of physiological repressors such as Bcl6 or BLIMP1 to suppress MYC over-expression. In addition, MYC alterations are often developed concurrently with other genetic alterations that counteract the proapoptotic function of MYC. In this review, we discuss the physiologic function of MYC and the role that MYC likely plays in the pathogenesis of B-cell lymphomas. We also summarize the role MYC plays in the diagnosis, prognostication and various strategies to detect MYC rearrangement and expression.
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Affiliation(s)
- Qingqing Cai
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - L. Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xiaolu Xu
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Ken H. Young
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- The University of Texas School of Medicine, Graduate School of Biomedical Sciences, Houston, Texas, USA
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