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Deng J, Teng J, Xiao T, Wen J, Meng W. MAD1 deficiency accelerates hepatocellular proliferation via suppressing TGF-β signaling. Heliyon 2024; 10:e31312. [PMID: 38813231 PMCID: PMC11133804 DOI: 10.1016/j.heliyon.2024.e31312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 05/31/2024] Open
Abstract
Numerous researches have reported on the regulatory network of liver regeneration induced by partial hepatectomy (PH). However, information on key molecules and/or signaling pathways regulating the termination stage of liver regeneration remains limited. In this study, we identify hepatic mitotic arrest deficient 1 (MAD1) as a crucial regulator of transforming growth factor β (TGF-β) in the hepatocyte to repress liver regeneration. MAD1 has a low expression level at the rapid proliferation phase but significantly increases at the termination phase of liver regeneration. We show that MAD1 deficiency accelerates hepatocyte proliferation and enhances mitochondrial biogenesis and respiratory. Mechanistically, MAD1 deficiency in hepatocytes enhances mitochondrial function and promotes hepatocyte proliferation by suppressing TGF-β signaling. Our study reveals MAD1 as a novel suppressor of hepatocyte proliferation, which may provide a new therapeutic target for the recovery of liver function after liver transplant and partial hepatectomy.
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Affiliation(s)
- Jiangming Deng
- National Clinical Research Center for Metabolic Diseases and the Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
- The Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
- Departments of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Jianhui Teng
- National Clinical Research Center for Metabolic Diseases and the Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
- The Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Ting Xiao
- The Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
- Department of Hepatology, Hunan Children's Hospital, Changsha, 410000, Hunan, China
| | - Jie Wen
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
| | - Wen Meng
- National Clinical Research Center for Metabolic Diseases and the Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
- The Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
- Departments of Oncology, the Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
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2
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Shi YB, Fu L, Tanizaki Y. Intestinal remodeling during Xenopus metamorphosis as a model for studying thyroid hormone signaling and adult organogenesis. Mol Cell Endocrinol 2024; 586:112193. [PMID: 38401883 PMCID: PMC10999354 DOI: 10.1016/j.mce.2024.112193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024]
Abstract
Intestinal development takes places in two phases, the initial formation of neonatal (mammals)/larval (anurans) intestine and its subsequent maturation into the adult form. This maturation occurs during postembryonic development when plasma thyroid hormone (T3) level peaks. In anurans such as the highly related Xenopus laevis and Xenopus tropicalis, the larval/tadpole intestine is drastically remodeled from a simple tubular structure to a complex, multi-folded adult organ during T3-dependent metamorphosis. This involved complete degeneration of larval epithelium via programmed cell death and de novo formation of adult epithelium, with concurrent maturation of the muscles and connective tissue. Here, we will summarize our current understanding of the underlying molecular mechanisms, with a focus on more recent genetic and genome-wide studies.
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Affiliation(s)
- Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.
| | - Liezhen Fu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Yuta Tanizaki
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
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3
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Sandhya S, Talukdar J, Gogoi G, Dey KS, Das B, Baishya D. Impact of coconut kernel extract on carcinogen-induced skin cancer model: Oxidative stress, C-MYC proto-oncogene and tumor formation. Heliyon 2024; 10:e29385. [PMID: 38665592 PMCID: PMC11043960 DOI: 10.1016/j.heliyon.2024.e29385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/07/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
This study aimed at analysing the effects of coconut (Cocos nucifera L.) kernel extract (CKE) on oxidative stress, C-MYC proto-oncogene, and tumour formation in a skin cancer model. Tumorigenesis was induced by dimethylbenz[a]anthracene (DMBA)/12-O-tetradecanoylphorbol-13-acetate (TPA). In vitro antioxidant activity of CKE was assessed using 2, 2-diphenyl-1-picrylhydrazyl (DPPH), hydrogen peroxide (H2O2), total phenolic and flavonoid content assays. CKE showed a higher antioxidant activity then ascorbic acid (*P < 0.05, ****P < 0.0001). HPLC and NMR study of the CKE revealed the presence of lauric acid (LA). Following the characterization of CKE, mice were randomly assigned to receive DMBA/TPA Induction and CKE treatment at different doses (50, 100, and 200 mg/kg) of body weight. LA 100 mg/kg of body weight used as standard. Significantly, the CKE200 and control groups' mice did not develop tumors; however, the CKE100 and CKE50 treated groups did develop tumors less frequently than the DMBA/TPA-treated mice. Histopathological analysis revealed that the epidermal layer in DMBA-induced mice was thicker and had squamous pearls along with a hyperplasia/dysplasia lesion, indicating skin squamous cell carcinoma (SCC), whereas the epidermal layers in CKE200-treated and control mice were normal. Additionally, the CKE treatment demonstrated a significant stimulatory effect on the activities of reactive oxygen species (ROS), glutathione (GSH), catalase (CAT), and superoxide dismutase (SOD), as well as an inhibitory effect on lipid peroxidase (*P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001) and c-MYC protein expression (*P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001). In conclusion, CKE prevents the growth of tumors on mouse skin by reducing oxidative stress and suppressing c-MYC overexpression brought on by DMBA/TPA induction. This makes it an effective dietary antioxidant with anti-tumor properties.
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Affiliation(s)
- Sorra Sandhya
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam, India
- Department of Cancer and Stem Cell Biology, KaviKrishna Laboratory, Indian Institute of Technology-Guwahati Research Park, Assam, India
| | - Joyeeta Talukdar
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam, India
- Department of Cancer and Stem Cell Biology, KaviKrishna Laboratory, Indian Institute of Technology-Guwahati Research Park, Assam, India
| | - Gayatri Gogoi
- Department of Pathology, Assam Medical College and Hospital (AMCH), Assam, India
| | | | - Bikul Das
- Department of Cancer and Stem Cell Biology, KaviKrishna Laboratory, Indian Institute of Technology-Guwahati Research Park, Assam, India
- Department of Stem Cell and Infection, Thoreau Lab for Global Health, University of Massachusetts, Lowell, MA, USA
| | - Debabrat Baishya
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam, India
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4
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Shukla K, Idanwekhai K, Naradikian M, Ting S, Schoenberger SP, Brunk E. Machine Learning of Three-Dimensional Protein Structures to Predict the Functional Impacts of Genome Variation. J Chem Inf Model 2024. [PMID: 38635316 DOI: 10.1021/acs.jcim.3c01967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Research in the human genome sciences generates a substantial amount of genetic data for hundreds of thousands of individuals, which concomitantly increases the number of variants of unknown significance (VUS). Bioinformatic analyses can successfully reveal rare variants and variants with clear associations with disease-related phenotypes. These studies have had a significant impact on how clinical genetic screens are interpreted and how patients are stratified for treatment. There are few, if any, computational methods for variants comparable to biological activity predictions. To address this gap, we developed a machine learning method that uses protein three-dimensional structures from AlphaFold to predict how a variant will influence changes to a gene's downstream biological pathways. We trained state-of-the-art machine learning classifiers to predict which protein regions will most likely impact transcriptional activities of two proto-oncogenes, nuclear factor erythroid 2 (NFE2L2)-related factor 2 (NRF2) and c-Myc. We have identified classifiers that attain accuracies higher than 80%, which have allowed us to identify a set of key protein regions that lead to significant perturbations in c-Myc or NRF2 transcriptional pathway activities.
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Affiliation(s)
- Kriti Shukla
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
| | - Kelvin Idanwekhai
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
- School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
| | - Martin Naradikian
- La Jolla Institute for Immunology, San Diego, California 92093, United States
| | - Stephanie Ting
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
| | | | - Elizabeth Brunk
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
- Integrative Program for Biological and Genome Sciences (IBGS), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
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5
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Gandhi P, Wang Y, Li G, Wang S. The role of long noncoding RNAs in ocular angiogenesis and vascular oculopathy. Cell Biosci 2024; 14:39. [PMID: 38521951 PMCID: PMC10961000 DOI: 10.1186/s13578-024-01217-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/05/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are RNA transcripts over 200 nucleotides in length that do not code for proteins. Initially considered a genomic mystery, an increasing number of lncRNAs have been shown to have vital roles in physiological and pathological conditions by regulating gene expression through diverse mechanisms depending on their subcellular localization. Dysregulated angiogenesis is responsible for various vascular oculopathies, including diabetic retinopathy, retinopathy of prematurity, age-related macular degeneration, and corneal neovascularization. While anti-VEGF treatment is available, it is not curative, and long-term outcomes are suboptimal, and some patients are unresponsive. To better understand these diseases, researchers have investigated the role of lncRNAs in regulating angiogenesis and models of vascular oculopathies. This review summarizes recent research on lncRNAs in ocular angiogenesis, including the pro-angiogenic lncRNAs ANRIL, HOTAIR, HOTTIP, H19, IPW, MALAT1, MIAT, NEAT1, and TUG1, the anti-angiogenic lncRNAs MEG3 and PKNY, and the human/primate specific lncRNAs lncEGFL7OS, discussing their functions and mechanisms of action in vascular oculopathies.
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Affiliation(s)
- Pranali Gandhi
- Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Yuzhi Wang
- Louisiana State University School of Medicine, New Orleans, LA, 70112, USA
| | - Guigang Li
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei province, P.R. China.
| | - Shusheng Wang
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, 70118, USA.
- Department of Ophthalmology, Tulane University, New Orleans, LA, 70112, USA.
- Tulane Personalized Health Institute, Tulane University, New Orleans, LA, 70112, USA.
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6
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Venkatraman S, Balasubramanian B, Thuwajit C, Meller J, Tohtong R, Chutipongtanate S. Targeting MYC at the intersection between cancer metabolism and oncoimmunology. Front Immunol 2024; 15:1324045. [PMID: 38390324 PMCID: PMC10881682 DOI: 10.3389/fimmu.2024.1324045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
MYC activation is a known hallmark of cancer as it governs the gene targets involved in various facets of cancer progression. Of interest, MYC governs oncometabolism through the interactions with its partners and cofactors, as well as cancer immunity via its gene targets. Recent investigations have taken interest in characterizing these interactions through multi-Omic approaches, to better understand the vastness of the MYC network. Of the several gene targets of MYC involved in either oncometabolism or oncoimmunology, few of them overlap in function. Prominent interactions have been observed with MYC and HIF-1α, in promoting glucose and glutamine metabolism and activation of antigen presentation on regulatory T cells, and its subsequent metabolic reprogramming. This review explores existing knowledge of the role of MYC in oncometabolism and oncoimmunology. It also unravels how MYC governs transcription and influences cellular metabolism to facilitate the induction of pro- or anti-tumoral immunity. Moreover, considering the significant roles MYC holds in cancer development, the present study discusses effective direct or indirect therapeutic strategies to combat MYC-driven cancer progression.
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Affiliation(s)
- Simran Venkatraman
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Brinda Balasubramanian
- Division of Cancer and Stem Cells, Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jaroslaw Meller
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Rutaiwan Tohtong
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Somchai Chutipongtanate
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Milk, microbiome, Immunity and Lactation research for Child Health (MILCH) and Novel Therapeutics Lab, Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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7
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Lu Y, Berenson A, Lane R, Guelin I, Li Z, Chen Y, Shah S, Yin M, Soto-Ugaldi LF, Fiszbein A, Fuxman Bass JI. A large-scale cancer-specific protein-DNA interaction network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577099. [PMID: 38352498 PMCID: PMC10862707 DOI: 10.1101/2024.01.24.577099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Cancer development and progression are generally associated with dysregulation of gene expression, often resulting from changes in transcription factor (TF) sequence or expression. Identifying key TFs involved in cancer gene regulation provides a framework for potential new therapeutics. This study presents a large-scale cancer gene TF-DNA interaction network as well as an extensive promoter clone resource for future studies. Most highly connected TFs do not show a preference for binding to promoters of genes associated with either good or poor cancer prognosis, suggesting that emerging strategies aimed at shifting gene expression balance between these two prognostic groups may be inherently complex. However, we identified potential for oncogene targeted therapeutics, with half of the tested oncogenes being potentially repressed by influencing specific activator or bifunctional TFs. Finally, we investigate the role of intrinsically disordered regions within the key cancer-related TF estrogen receptor ɑ (ESR1) on DNA binding and transcriptional activity, and found that these regions can have complex trade-offs in TF function. Altogether, our study not only broadens our knowledge of TFs involved in the cancer gene regulatory network but also provides a valuable resource for future studies, laying a foundation for potential therapeutic strategies targeting TFs in cancer.
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Affiliation(s)
- Yunwei Lu
- Biology Department, Boston University, Boston, MA, 02215, USA
| | - Anna Berenson
- Biology Department, Boston University, Boston, MA, 02215, USA
- Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, 02215, USA
| | - Ryan Lane
- Biology Department, Boston University, Boston, MA, 02215, USA
| | - Isabelle Guelin
- Biology Department, Boston University, Boston, MA, 02215, USA
| | - Zhaorong Li
- Bioinformatics Program, Boston University, Boston, MA, 02215, USA
| | - Yilin Chen
- Biology Department, Boston University, Boston, MA, 02215, USA
| | - Sakshi Shah
- Biology Department, Boston University, Boston, MA, 02215, USA
| | - Meimei Yin
- Biology Department, Boston University, Boston, MA, 02215, USA
| | | | - Ana Fiszbein
- Biology Department, Boston University, Boston, MA, 02215, USA
- Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, 02215, USA
- Bioinformatics Program, Boston University, Boston, MA, 02215, USA
| | - Juan Ignacio Fuxman Bass
- Biology Department, Boston University, Boston, MA, 02215, USA
- Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, 02215, USA
- Bioinformatics Program, Boston University, Boston, MA, 02215, USA
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8
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Epasto LM, Pötzl C, Peterlik H, Khalil M, Saint‐Pierre C, Gasparutto D, Sicoli G, Kurzbach D. NMR-identification of the interaction between BRCA1 and the intrinsically disordered monomer of the Myc-associated factor X. Protein Sci 2024; 33:e4849. [PMID: 38037490 PMCID: PMC10731500 DOI: 10.1002/pro.4849] [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: 09/20/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
The breast cancer susceptibility 1 (BRCA1) protein plays a pivotal role in modulating the transcriptional activity of the vital intrinsically disordered transcription factor MYC. In this regard, mutations of BRCA1 and interruption of its regulatory activity are related to hereditary breast and ovarian cancer (HBOC). Interestingly, so far, MYC's main dimerization partner MAX (MYC-associated factor X) has not been found to bind BRCA1 despite a high sequence similarity between both oncoproteins. Herein, we show that a potential reason for this discrepancy is the heterogeneous conformational space of MAX, which encloses a well-documented folded coiled-coil homodimer as well as a less common intrinsically disordered monomer state-contrary to MYC, which exists mostly as intrinsically disordered protein in the absence of any binding partner. We show that when the intrinsically disordered state of MAX is artificially overpopulated, the binding of MAX to BRCA1 can readily be observed. We characterize this interaction by nuclear magnetic resonance (NMR) spectroscopy chemical shift and relaxation measurements, complemented with ITC and SAXS data. Our results suggest that BRCA1 directly binds the MAX monomer to form a disordered complex. Though probed herein under biomimetic in-vitro conditions, this finding can potentially stimulate new perspectives on the regulatory network around BRCA1 and its involvement in MYC:MAX regulation.
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Affiliation(s)
- Ludovica Martina Epasto
- Faculty of Chemistry, Institute for Biological ChemistryUniversity of ViennaViennaAustria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaViennaAustria
| | - Christopher Pötzl
- Faculty of Chemistry, Institute for Biological ChemistryUniversity of ViennaViennaAustria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaViennaAustria
| | | | - Mahdi Khalil
- CNRS UMR 8516, LASIREUniversity of LilleVilleneuve d'Ascq CedexFrance
| | | | | | - Giuseppe Sicoli
- CNRS UMR 8516, LASIREUniversity of LilleVilleneuve d'Ascq CedexFrance
| | - Dennis Kurzbach
- Faculty of Chemistry, Institute for Biological ChemistryUniversity of ViennaViennaAustria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaViennaAustria
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9
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Barakat S, Ezen E, Devecioğlu İ, Gezen M, Piepoli S, Erman B. Dimerization choice and alternative functions of ZBTB transcription factors. FEBS J 2024; 291:237-255. [PMID: 37450366 DOI: 10.1111/febs.16905] [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: 09/20/2022] [Revised: 06/09/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Zinc Finger DNA-binding domain-containing proteins are the most populous family among eukaryotic transcription factors. Among these, members of the BTB domain-containing ZBTB sub-family are mostly known for their transcriptional repressive functions. In this Viewpoint article, we explore molecular mechanisms that potentially diversify the function of ZBTB proteins based on their homo and heterodimerization, alternative splicing and post-translational modifications. We describe how the BTB domain is as much a scaffold for the assembly of co-repressors, as a domain that regulates protein stability. We highlight another mechanism that regulates ZBTB protein stability: phosphorylation in the zinc finger domain. We explore the non-transcriptional, structural roles of ZBTB proteins and highlight novel findings that describe the ability of ZBTB proteins to associate with poly adenosine ribose in the nucleus during the DNA damage response. Herein, we discuss the contribution of BTB domain scaffolds to the formation of transcriptional repressive complexes, to chromosome compartmentalization and their non-transcriptional, purely structural functions in the nucleus.
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Affiliation(s)
- Sarah Barakat
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Ege Ezen
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - İzem Devecioğlu
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Melike Gezen
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Sofia Piepoli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Batu Erman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
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10
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Abidi SNF, Hsu FTY, Smith-Bolton RK. Regenerative growth is constrained by brain tumor to ensure proper patterning in Drosophila. PLoS Genet 2023; 19:e1011103. [PMID: 38127821 PMCID: PMC10769103 DOI: 10.1371/journal.pgen.1011103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 01/05/2024] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Some animals respond to injury by inducing new growth to regenerate the lost structures. This regenerative growth must be carefully controlled and constrained to prevent aberrant growth and to allow correct organization of the regenerating tissue. However, the factors that restrict regenerative growth have not been identified. Using a genetic ablation system in the Drosophila wing imaginal disc, we have identified one mechanism that constrains regenerative growth, impairment of which also leads to erroneous patterning of the final appendage. Regenerating discs with reduced levels of the RNA-regulator Brain tumor (Brat) exhibit enhanced regeneration, but produce adult wings with disrupted margins that are missing extensive tracts of sensory bristles. In these mutants, aberrantly high expression of the pro-growth factor Myc and its downstream targets likely contributes to this loss of cell-fate specification. Thus, Brat constrains the expression of pro-regeneration genes and ensures that the regenerating tissue forms the proper final structure.
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Affiliation(s)
- Syeda Nayab Fatima Abidi
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Felicity Ting-Yu Hsu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Rachel K. Smith-Bolton
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Carle R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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11
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Burioli EAV, Hammel M, Vignal E, Vidal-Dupiol J, Mitta G, Thomas F, Bierne N, Destoumieux-Garzón D, Charrière GM. Transcriptomics of mussel transmissible cancer MtrBTN2 suggests accumulation of multiple cancer traits and oncogenic pathways shared among bilaterians. Open Biol 2023; 13:230259. [PMID: 37816387 PMCID: PMC10564563 DOI: 10.1098/rsob.230259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
Transmissible cancer cell lines are rare biological entities giving rise to diseases at the crossroads of cancer and parasitic diseases. These malignant cells have acquired the amazing capacity to spread from host to host. They have been described only in dogs, Tasmanian devils and marine bivalves. The Mytilus trossulus bivalve transmissible neoplasia 2 (MtrBTN2) lineage has even acquired the capacity to spread inter-specifically between marine mussels of the Mytilus edulis complex worldwide. To identify the oncogenic processes underpinning the biology of these atypical cancers we performed transcriptomics of MtrBTN2 cells. Differential expression, enrichment, protein-protein interaction network, and targeted analyses were used. Overall, our results suggest the accumulation of multiple cancerous traits that may be linked to the long-term evolution of MtrBTN2. We also highlight that vertebrate and lophotrochozoan cancers could share a large panel of common drivers, which supports the hypothesis of an ancient origin of oncogenic processes in bilaterians.
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Affiliation(s)
- E A V Burioli
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - M Hammel
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - E Vignal
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - J Vidal-Dupiol
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - G Mitta
- IFREMER, UMR 241 Écosystèmes Insulaires Océaniens, Labex Corail, Centre Ifremer du Pacifique, Tahiti, Polynésie française
| | - F Thomas
- CREEC/CANECEV (CREES), MIVEGEC, Unité Mixte de Recherches, IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France
| | - N Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - D Destoumieux-Garzón
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - G M Charrière
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
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12
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Caglayan E, Konopka G. Decoding DNA sequence-driven evolution of the human brain epigenome at cellular resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557820. [PMID: 37745404 PMCID: PMC10515917 DOI: 10.1101/2023.09.14.557820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
DNA-based evolutionary comparisons of regulatory genomic elements enable insight into functional changes, overcoming tissue inaccessibility. Here, we harnessed adult and fetal cortex single-cell ATAC-seq datasets to uncover DNA substitutions specific to the human and human-ancestral lineages within apes. We found that fetal microglia identity is evolutionarily divergent in all lineages, whereas other cell types are conserved. Using multiomic datasets, we further identified genes linked to multiple lineage-divergent gene regulatory elements and implicated biological pathways associated with these divergent features. We also uncovered patterns of transcription factor binding site evolution across lineages and identified expansion of bHLH-PAS factor targets in human-hominin lineages, and MEF2 factor targets in the ape lineage. Finally, conserved features were more enriched in brain disease variants, whereas there was no distinct enrichment on the human lineage compared to its ancestral lineages. Our study identifies major evolutionary patterns in the human brain epigenome at cellular resolution.
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Affiliation(s)
- Emre Caglayan
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
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13
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Ungureanu AR, Popovici V, Oprean C, Danciu C, Schröder V, Olaru OT, Mihai DP, Popescu L, Luță EA, Chițescu CL, Gîrd CE. Cytotoxicity Analysis and In Silico Studies of Three Plant Extracts with Potential Application in Treatment of Endothelial Dysfunction. Pharmaceutics 2023; 15:2125. [PMID: 37631338 PMCID: PMC10459174 DOI: 10.3390/pharmaceutics15082125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/06/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Endothelial dysfunction is the basis of the physiopathological mechanisms of vascular diseases. In addition to the therapeutic activity of plant extracts, cytotoxicity is significant. This research evaluates the cytotoxicity of three vegetal extracts (Calendulae flos extract-CE, Ginkgo bilobae folium extract-GE, and Sophorae flos extract-SE). In vitro evaluation was performed using an endothelial cell line model (Human Pulmonary Artery Endothelial Cells-HPAEC) when a dose-dependent cytotoxic activity was observed after 72 h. The IC50 values were calculated for all extracts: Calendulae flos extract (IC50 = 91.36 μg/mL), Sophorae flos extract (IC50 = 68.61 μg/mL), and Ginkgo bilobae folium extract (IC50 = 13.08 μg/mL). Therefore, at the level of HPAEC cells, the cytotoxicity of the extracts follows the order GE > SE > CE. The apoptotic mechanism implied in cell death was predicted for several phytocompounds using the PASS algorithm and molecular docking simulations, highlighting potential interactions with caspases-3 and -8. In vivo analysis was performed through brine shrimp lethality assay (BSLA) when lethal, behavioral, and cytological effects were evaluated on Artemia salina larvae. The viability examined after 24 h (assessment of lethal effects) follows the same sequence: CE > SE > GE. In addition, the predicted cell permeability was observed mainly for GE constituents through in silico studies. However, the extracts can be considered nontoxic according to Clarckson's criteria because no BSL% was registered at 1200 µg/mL. The obtained data reveal that all three extracts are safe for human use and suitable for incorporation in further pharmaceutical formulations.
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Affiliation(s)
- Andreea Roxana Ungureanu
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.R.U.); (O.T.O.); (L.P.); (E.-A.L.); (C.E.G.)
| | - Violeta Popovici
- Department of Microbiology and Immunology, Faculty of Dental Medicine, Ovidius University of Constanta, 7 Ilarie Voronca Street, 900684 Constanta, Romania;
| | - Camelia Oprean
- Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania;
- OncoGen Centre, County Hospital’ Pius Branzeu’, Blvd. Liviu Rebreanu 156, 300723 Timisoara, Romania
| | - Corina Danciu
- Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania;
| | - Verginica Schröder
- Department of Cellular and Molecular Biology, Faculty of Pharmacy, Ovidius University of Constanta, 6 Capitan Al. Serbanescu Street, 900001 Constanta, Romania;
| | - Octavian Tudorel Olaru
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.R.U.); (O.T.O.); (L.P.); (E.-A.L.); (C.E.G.)
| | - Dragoș Paul Mihai
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.R.U.); (O.T.O.); (L.P.); (E.-A.L.); (C.E.G.)
| | - Liliana Popescu
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.R.U.); (O.T.O.); (L.P.); (E.-A.L.); (C.E.G.)
| | - Emanuela-Alice Luță
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.R.U.); (O.T.O.); (L.P.); (E.-A.L.); (C.E.G.)
| | - Carmen Lidia Chițescu
- Faculty of Medicine and Pharmacy, “Dunărea de Jos” University of Galați, A.I. Cuza 35, 800010 Galați, Romania;
| | - Cerasela Elena Gîrd
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.R.U.); (O.T.O.); (L.P.); (E.-A.L.); (C.E.G.)
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14
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Tanizaki Y, Shibata Y, Na W, Shi YB. Cell cycle activation in thyroid hormone-induced apoptosis and stem cell development during Xenopus intestinal metamorphosis. Front Endocrinol (Lausanne) 2023; 14:1184013. [PMID: 37265708 PMCID: PMC10230048 DOI: 10.3389/fendo.2023.1184013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/03/2023] [Indexed: 06/03/2023] Open
Abstract
Amphibian metamorphosis resembles mammalian postembryonic development, a period around birth when many organs mature into their adult forms and when plasma thyroid hormone (T3) concentration peaks. T3 plays a causative role for amphibian metamorphosis. This and its independence from maternal influence make metamorphosis of amphibians, particularly anurans such as pseudo-tetraploid Xenopus laevis and its highly related diploid species Xenopus tropicalis, an excellent model to investigate how T3 regulates adult organ development. Studies on intestinal remodeling, a process that involves degeneration of larval epithelium via apoptosis and de novo formation of adult stem cells followed by their proliferation and differentiation to form the adult epithelium, have revealed important molecular insights on T3 regulation of cell fate during development. Here, we review some evidence suggesting that T3-induced activation of cell cycle program is important for T3-induced larval epithelial cell death and de novo formation of adult intestinal stem cells.
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15
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Kalakoti Y, Clarancia Peter S, Gawande S, Sundar D. Modulation of DNA-protein interactions by proximal genetic elements as uncovered by interpretable deep learning. J Mol Biol 2023; 435:168121. [PMID: 37100167 DOI: 10.1016/j.jmb.2023.168121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
Abstract
Transcription factors (TF) recognize specific motifs in the genome that are typically 6-12 bp long to regulate various aspects of the cellular machinery. Presence of binding motifs and favorable genome accessibility are key drivers for a consistent TF-DNA interaction. Although these pre-requisites may occur thousands of times in the genome, there seems to be a high degree of selectivity for the sites that are actually bound. Here, we present a deep-learning framework that identifies and characterizes the upstream and downstream genetic elements to the binding motif, for their role in enforcing the mentioned selectivity. The proposed framework is based on an interpretable recurrent neural network architecture that enables for the relative analysis of sequence context features. We apply the framework to model twenty-six transcription factors and score the TF-DNA binding at a base-pair resolution. We find significant differences in activations of DNA context features for bound and unbound sequences. In addition to standardized evaluation protocols, we offer outstanding interpretability that enables us to identify and annotate DNA sequence with possible elements that modulate TF-DNA binding. Also, differences in data processing have a huge influence on the overall model performance. Overall, the proposed framework allows for novel insights on the non-coding genetic elements and their role in facilitating a stable TF-DNA interaction.
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Affiliation(s)
- Yogesh Kalakoti
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi - 110016, India.
| | | | - Swaraj Gawande
- Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Delhi - 110016, India.
| | - Durai Sundar
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi - 110016, India; Yardi School of Artificial Intelligence, Indian Institute of Technology (IIT) Delhi, New Delhi - 110016, India.
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16
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Harada T, Perez MW, Kalfon J, Braes FD, Batley R, Eagle K, Nabet B, Leifer B, Kruell J, Paralkar VR, Stegmaier K, Koehler AN, Orkin SH, Pimkin M. Rapid-kinetics degron benchmarking reveals off-target activities and mixed agonism-antagonism of MYB inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536032. [PMID: 37066194 PMCID: PMC10104119 DOI: 10.1101/2023.04.07.536032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Attenuating aberrant transcriptional circuits holds great promise for the treatment of numerous diseases, including cancer. However, development of transcriptional inhibitors is hampered by the lack of a generally accepted functional cellular readout to characterize their target specificity and on-target activity. We benchmarked the direct gene-regulatory signatures of six agents reported as inhibitors of the oncogenic transcription factor MYB against targeted MYB degradation in a nascent transcriptomics assay. The inhibitors demonstrated partial specificity for MYB target genes but displayed significant off-target activity. Unexpectedly, the inhibitors displayed bimodal on-target effects, acting as mixed agonists-antagonists. Our data uncover unforeseen agonist effects of small molecules originally developed as TF inhibitors and argue that rapid-kinetics benchmarking against degron models should be used for functional characterization of transcriptional modulators.
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Affiliation(s)
- Taku Harada
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Monika W. Perez
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Jérémie Kalfon
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Flora Dievenich Braes
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Rashad Batley
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Kenneth Eagle
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Ken Eagle Consulting, Houston, TX, 77494, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Becky Leifer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jasmin Kruell
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Vikram R. Paralkar
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kimberly Stegmaier
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Angela N. Koehler
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stuart H. Orkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Howard Hughes Medical Institute, Boston, MA, 02215, USA
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
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17
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Melnik BC, Schmitz G. Milk Exosomal microRNAs: Postnatal Promoters of β Cell Proliferation but Potential Inducers of β Cell De-Differentiation in Adult Life. Int J Mol Sci 2022; 23:ijms231911503. [PMID: 36232796 PMCID: PMC9569743 DOI: 10.3390/ijms231911503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Pancreatic β cell expansion and functional maturation during the birth-to-weaning period is driven by epigenetic programs primarily triggered by growth factors, hormones, and nutrients provided by human milk. As shown recently, exosomes derived from various origins interact with β cells. This review elucidates the potential role of milk-derived exosomes (MEX) and their microRNAs (miRs) on pancreatic β cell programming during the postnatal period of lactation as well as during continuous cow milk exposure of adult humans to bovine MEX. Mechanistic evidence suggests that MEX miRs stimulate mTORC1/c-MYC-dependent postnatal β cell proliferation and glycolysis, but attenuate β cell differentiation, mitochondrial function, and insulin synthesis and secretion. MEX miR content is negatively affected by maternal obesity, gestational diabetes, psychological stress, caesarean delivery, and is completely absent in infant formula. Weaning-related disappearance of MEX miRs may be the critical event switching β cells from proliferation to TGF-β/AMPK-mediated cell differentiation, whereas continued exposure of adult humans to bovine MEX miRs via intake of pasteurized cow milk may reverse β cell differentiation, promoting β cell de-differentiation. Whereas MEX miR signaling supports postnatal β cell proliferation (diabetes prevention), persistent bovine MEX exposure after the lactation period may de-differentiate β cells back to the postnatal phenotype (diabetes induction).
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Affiliation(s)
- Bodo C. Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, D-49076 Osnabrück, Germany
- Correspondence: ; Tel.: +49-52-4198-8060
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital of Regensburg, University of Regensburg, D-93053 Regensburg, Germany
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18
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Ferraiuolo RM, Fifield BA, Hamm C, Porter LA. Stabilization of c-Myc by the atypical cell cycle regulator, Spy1, decreases efficacy of breast cancer treatments. Breast Cancer Res Treat 2022; 196:17-30. [PMID: 36029387 DOI: 10.1007/s10549-022-06715-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/14/2022] [Indexed: 11/02/2022]
Abstract
PURPOSE c-Myc is frequently upregulated in breast cancers, however, targeting c-Myc has proven to be a challenge. Targeting of downstream mediators of c-Myc, such as the 'cyclin-like' cell cycle regulator Spy1, may be a viable therapeutic option in a subset of breast cancer subtypes. METHODS Mouse mammary tumor cells isolated from MMTV-Myc mice and human breast cancer cell lines were used to manipulate Spy1 levels followed by tamoxifen or chemotherapeutic treatment with a variety of endpoints. Patient samples from TNBC patients were obtained and constructed into a TMA and stained for c-Myc and Spy1 protein levels. RESULTS Over time, MMTV-Myc cells show a decreased response to tamoxifen treatment with increasing levels of Spy1 in the tamoxifen-resistant cells. shRNA against Spy1 re-establishes tamoxifen sensitivity. Spy1 was found to be highly elevated in human TNBC cell and patient samples, correlating to c-Myc protein levels. c-Myc was found to be stabilized by Spy1 and knocking down Spy1 in TNBC cells shows a significant increase in response to chemotherapy treatments. CONCLUSION Understanding the interplay between protein expression level and response to treatment is a critical factor in developing novel treatment options for breast cancer patients. These data have shown a connection between Spy1 and c-Myc protein levels in more aggressive breast cancer cells and patient samples. Furthermore, targeting c-Myc has proven difficult, these data suggest targeting Spy1 even when c-Myc is elevated can confer an advantage to current chemotherapies.
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Affiliation(s)
- Rosa-Maria Ferraiuolo
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Bre-Anne Fifield
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, N9B 3P4, Canada.,WE-SPARK Health Institute, Windsor, ON, N9B 3P4, Canada
| | - Caroline Hamm
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, N9B 3P4, Canada.,Windsor Regional Cancer Centre, Windsor Regional Hospital, Windsor, ON, N9C 3E6, Canada.,Western University, Windsor, ON, N9B 3P4, Canada.,WE-SPARK Health Institute, Windsor, ON, N9B 3P4, Canada
| | - Lisa A Porter
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, N9B 3P4, Canada. .,WE-SPARK Health Institute, Windsor, ON, N9B 3P4, Canada.
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19
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Epasto LM, Che K, Kozak F, Selimovic A, Kadeřávek P, Kurzbach D. Toward protein NMR at physiological concentrations by hyperpolarized water-Finding and mapping uncharted conformational spaces. SCIENCE ADVANCES 2022; 8:eabq5179. [PMID: 35930648 PMCID: PMC9355353 DOI: 10.1126/sciadv.abq5179] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a key method for determining the structural dynamics of proteins in their native solution state. However, the low sensitivity of NMR typically necessitates nonphysiologically high sample concentrations, which often limit the relevance of the recorded data. We show how to use hyperpolarized water by dissolution dynamic nuclear polarization (DDNP) to acquire protein spectra at concentrations of 1 μM within seconds and with a high signal-to-noise ratio. The importance of approaching physiological concentrations is demonstrated for the vital MYC-associated factor X, which we show to switch conformations when diluted. While in vitro conditions lead to a population of the well-documented dimer, concentrations lowered by more than two orders of magnitude entail dimer dissociation and formation of a globularly folded monomer. We identified this structure by integrating DDNP with computational techniques to overcome the often-encountered constraint of DDNP of limited structural information provided by the typically detected one-dimensional spectra.
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Affiliation(s)
- Ludovica M. Epasto
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
| | - Kateryna Che
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
| | - Fanny Kozak
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
| | - Albina Selimovic
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
| | - Pavel Kadeřávek
- Masaryk University, CEITEC, Kamenice 5, 625 00 Brno, Czech Republic
| | - Dennis Kurzbach
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
- Corresponding author.
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20
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Bentsen M, Heger V, Schultheis H, Kuenne C, Looso M. TF-COMB - discovering grammar of transcription factor binding sites. Comput Struct Biotechnol J 2022; 20:4040-4051. [PMID: 35983231 PMCID: PMC9358416 DOI: 10.1016/j.csbj.2022.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/12/2022] [Indexed: 02/07/2023] Open
Abstract
Cooperativity between transcription factors is important to regulate target gene expression. In particular, the binding grammar of TFs in relation to each other, as well as in the context of other genomic elements, is crucial for TF functionality. However, tools to easily uncover co-occurrence between DNA-binding proteins, and investigate the regulatory modules of TFs, are limited. Here we present TF-COMB (Transcription Factor Co-Occurrence using Market Basket analysis) - a tool to investigate co-occurring TFs and binding grammar within regulatory regions. We found that TF-COMB can accurately identify known co-occurring TFs from ChIP-seq data, as well as uncover preferential localization to other genomic elements. With the use of ATAC-seq footprinting and TF motif locations, we found that TFs exhibit both preferred orientation and distance in relation to each other, and that these are biologically significant. Finally, we extended the analysis to not only investigate individual TF pairs, but also TF pairs in the context of networks, which enabled the investigation of TF complexes and TF hubs. In conclusion, TF-COMB is a flexible tool to investigate various aspects of TF binding grammar.
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Affiliation(s)
- Mette Bentsen
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Vanessa Heger
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Hendrik Schultheis
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Carsten Kuenne
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Corresponding author at: Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
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21
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The Functional Interaction of EGFR with AT1R or TP in Primary Vascular Smooth Muscle Cells Triggers a Synergistic Regulation of Gene Expression. Cells 2022; 11:cells11121936. [PMID: 35741065 PMCID: PMC9222111 DOI: 10.3390/cells11121936] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/11/2022] [Accepted: 06/15/2022] [Indexed: 02/01/2023] Open
Abstract
In vivo, cells are simultaneously exposed to multiple stimuli whose effects are difficult to distinguish. Therefore, they are often investigated in experimental cell culture conditions where stimuli are applied separately. However, it cannot be presumed that their individual effects simply add up. As a proof-of-principle to address the relevance of transcriptional signaling synergy, we investigated the interplay of the Epidermal Growth Factor Receptor (EGFR) with the Angiotensin-II (AT1R) or the Thromboxane-A2 (TP) receptors in murine primary aortic vascular smooth muscle cells. Transcriptome analysis revealed that EGFR-AT1R or EGFR-TP simultaneous activations led to different patterns of regulated genes compared to individual receptor activations (qualitative synergy). Combined EGFR-TP activation also caused a variation of amplitude regulation for a defined set of genes (quantitative synergy), including vascular injury-relevant ones (Klf15 and Spp1). Moreover, Gene Ontology enrichment suggested that EGFR and TP-induced gene expression changes altered processes critical for vascular integrity, such as cell cycle and senescence. These bioinformatics predictions regarding the functional relevance of signaling synergy were experimentally confirmed. Therefore, by showing that the activation of more than one receptor can trigger a synergistic regulation of gene expression, our results epitomize the necessity to perform comprehensive network investigations, as the study of individual receptors may not be sufficient to understand their physiological or pathological impact.
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22
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Monti N, Verna R, Piombarolo A, Querqui A, Bizzarri M, Fedeli V. Paradoxical Behavior of Oncogenes Undermines the Somatic Mutation Theory. Biomolecules 2022; 12:662. [PMID: 35625590 PMCID: PMC9138429 DOI: 10.3390/biom12050662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 12/04/2022] Open
Abstract
The currently accepted theory on the influence of DNA mutations on carcinogenesis (the Somatic Mutation Theory, SMT) is facing an increasing number of controversial results that undermine the explanatory power of mutated genes considered as "causative" factors. Intriguing results have demonstrated that several critical genes may act differently, as oncogenes or tumor suppressors, while phenotypic reversion of cancerous cells/tissues can be achieved by modifying the microenvironment, the mutations they are carrying notwithstanding. Furthermore, a high burden of mutations has been identified in many non-cancerous tissues without any apparent pathological consequence. All things considered, a relevant body of unexplained inconsistencies calls for an in depth rewiring of our theoretical models. Ignoring these paradoxes is no longer sustainable. By avoiding these conundrums, the scientific community will deprive itself of the opportunity to achieve real progress in this important biomedical field. To remedy this situation, we need to embrace new theoretical perspectives, taking the cell-microenvironment interplay as the privileged pathogenetic level of observation, and by assuming new explanatory models based on truly different premises. New theoretical frameworks dawned in the last two decades principally focus on the complex interaction between cells and their microenvironment, which is thought to be the critical level from which carcinogenesis arises. Indeed, both molecular and biophysical components of the stroma can dramatically drive cell fate commitment and cell outcome in opposite directions, even in the presence of the same stimulus. Therefore, such a novel approach can help in solving apparently inextricable paradoxes that are increasingly observed in cancer biology.
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Affiliation(s)
| | | | | | | | | | - Valeria Fedeli
- Systems Biology Group Lab, Department of Experimental Medicine, “Sapienza” University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (N.M.); (R.V.); (A.P.); (A.Q.); (M.B.)
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23
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Tanizaki Y, Zhang H, Shibata Y, Shi YB. Thyroid hormone receptor α controls larval intestinal epithelial cell death by regulating the CDK1 pathway. Commun Biol 2022; 5:112. [PMID: 35132135 PMCID: PMC8821549 DOI: 10.1038/s42003-022-03061-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/18/2022] [Indexed: 12/13/2022] Open
Abstract
Thyroid hormone (T3) regulates adult intestine development through T3 receptors (TRs). It is difficult to study TR function during postembryonic intestinal maturation in mammals due to maternal influence. We chose intestinal remodeling during Xenopus tropicalis metamorphosis as a model to study TR function in adult organ development. By using ChIP (chromatin immunoprecipitation)-Seq, we identified over 3000 TR-bound genes in the intestine of premetamorphic wild type or TRα (the major TR expressed during premetamorphosis)-knockout tadpoles. Surprisingly, cell cycle-related GO (gene ontology) terms and biological pathways were highly enriched among TR target genes even though the first major event during intestinal metamorphosis is larval epithelial cell death, and TRα knockout drastically reduced this enrichment. More importantly, treatment of tadpoles with cell cycle inhibitors blocked T3-induced intestinal remodeling, especially larval epithelial cell death, suggesting that TRα-dependent activation of cell cycle is important for T3-induced apoptosis during intestinal remodeling. Tanizaki et al use ChIP-Seq to identify over 3000 Thyroid hormone (T3) receptor (TR)-bound genes in the intestine of premetamorphic wild type Xenopus tropicalis tadpoles and in TRα-knockouts. They show that treatment of tadpoles with cell cycle inhibitors blocked T3-induced intestinal remodeling, suggesting that TRα-dependent activation of the cell cycle is important for T3-induced apoptosis during intestinal remodelling.
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Affiliation(s)
- Yuta Tanizaki
- Section on Molecular Morphogenesis, Cell Regulation and Development Affinity Group, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Hongen Zhang
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yuki Shibata
- Section on Molecular Morphogenesis, Cell Regulation and Development Affinity Group, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Cell Regulation and Development Affinity Group, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA.
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MXD3 Promotes Obesity and the Androgen Receptor Signaling Pathway in Gender-Disparity Hepatocarcinogenesis. Cells 2021; 10:cells10123434. [PMID: 34943942 PMCID: PMC8700344 DOI: 10.3390/cells10123434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/02/2021] [Accepted: 12/04/2021] [Indexed: 12/26/2022] Open
Abstract
Obesity is closely linked to metabolic diseases, particularly non-alcoholic steatohepatitis (NASH) or non-alcoholic fatty liver disease (NAFLD), ultimately leading to hepatocellular carcinoma (HCC). However, the molecular mechanisms of NASH-associated HCC (NAHCC) remain elusive. To explore the impact of Max dimerization protein 3 (MXD3), a transcription factor that regulates several cellular functions in disorders associated with metabolic diseases, we conditionally expressed Mxd3 proteins using Tet-on mxd3 transgenic zebrafish (MXs) with doxycycline (MXs + Dox) or without doxycycline (MXs − Dox) treatment. Overexpression of global MXD3 (gMX) or hepatic Mxd3 (hMX) was associated with obesity-related NAFLD pathophysiology in gMX + Dox, and liver fibrosis and HCC in hMX + Dox. Oil Red O (ORO)-stained signals were seen in intravascular blood vessels and liver buds of larval gMX + Dox, indicating that Mxd3 functionally promotes lipogenesis. The gMX + Dox-treated young adults exhibited an increase in body weight and visceral fat accumulation. The hMX + Dox-treated young adults showed normal body characteristics but exhibited liver steatosis and NASH-like phenotypes. Subsequently, steatohepatitis, liver fibrosis, and NAHCC were found in 6-month-old gMX + Dox adults compared with gMX − Dox adults at the same stage. Overexpression of Mxd3 also enhanced AR expression accompanied by the increase of AR-signaling pathways resulting in hepatocarcinogenesis in males. Our results demonstrate that global actions of Mxd3 are central to the initiation of obesity in the gMX zebrafish through their effects on adipogenesis and that MXD3 could serve as a therapeutic target for obesity-associated liver diseases.
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Novikova S, Tikhonova O, Kurbatov L, Farafonova T, Vakhrushev I, Lupatov A, Yarygin K, Zgoda V. Omics Technologies to Decipher Regulatory Networks in Granulocytic Cell Differentiation. Biomolecules 2021; 11:biom11060907. [PMID: 34207065 PMCID: PMC8233756 DOI: 10.3390/biom11060907] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 01/01/2023] Open
Abstract
Induced granulocytic differentiation of human leukemic cells under all-trans-retinoid acid (ATRA) treatment underlies differentiation therapy of acute myeloid leukemia. Knowing the regulation of this process it is possible to identify potential targets for antileukemic drugs and develop novel approaches to differentiation therapy. In this study, we have performed transcriptomic and proteomic profiling to reveal up- and down-regulated transcripts and proteins during time-course experiments. Using data on differentially expressed transcripts and proteins we have applied upstream regulator search and obtained transcriptome- and proteome-based regulatory networks of induced granulocytic differentiation that cover both up-regulated (HIC1, NFKBIA, and CASP9) and down-regulated (PARP1, VDR, and RXRA) elements. To verify the designed network we measured HIC1 and PARP1 protein abundance during granulocytic differentiation by selected reaction monitoring (SRM) using stable isotopically labeled peptide standards. We also revealed that transcription factor CEBPB and LYN kinase were involved in differentiation onset, and evaluated their protein levels by SRM technique. Obtained results indicate that the omics data reflect involvement of the DNA repair system and the MAPK kinase cascade as well as show the balance between the processes of the cell survival and apoptosis in a p53-independent manner. The differentially expressed transcripts and proteins, predicted transcriptional factors, and key molecules such as HIC1, CEBPB, LYN, and PARP1 may be considered as potential targets for differentiation therapy of acute myeloid leukemia.
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Bartlett T. Fusion of single-cell transcriptome and DNA-binding data, for genomic network inference in cortical development. BMC Bioinformatics 2021; 22:301. [PMID: 34088262 PMCID: PMC8176738 DOI: 10.1186/s12859-021-04201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Network models are well-established as very useful computational-statistical tools in cell biology. However, a genomic network model based only on gene expression data can, by definition, only infer gene co-expression networks. Hence, in order to infer gene regulatory patterns, it is necessary to also include data related to binding of regulatory factors to DNA. RESULTS We propose a new dynamic genomic network model, for inferring patterns of genomic regulatory influence in dynamic processes such as development. Our model fuses experiment-specific gene expression data with publicly available DNA-binding data. The method we propose is computationally efficient, and can be applied to genome-wide data with tens of thousands of transcripts. Thus, our method is well suited for use as an exploratory tool for genome-wide data. We apply our method to data from human fetal cortical development, and our findings confirm genomic regulatory patterns which are recognised as being fundamental to neuronal development. CONCLUSIONS Our method provides a mathematical/computational toolbox which, when coupled with targeted experiments, will reveal and confirm important new functional genomic regulatory processes in mammalian development.
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Affiliation(s)
- Thomas Bartlett
- University College London, Gower Street, London, WC1E 6BT, UK.
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Lee JEA, Parsons LM, Quinn LM. MYC function and regulation in flies: how Drosophila has enlightened MYC cancer biology. AIMS GENETICS 2021. [DOI: 10.3934/genet.2014.1.81] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractProgress in our understanding of the complex signaling events driving human cancer would have been unimaginably slow without discoveries from Drosophila genetic studies. Significantly, many of the signaling pathways now synonymous with cancer biology were first identified as a result of elegant screens for genes fundamental to metazoan development. Indeed the name given to many core cancer-signaling cascades tells of their history as developmental patterning regulators in flies—e.g. Wingless (Wnt), Notch and Hippo. Moreover, astonishing insight has been gained into these complex signaling networks, and many other classic oncogenic signaling networks (e.g. EGFR/RAS/RAF/ERK, InR/PI3K/AKT/TOR), using sophisticated fly genetics. Of course if we are to understand how these signaling pathways drive cancer, we must determine the downstream program(s) of gene expression activated to promote the cell and tissue over growth fundamental to cancer. Here we discuss one commonality between each of these pathways: they are all implicated as upstream activators of the highly conserved MYC oncogene and transcription factor. MYC can drive all aspects of cell growth and cell cycle progression during animal development. MYC is estimated to be dysregulated in over 50% of all cancers, underscoring the importance of elucidating the signals activating MYC. We also discuss the FUBP1/FIR/FUSE system, which acts as a ‘cruise control’ on the MYC promoter to control RNA Polymerase II pausing and, therefore, MYC transcription in response to the developmental signaling environment. Importantly, the striking conservation between humans and flies within these major axes of MYC regulation has made Drosophila an extremely valuable model organism for cancer research. We therefore discuss how Drosophila studies have helped determine the validity of signaling pathways regulating MYC in vivo using sophisticated genetics, and continue to provide novel insight into cancer biology.
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Affiliation(s)
- Jue Er Amanda Lee
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville 3010, Melbourne, Australia
| | - Linda May Parsons
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville 3010, Melbourne, Australia
| | - Leonie M. Quinn
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville 3010, Melbourne, Australia
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Bravo-Ruiz I, Medina MÁ, Martínez-Poveda B. From Food to Genes: Transcriptional Regulation of Metabolism by Lipids and Carbohydrates. Nutrients 2021; 13:nu13051513. [PMID: 33946267 PMCID: PMC8145205 DOI: 10.3390/nu13051513] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 04/28/2021] [Indexed: 12/31/2022] Open
Abstract
Lipids and carbohydrates regulate gene expression by means of molecules that sense these macronutrients and act as transcription factors. The peroxisome proliferator-activated receptor (PPAR), activated by some fatty acids or their derivatives, and the carbohydrate response element binding protein (ChREBP), activated by glucose-derived metabolites, play a key role in metabolic homeostasis, especially in glucose and lipid metabolism. Furthermore, the action of both factors in obesity, diabetes and fatty liver, as well as the pharmacological development in the treatment of these pathologies are indeed of high relevance. In this review we present an overview of the discovery, mechanism of activation and metabolic functions of these nutrient-dependent transcription factors in different tissues contexts, from the nutritional genomics perspective. The possibility of targeting these factors in pharmacological approaches is also discussed. Lipid and carbohydrate-dependent transcription factors are key players in the complex metabolic homeostasis, but these factors also drive an adaptive response to non-physiological situations, such as overeating. Possibly the decisive role of ChREBP and PPAR in metabolic regulation points to them as ideal therapeutic targets, but their pleiotropic functions in different tissues makes it difficult to "hit the mark".
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Affiliation(s)
- Inés Bravo-Ruiz
- Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, E-29071 Málaga, Spain; (I.B.-R.); (M.Á.M.)
| | - Miguel Ángel Medina
- Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, E-29071 Málaga, Spain; (I.B.-R.); (M.Á.M.)
- Instituto de Investigación Biomédica de Málaga (IBIMA), E-29071 Málaga, Spain
- CIBER de Enfermedades Raras (CIBERER), E-29071 Málaga, Spain
| | - Beatriz Martínez-Poveda
- Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, E-29071 Málaga, Spain; (I.B.-R.); (M.Á.M.)
- Instituto de Investigación Biomédica de Málaga (IBIMA), E-29071 Málaga, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), E-28029 Madrid, Spain
- Correspondence:
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Shi YB, Shibata Y, Tanizaki Y, Fu L. The development of adult intestinal stem cells: Insights from studies on thyroid hormone-dependent anuran metamorphosis. VITAMINS AND HORMONES 2021; 116:269-293. [PMID: 33752821 DOI: 10.1016/bs.vh.2021.02.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Vertebrates organ development often takes place in two phases: initial formation and subsequent maturation into the adult form. This is exemplified by the intestine. In mouse, the intestine at birth has villus, where most differentiated epithelial cells are located, but lacks any crypts, where adult intestinal stem cells reside. The crypt is formed during the first 3 weeks after birth when plasma thyroid hormone (T3) levels are high. Similarly, in anurans, the intestine undergoes drastic remodeling into the adult form during metamorphosis in a process completely dependent on T3. Studies on Xenopus metamorphosis have revealed important clues on the formation of the adult intestine during metamorphosis. Here we will review our current understanding on how T3 induces the degeneration of larval epithelium and de novo formation of adult intestinal stem cells. We will also discuss the mechanistic conservations in intestinal development between anurans and mammals.
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Affiliation(s)
- Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States.
| | - Yuki Shibata
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Yuta Tanizaki
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Liezhen Fu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
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Shimizu T, Hisamoto N. Factors regulating axon regeneration via JNK MAP kinase in Caenorhabditis elegans. J Biochem 2021; 167:433-439. [PMID: 32091576 DOI: 10.1093/jb/mvaa020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 01/23/2020] [Indexed: 12/25/2022] Open
Abstract
Axon regeneration following nerve injury is a highly conserved process in animals. The nematode Caenorhabditis elegans is an excellent model for investigating the molecular mechanisms of axon regeneration. Recent studies using C. elegans have shown that the c-Jun N-terminal kinase (JNK) plays the important role in axon regeneration. Furthermore, many factors have been identified that act upstream of the JNK cascade after axotomy. This review introduces these factors and describes their roles during the regulation of axon regeneration.
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Affiliation(s)
- Tatsuhiro Shimizu
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Naoki Hisamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
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Caenorhabditis elegans F-Box Protein Promotes Axon Regeneration by Inducing Degradation of the Mad Transcription Factor. J Neurosci 2021; 41:2373-2381. [PMID: 33514673 PMCID: PMC7984584 DOI: 10.1523/jneurosci.1024-20.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 01/19/2023] Open
Abstract
In Caenorhabditis elegans, axon regeneration is activated by a signaling cascade through the receptor tyrosine kinase (RTK) SVH-2. Axonal injury induces svh-2 gene expression by degradation of the Mad-like transcription factor MDL-1. In this study, we identify the svh-24/sdz-33 gene encoding a protein containing F-box and F-box-associated domains as a regulator of axon regeneration in motor neurons. We find that sdz-33 is required for axon injury-induced svh-2 expression. In Caenorhabditis elegans, axon regeneration is activated by a signaling cascade through the receptor tyrosine kinase (RTK) SVH-2. Axonal injury induces svh-2 gene expression by degradation of the Mad-like transcription factor MDL-1. In this study, we identify the svh-24/sdz-33 gene encoding a protein containing F-box and F-box-associated domains as a regulator of axon regeneration in motor neurons. We find that sdz-33 is required for axon injury-induced svh-2 expression. SDZ-33 targets MDL-1 for poly-ubiquitylation and degradation. Furthermore, we demonstrate that SDZ-33 promotes axotomy-induced nuclear degradation of MDL-1, resulting in the activation of svh-2 expression in animals. These results suggest that the F-box protein is required for RTK signaling in the control of axon regeneration. SIGNIFICANCE STATEMENT In Caenorhabditis elegans, axon regeneration is positively regulated by the growth factor SVH-1 and its receptor tyrosine kinase SVH-2. Expression of the svh-2 gene is induced by axonal injury via the Ets-like transcription factor ETS-4, whose transcriptional activity is inhibited by the Mad-like transcription factor MDL-1. Axon injury leads to the degradation of MDL-1, and this is linked to the activation of ETS-4 transcriptional activity. In this study, we identify the sdz-33 gene encoding a protein containing an F-box domain as a regulator of axon regeneration. We demonstrate that MDL-1 is poly-ubiquitylated and degraded through the SDZ-33-mediated 26S proteasome pathway. These results reveal that an F-box protein promotes axon regeneration by degrading the Mad transcription factor.
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32
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Inamoto I, Sheoran I, Popa SC, Hussain M, Shin JA. Combining Rational Design and Continuous Evolution on Minimalist Proteins That Target the E-box DNA Site. ACS Chem Biol 2021; 16:35-44. [PMID: 33370105 DOI: 10.1021/acschembio.0c00684] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-based therapeutics are part of the next-generation arsenal of drugs being developed against proto-oncoprotein Myc. We designed protein MEF to mimic the basic region/helix-loop-helix/leucine zipper (bHLHZ) domain of Max and Myc, which bind to the E-box motif (enhancer box, CACGTG). To make MEF, we started with our rationally designed ME47, a hybrid of the Max basic region and E47 HLH, that effectively inhibited tumor growth in a mouse model of breast cancer. We used phage-assisted continuous evolution (PACE), which uncovered mutations at Arg12 that contact the DNA phosphodiester backbone. The Arg12 mutations improved ME47's stability. We replaced Cys29 with Ala to eliminate potential undesired disulfide formation and fused the designed FosW leucine zipper to mutated ME47 to increase the dimerization interface and E-box targeting activity. This "franken-protein" MEF comprises the Max basic region, E47 HLH, and FosW leucine zipper. Compared with ME47, MEF gives 2-fold stronger binding to E-box and 4-fold increased specificity for E-box over nonspecific DNA. The synergistic combination of rational design and PACE allowed us to make MEF and demonstrates the power and utility of our two-pronged approach toward development of promising protein drugs with robust structure and DNA-binding function.
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Affiliation(s)
- Ichiro Inamoto
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Inder Sheoran
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Serban C. Popa
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Montdher Hussain
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Jumi A. Shin
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
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Sicoli G, Kress T, Vezin H, Ledolter K, Kurzbach D. A Switch between Two Intrinsically Disordered Conformational Ensembles Modulates the Active Site of a Basic-Helix-Loop-Helix Transcription Factor. J Phys Chem Lett 2020; 11:8944-8951. [PMID: 33030907 PMCID: PMC7649839 DOI: 10.1021/acs.jpclett.0c02242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We report a conformational switch between two distinct intrinsically disordered subensembles within the active site of a transcription factor. This switch highlights an evolutionary benefit conferred by the high plasticity of intrinsically disordered domains, namely, their potential to dynamically sample a heterogeneous conformational space housing multiple states with tailored properties. We focus on proto-oncogenic basic-helix-loop-helix (bHLH)-type transcription factors, as these play key roles in cell regulation and function. Despite intense research efforts, the understanding of structure-function relations of these transcription factors remains incomplete as they feature intrinsically disordered DNA-interaction domains that are difficult to characterize, theoretically as well as experimentally. Here we characterize the structural dynamics of the intrinsically disordered region DNA-binding site of the vital MYC-associated transcription factor X (MAX). Integrating nuclear magnetic resonance (NMR) measurements, molecular dynamics (MD) simulations, and electron paramagnetic resonance (EPR) measurements, we show that, in the absence of DNA, the binding site of the free MAX2 homodimer samples two intrinsically disordered conformational subensembles. These feature distinct structural properties: one subensemble consists of a set of highly flexible and spatially extended conformers, while the second features a set of "hinged" conformations. In this latter ensemble, the disordered N-terminal tails of MAX2 fold back along the dimer, forming transient long-range contacts with the HLH-region and thereby exposing the DNA binding site to the solvent. The features of these divergent substates suggest two mechanisms by which protein conformational dynamics in MAX2 might modulate DNA-complex formation: by enhanced initial recruitment of free DNA ligands, as a result of the wider conformational space sampled by the extended ensemble, and by direct exposure of the binding site and the corresponding strong electrostatic attractions presented while in the hinged conformations.
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Affiliation(s)
- Giuseppe Sicoli
- Laboratoire
Avancé de Spectroscopie pour les Interactions, la Réactivité
et l’Environnement (LASIRE), UMR CNRS 8516, Université de Lille, Avenue Paul Langevin − C4, F-59655 Villeneuve d’Ascq, France
| | - Thomas Kress
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Hervé Vezin
- Laboratoire
Avancé de Spectroscopie pour les Interactions, la Réactivité
et l’Environnement (LASIRE), UMR CNRS 8516, Université de Lille, Avenue Paul Langevin − C4, F-59655 Villeneuve d’Ascq, France
| | - Karin Ledolter
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University Vienna, Campus Vienna BioCenter 5, 1030 Vienna, Austria
| | - Dennis Kurzbach
- Faculty
of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
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Liu Y, Shi N, Regev A, He S, Hemann MT. Integrated regulatory models for inference of subtype-specific susceptibilities in glioblastoma. Mol Syst Biol 2020; 16:e9506. [PMID: 32974985 PMCID: PMC7516378 DOI: 10.15252/msb.20209506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/15/2022] Open
Abstract
Glioblastoma multiforme (GBM) is a highly malignant form of cancer that lacks effective treatment options or well-defined strategies for personalized cancer therapy. The disease has been stratified into distinct molecular subtypes; however, the underlying regulatory circuitry that gives rise to such heterogeneity and its implications for therapy remain unclear. We developed a modular computational pipeline, Integrative Modeling of Transcription Regulatory Interactions for Systematic Inference of Susceptibility in Cancer (inTRINSiC), to dissect subtype-specific regulatory programs and predict genetic dependencies in individual patient tumors. Using a multilayer network consisting of 518 transcription factors (TFs), 10,733 target genes, and a signaling layer of 3,132 proteins, we were able to accurately identify differential regulatory activity of TFs that shape subtype-specific expression landscapes. Our models also allowed inference of mechanisms for altered TF behavior in different GBM subtypes. Most importantly, we were able to use the multilayer models to perform an in silico perturbation analysis to infer differential genetic vulnerabilities across GBM subtypes and pinpoint the MYB family member MYBL2 as a drug target specific for the Proneural subtype.
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Affiliation(s)
- Yunpeng Liu
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- MIT Koch Institute for Integrative Cancer ResearchCambridgeMAUSA
- Broad Institute of MIT and HarvardCambridgeMAUSA
| | - Ning Shi
- School of Computer ScienceUniversity of BirminghamBirminghamUK
| | - Aviv Regev
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- MIT Koch Institute for Integrative Cancer ResearchCambridgeMAUSA
- Broad Institute of MIT and HarvardCambridgeMAUSA
| | - Shan He
- School of Computer ScienceUniversity of BirminghamBirminghamUK
| | - Michael T Hemann
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- MIT Koch Institute for Integrative Cancer ResearchCambridgeMAUSA
- Broad Institute of MIT and HarvardCambridgeMAUSA
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35
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Baumeister J, Chatain N, Hubrich A, Maié T, Costa IG, Denecke B, Han L, Küstermann C, Sontag S, Seré K, Strathmann K, Zenke M, Schuppert A, Brümmendorf TH, Kranc KR, Koschmieder S, Gezer D. Hypoxia-inducible factor 1 (HIF-1) is a new therapeutic target in JAK2V617F-positive myeloproliferative neoplasms. Leukemia 2020; 34:1062-1074. [PMID: 31728053 DOI: 10.1038/s41375-019-0629-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 10/17/2019] [Accepted: 11/03/2019] [Indexed: 12/18/2022]
Abstract
Classical Philadelphia chromosome-negative myeloproliferative neoplasms (MPN) are a heterogeneous group of hematopoietic malignancies including polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). The JAK2V617F mutation plays a central role in these disorders and can be found in 90% of PV and ~50-60% of ET and PMF. Hypoxia-inducible factor 1 (HIF-1) is a master transcriptional regulator of the response to decreased oxygen levels. We demonstrate the impact of pharmacological inhibition and shRNA-mediated knockdown (KD) of HIF-1α in JAK2V617F-positive cells. Inhibition of HIF-1 binding to hypoxia response elements (HREs) with echinomycin, verified by ChIP, impaired growth and survival by inducing apoptosis and cell cycle arrest in Jak2V617F-positive 32D cells, but not Jak2WT controls. Echinomycin selectively abrogated clonogenic growth of JAK2V617F cells and decreased growth, survival, and colony formation of bone marrow and peripheral blood mononuclear cells and iPS cell-derived progenitor cells from JAK2V617F-positive patients, while cells from healthy donors were unaffected. We identified HIF-1 target genes involved in the Warburg effect as a possible underlying mechanism, with increased expression of Pdk1, Glut1, and others. That was underlined by transcriptome analysis of primary patient samples. Collectively, our data show that HIF-1 is a new potential therapeutic target in JAK2V617F-positive MPN.
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Affiliation(s)
- Julian Baumeister
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Nicolas Chatain
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Annika Hubrich
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Tiago Maié
- Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
| | - Ivan G Costa
- Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
| | - Bernd Denecke
- Interdisciplinary Center for Clinical Research Aachen, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Lijuan Han
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Caroline Küstermann
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Institute of Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, Aachen, Germany; Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Stephanie Sontag
- Institute of Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, Aachen, Germany; Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Kristin Seré
- Institute of Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, Aachen, Germany; Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Klaus Strathmann
- Institute for Transfusion Medicine, RWTH Aachen University Medical School, Aachen, Germany
| | - Martin Zenke
- Institute of Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, Aachen, Germany; Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Andreas Schuppert
- Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Kamil R Kranc
- Laboratory of Haematopoietic Stem Cell & Leukaemia Biology, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Deniz Gezer
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany.
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Caggiano C, Pieraccioli M, Panzeri V, Sette C, Bielli P. c-MYC empowers transcription and productive splicing of the oncogenic splicing factor Sam68 in cancer. Nucleic Acids Res 2020; 47:6160-6171. [PMID: 31066450 PMCID: PMC6614821 DOI: 10.1093/nar/gkz344] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 04/19/2019] [Accepted: 04/24/2019] [Indexed: 02/07/2023] Open
Abstract
The splicing factor Sam68 is upregulated in many human cancers, including prostate cancer (PCa) where it promotes cell proliferation and survival. Nevertheless, in spite of its frequent upregulation in cancer, the mechanism(s) underlying its expression are largely unknown. Herein, bioinformatics analyses identified the promoter region of the Sam68 gene (KHDRBS1) and the proto-oncogenic transcription factor c-MYC as a key regulator of Sam68 expression. Upregulation of Sam68 and c-MYC correlate in PCa patients. c-MYC directly binds to and activates the Sam68 promoter. Furthermore, c-MYC affects productive splicing of the nascent Sam68 transcript by modulating the transcriptional elongation rate within the gene. Importantly, c-MYC-dependent expression of Sam68 is under the tight control of external cues, such as androgens and/or mitogens. These findings uncover an unexpected coordination of transcription and splicing of Sam68 by c-MYC, which may represent a key step in PCa tumorigenesis.
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Affiliation(s)
- Cinzia Caggiano
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Marco Pieraccioli
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Valentina Panzeri
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Science medical/chirurgic and translational medicine, University of Rome Sapienza,00189 Rome, Italy
| | - Claudio Sette
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.,Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Hearth, 00168 Rome, Italy
| | - Pamela Bielli
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
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Zhang Y, Shao Y, Lv Z, Li C. MYC regulates coelomocytes apoptosis by targeting Bax expression in sea cucumber Apostichopus japonicus. FISH & SHELLFISH IMMUNOLOGY 2020; 97:27-33. [PMID: 31843700 DOI: 10.1016/j.fsi.2019.12.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/28/2019] [Accepted: 12/12/2019] [Indexed: 06/10/2023]
Abstract
Myelocytomatosis viral oncogene (MYC), a multifunctional transcription factor, (TF) exerts various physiological and pathological effects on animals. AjMYC could induce coelomocyte apoptosis in Apostichopus japonicus, but the underlying molecular mechanism remains poorly understood. In this study, the promoter sequence of apoptosis regulator Bcl-2-associated X (Bax) was cloned by genomic walking. The AjBax promoter region spaning 1189 bp, containing several transcription factor binding sites, included four potential E-boxes (-1030 bp to -1019 bp, -785 bp to -774 bp, -570 bp to -559 bp, -100 bp to -89 bp), two P53 binding sites (-439 bp to -430 bp, -845 bp to -836 bp), and one NF-κB site (-191 bp to -182 bp). Transient transfection of EPC cells with 5'-deletion constructs linked to luciferase reporter revealed that the region -1189/+454 contributed importantly to the expression of the AjBax. In addition, the AjBax promoter was induced by LPS, PGN or MAN. The four potential MYC binding sites were cotransfected with AjMYC in EPC cell whether AjMYC could activate AjBax expression as a transcriptional factor. Only P1 (-1189/+454) fragment containing the first MYC binding site transfection increased the luciferase activity by 2.08-fold (p < 0.01) compared with the control. The first MYC binding site -1030/-1019 was essential to induce AjBax transcription. Further functional assay indicated that AjBax was significantly induced by 3.54-fold increase (p < 0.01) after AjMYC overexpression in sea cucumber coelomocytes. All our findings supported that AjMYC could regulate coelomocyte apoptosis by directly targeting AjBax expression in A. japonicus.
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Affiliation(s)
- Yi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China
| | - Yina Shao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China
| | - Zhimeng Lv
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China.
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38
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Sicoli G, Vezin H, Ledolter K, Kress T, Kurzbach D. Conformational tuning of a DNA-bound transcription factor. Nucleic Acids Res 2019; 47:5429-5435. [PMID: 31020309 PMCID: PMC6547406 DOI: 10.1093/nar/gkz291] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 04/05/2019] [Accepted: 04/10/2019] [Indexed: 11/14/2022] Open
Abstract
Transcription factors are involved in many cellular processes that take place remote from their cognate DNA sequences. The efficiencies of these activities are thus in principle counteracted by high binding affinities of the factors to their cognate DNAs. Models such as facilitated diffusion or dissociation address this apparent contradiction. We show that the MYC associated transcription factor X (MAX) undergoes nanoscale conformational fluctuations in the DNA-bound state, which is consistent with facilitated dissociation from or diffusion along DNA strands by transiently reducing binding energies. An integrative approach involving EPR, NMR, crystallographic and molecular dynamics analyses demonstrates that the N-terminal domain of MAX constantly opens and closes around a bound DNA ligand thereby dynamically tuning the binding epitope and the mode of interaction.
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Affiliation(s)
- Giuseppe Sicoli
- Univ. Lille, CNRS, UMR 8516 - LASIR - Laboratoire de Spectrochimie Infrarouge et Raman, F-59000 Lille, France
| | - Hervé Vezin
- Univ. Lille, CNRS, UMR 8516 - LASIR - Laboratoire de Spectrochimie Infrarouge et Raman, F-59000 Lille, France
| | - Karin Ledolter
- University Vienna, Department for Structural and Computational Biology, Max F. Perutz Laboratories, Campus Vienna BioCenter 5, 1030 Vienna, Austria
| | - Thomas Kress
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.,University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
| | - Dennis Kurzbach
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
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Popa SC, Shin JA. The Intrinsically Disordered Loop in the USF1 bHLHZ Domain Modulates Its DNA-Binding Sequence Specificity in Hereditary Asthma. J Phys Chem B 2019; 123:9862-9871. [PMID: 31670516 DOI: 10.1021/acs.jpcb.9b06719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
USF1, a basic region/helix-loop-helix/leucine zipper (bHLHZ) transcription factor, binds to the E-box in the PAI-1 (plasminogen activator inhibitor) promoter. Two alleles containing the E-box control PAI-1 transcription; these alleles are termed "4G" and "5G" based on the G tract flanking E-box. USF1-governed transcription of PAI-1 is elevated in heritable asthma sufferers: the 4G/4G genotype has the highest plasma levels of PAI-1. While USF1 uses its basic region to bind E-box, we found that it uses its 12 amino-acid loop to recognize the flanking sequence and discern the single-nucleotide difference between the alleles. We used the bacterial one-hybrid and electrophoretic mobility shift assays to assess protein-DNA recognition, and circular dichroism to examine protein secondary structure. We mutated Ser233 and Thr234 in the USF1 bHLHZ loop to Ala to generate S233A and T234A. Interestingly, USF1 bHLHZ, S233A, and T234A prefer the 5G sequence (USF1 bHLHZ Kd values 4.1 ± 0.3 nM and 7.0 ± 0.4 nM for 5G and 4G, respectively), whereas studies in stimulated human mast cells showed a preference for 4G. We replaced the 8 amino-acid loop of transcription factor Max bHLHZ with the 12 amino-acid USF1 loop: this mutant now distinguishes the 4G/5G polymorphism-while Max bHLHZ does not-confirming that USF1 differentiation of the 4G/5G is driven by the loop.
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Affiliation(s)
- Serban C Popa
- Department of Chemistry , University of Toronto , 3359 Mississauga Road , Mississauga , Ontario L5L 1C6 , Canada
| | - Jumi A Shin
- Department of Chemistry , University of Toronto , 3359 Mississauga Road , Mississauga , Ontario L5L 1C6 , Canada
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40
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Tarczewska A, Greb-Markiewicz B. The Significance of the Intrinsically Disordered Regions for the Functions of the bHLH Transcription Factors. Int J Mol Sci 2019; 20:E5306. [PMID: 31653121 PMCID: PMC6862971 DOI: 10.3390/ijms20215306] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/22/2019] [Accepted: 10/22/2019] [Indexed: 11/17/2022] Open
Abstract
The bHLH proteins are a family of eukaryotic transcription factors regulating expression of a wide range of genes involved in cell differentiation and development. They contain the Helix-Loop-Helix (HLH) domain, preceded by a stretch of basic residues, which are responsible for dimerization and binding to E-box sequences. In addition to the well-preserved DNA-binding bHLH domain, these proteins may contain various additional domains determining the specificity of performed transcriptional regulation. According to this, the family has been divided into distinct classes. Our aim was to emphasize the significance of existing disordered regions within the bHLH transcription factors for their functionality. Flexible, intrinsically disordered regions containing various motives and specific sequences allow for multiple interactions with transcription co-regulators. Also, based on in silico analysis and previous studies, we hypothesize that the bHLH proteins have a general ability to undergo spontaneous phase separation, forming or participating into liquid condensates which constitute functional centers involved in transcription regulation. We shortly introduce recent findings on the crucial role of the thermodynamically liquid-liquid driven phase separation in transcription regulation by disordered regions of regulatory proteins. We believe that further experimental studies should be performed in this field for better understanding of the mechanism of gene expression regulation (among others regarding oncogenes) by important and linked to many diseases the bHLH transcription factors.
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Affiliation(s)
- Aneta Tarczewska
- Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Beata Greb-Markiewicz
- Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
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41
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Reddy GP, Reddy LV, Kim S. CANCER BIOLOGY AND PATHOLOGY. Cancer 2019. [DOI: 10.1002/9781119645214.ch2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Sakai Y, Hanafusa H, Pastuhov SI, Shimizu T, Li C, Hisamoto N, Matsumoto K. TDP2 negatively regulates axon regeneration by inducing SUMOylation of an Ets transcription factor. EMBO Rep 2019; 20:e47517. [PMID: 31393064 PMCID: PMC6776894 DOI: 10.15252/embr.201847517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 07/03/2019] [Accepted: 07/15/2019] [Indexed: 12/02/2022] Open
Abstract
In Caenorhabditis elegans, the JNK MAP kinase (MAPK) pathway is important for axon regeneration. The JNK pathway is activated by a signaling cascade consisting of the growth factor SVH‐1 and its receptor tyrosine kinase SVH‐2. Expression of the svh‐2 gene is induced by axonal injury in a process involving the transcription factors ETS‐4 and CEBP‐1. Here, we find that svh‐14/mxl‐1, a gene encoding a Max‐like transcription factor, is required for activation of svh‐2 expression in response to axonal injury. We show that MXL‐1 binds to and inhibits the function of TDPT‐1, a C. elegans homolog of mammalian tyrosyl‐DNA phosphodiesterase 2 [TDP2; also called Ets1‐associated protein II (EAPII)]. Deletion of tdpt‐1 suppresses the mxl‐1 defect, but not the ets‐4 defect, in axon regeneration. TDPT‐1 induces SUMOylation of ETS‐4, which inhibits ETS‐4 transcriptional activity, and MXL‐1 counteracts this effect. Thus, TDPT‐1 interacts with two different transcription factors in axon regeneration.
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Affiliation(s)
- Yoshiki Sakai
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Hiroshi Hanafusa
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Strahil Iv Pastuhov
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Tatsuhiro Shimizu
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Chun Li
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Naoki Hisamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kunihiro Matsumoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
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Mukamel EA, Ngai J. Perspectives on defining cell types in the brain. Curr Opin Neurobiol 2019; 56:61-68. [PMID: 30530112 PMCID: PMC6551297 DOI: 10.1016/j.conb.2018.11.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/10/2018] [Accepted: 11/21/2018] [Indexed: 12/11/2022]
Abstract
The diversity of brain cell types was one of the earliest observations in modern neuroscience and continues to be one of the central concerns of current neuroscience research. Despite impressive recent progress, including single cell transcriptome and epigenome profiling as well as anatomical methods, we still lack a complete census or taxonomy of brain cell types. We argue this is due partly to the conceptual difficulty in defining a cell type. By considering the biological drivers of cell identity, such as networks of genes and gene regulatory elements, we propose a definition of cell type that emphasizes self-stabilizing regulation. We explore the predictions and hypotheses that arise from this definition. Integration of data from multiple modalities, including molecular profiling of genes and gene products, epigenetic landscape, cellular morphology, connectivity, and physiology, will be essential for a meaningful and broadly useful definition of brain cell types.
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Affiliation(s)
- Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, CA 92037, United States.
| | - John Ngai
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, QB3 Functional Genomics Laboratory, University of California, Berkeley, CA 94720, United States.
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44
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Paglia S, Sollazzo M, Di Giacomo S, Strocchi S, Grifoni D. Exploring MYC relevance to cancer biology from the perspective of cell competition. Semin Cancer Biol 2019; 63:49-59. [PMID: 31102666 DOI: 10.1016/j.semcancer.2019.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/08/2019] [Accepted: 05/14/2019] [Indexed: 12/13/2022]
Abstract
Cancer has long been regarded and treated as a foreign body appearing by mistake inside a living organism. However, now we know that cancer cells communicate with neighbours, thereby creating modified environments able to support their unusual need for nutrients and space. Understanding the molecular basis of these bi-directional interactions is thus mandatory to approach the complex nature of cancer. Since their discovery, MYC proteins have been showing to regulate a steadily increasing number of processes impacting cell fitness, and are consistently found upregulated in almost all human tumours. Of interest, MYC takes part in cell competition, an evolutionarily conserved fitness comparison strategy aimed at detecting weakened cells, which are then committed to death, removed from the tissue and replaced by fitter neighbours. During physiological development, MYC-mediated cell competition is engaged to eliminate cells with suboptimal MYC levels, so as to guarantee selective growth of the fittest and proper homeostasis, while transformed cells expressing high levels of MYC coopt cell competition to subvert tissue constraints, ultimately disrupting homeostasis. Therefore, the interplay between cells with different MYC levels may result in opposite functional outcomes, depending on the nature of the players. In the present review, we describe the most recent findings on the role of MYC-mediated cell competition in different contexts, with a special emphasis on its impact on cancer initiation and progression. We also discuss the relevance of competition-associated cell death to cancer disease.
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Affiliation(s)
- Simona Paglia
- CanceЯEvolutionLab, University of Bologna, Department of Pharmacy and Biotechnology, Via Selmi 3, 40126, Bologna, Italy.
| | - Manuela Sollazzo
- CanceЯEvolutionLab, University of Bologna, Department of Pharmacy and Biotechnology, Via Selmi 3, 40126, Bologna, Italy.
| | - Simone Di Giacomo
- CanceЯEvolutionLab, University of Bologna, Department of Pharmacy and Biotechnology, Via Selmi 3, 40126, Bologna, Italy.
| | - Silvia Strocchi
- CanceЯEvolutionLab, University of Bologna, Department of Pharmacy and Biotechnology, Via Selmi 3, 40126, Bologna, Italy.
| | - Daniela Grifoni
- CanceЯEvolutionLab, University of Bologna, Department of Pharmacy and Biotechnology, Via Selmi 3, 40126, Bologna, Italy.
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NUTM1 Gene Fusions Characterize a Subset of Undifferentiated Soft Tissue and Visceral Tumors. Am J Surg Pathol 2019; 42:636-645. [PMID: 29356724 DOI: 10.1097/pas.0000000000001021] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
NUT midline carcinoma is an aggressive tumor that occurs mainly in the head and neck and, less frequently, the mediastinum and lung. Following identification of an index case of a NUTM1 fusion positive undifferentiated soft tissue tumor, we interrogated additional cases of primary undifferentiated soft tissue and visceral tumors for NUTM1 abnormalities. Targeted next-generation sequencing was performed on RNA extracted from formalin-fixed paraffin-embedded tissue, and results validated by fluorescence in situ hybridization using custom bacterial artificial chromosome probes. Six patients were identified: mean age of 42 years (range, 3 to 71 y); equal sex distribution; and, tumors involved the extremity soft tissues (N=2), kidney (N=2), stomach, and brain. On systemic work-up at presentation all patients lacked a distant primary tumor. Morphologically, the tumors were heterogenous, with undifferentiated round-epithelioid-rhabdoid cells arranged in solid sheets, nests, and cords. Mitotic activity was generally brisk. Four cases expressed pancytokeratin, but in only 2 cases was this diffuse. Next-generation sequencing demonstrated the following fusions: BRD4-NUTM1 (3 cases), BRD3-NUTM1, MXD1-NUTM1, and BCORL1-NUTM1. Independent testing by fluorescence in situ hybridization confirmed the presence of NUTM1 and partner gene rearrangement. This study establishes that NUT-associated tumors transgress the midline and account for a subset of primitive neoplasms occurring in soft tissue and viscera. Tumors harboring NUTM1 gene fusions are presumably underrecognized, and the extent to which they account for undifferentiated mesenchymal, neuroendocrine, and/or epithelial neoplasms is unclear. Moreover, the relationship, if any, between NUT-associated tumors in soft tissue and/or viscera, and conventional NUT carcinoma, remains to be elucidated.
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46
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Zhou Q, Yu B, Anderson C, Huang ZP, Hanus J, Zhang W, Han Y, Bhattacharjee PS, Srinivasan S, Zhang K, Wang DZ, Wang S. LncEGFL7OS regulates human angiogenesis by interacting with MAX at the EGFL7/miR-126 locus. eLife 2019; 8:e40470. [PMID: 30741632 PMCID: PMC6370342 DOI: 10.7554/elife.40470] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 01/11/2019] [Indexed: 01/02/2023] Open
Abstract
In an effort to identify human endothelial cell (EC)-enriched lncRNAs,~500 lncRNAs were shown to be highly restricted in primary human ECs. Among them, lncEGFL7OS, located in the opposite strand of the EGFL7/miR-126 gene, is regulated by ETS factors through a bidirectional promoter in ECs. It is enriched in highly vascularized human tissues, and upregulated in the hearts of dilated cardiomyopathy patients. LncEGFL7OS silencing impairs angiogenesis as shown by EC/fibroblast co-culture, in vitro/in vivo and ex vivo human choroid sprouting angiogenesis assays, while lncEGFL7OS overexpression has the opposite function. Mechanistically, lncEGFL7OS is required for MAPK and AKT pathway activation by regulating EGFL7/miR-126 expression. MAX protein was identified as a lncEGFL7OS-interacting protein that functions to regulate histone acetylation in the EGFL7/miR-126 promoter/enhancer. CRISPR-mediated targeting of EGLF7/miR-126/lncEGFL7OS locus inhibits angiogenesis, inciting therapeutic potential of targeting this locus. Our study establishes lncEGFL7OS as a human/primate-specific EC-restricted lncRNA critical for human angiogenesis.
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Affiliation(s)
- Qinbo Zhou
- Department of Cell and Molecular BiologyTulane UniversityNew OrleansUnited States
| | - Bo Yu
- Department of Cell and Molecular BiologyTulane UniversityNew OrleansUnited States
| | - Chastain Anderson
- Department of Cell and Molecular BiologyTulane UniversityNew OrleansUnited States
| | - Zhan-Peng Huang
- Department of CardiologyBoston Children’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Jakub Hanus
- Department of Cell and Molecular BiologyTulane UniversityNew OrleansUnited States
| | - Wensheng Zhang
- Department of Computer ScienceXavier UniversityNew OrleansUnited States
| | - Yu Han
- Aab Cardiovascular Research InstituteUniversity of Rochester School of Medicine and DentistryRochesterUnited States
| | | | - Sathish Srinivasan
- Cardiovascular Biology Research ProgramOklahoma Medical Research FoundationOklahomaUnited States
| | - Kun Zhang
- Department of Computer ScienceXavier UniversityNew OrleansUnited States
| | - Da-zhi Wang
- Department of CardiologyBoston Children’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Shusheng Wang
- Department of Cell and Molecular BiologyTulane UniversityNew OrleansUnited States
- Department of OphthalmologyTulane UniversityNew OrleansUnited States
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47
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Mitra S, Sharma P, Kaur S, Khursheed MA, Gupta S, Chaudhary M, Kurup AJ, Ramachandran R. Dual regulation of lin28a by Myc is necessary during zebrafish retina regeneration. J Cell Biol 2019; 218:489-507. [PMID: 30606747 PMCID: PMC6363449 DOI: 10.1083/jcb.201802113] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 08/31/2018] [Accepted: 10/29/2018] [Indexed: 02/06/2023] Open
Abstract
Cellular reprogramming leading to induction of Muller glia-derived progenitor cells (MGPCs) with stem cell characteristics is essential for zebrafish retina regeneration. Although several regeneration-specific genes are characterized, the significance of MGPC-associated Mycb induction remains unknown. Here, we show that early expression of Mycb induces expression of genes like ascl1a, a known activator of lin28a in MGPCs. Notably, mycb is simultaneously activated by Ascl1a and repressed by Insm1a in regenerating retina. Here, we unravel a dual role of Mycb in lin28a expression, both as an activator through Ascl1a in MGPCs and a repressor in combination with Hdac1 in neighboring cells. Myc inhibition reduces the number of MGPCs and abolishes normal regeneration. Myc in collaboration with Hdac1 inhibits her4.1, an effector of Delta-Notch signaling. Further, we also show the repressive role of Delta-Notch signaling on lin28a expression in post-injured retina. Our studies reveal mechanistic understanding of Myc pathway during zebrafish retina regeneration, which could pave way for therapeutic intervention during mammalian retina regeneration.
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Affiliation(s)
- Soumitra Mitra
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
| | - Poonam Sharma
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
| | - Simran Kaur
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
| | - Mohammad Anwar Khursheed
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
| | - Shivangi Gupta
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
| | - Mansi Chaudhary
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
| | - Akshai J Kurup
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
| | - Rajesh Ramachandran
- Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, India
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Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT. The Human Transcription Factors. Cell 2019; 172:650-665. [PMID: 29425488 DOI: 10.1016/j.cell.2018.01.029] [Citation(s) in RCA: 1464] [Impact Index Per Article: 292.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/15/2018] [Accepted: 01/22/2018] [Indexed: 12/13/2022]
Abstract
Transcription factors (TFs) recognize specific DNA sequences to control chromatin and transcription, forming a complex system that guides expression of the genome. Despite keen interest in understanding how TFs control gene expression, it remains challenging to determine how the precise genomic binding sites of TFs are specified and how TF binding ultimately relates to regulation of transcription. This review considers how TFs are identified and functionally characterized, principally through the lens of a catalog of over 1,600 likely human TFs and binding motifs for two-thirds of them. Major classes of human TFs differ markedly in their evolutionary trajectories and expression patterns, underscoring distinct functions. TFs likewise underlie many different aspects of human physiology, disease, and variation, highlighting the importance of continued effort to understand TF-mediated gene regulation.
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Affiliation(s)
- Samuel A Lambert
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Arttu Jolma
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Laura F Campitelli
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Pratyush K Das
- Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland
| | - Yimeng Yin
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Mihai Albu
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jussi Taipale
- Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland; Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden; Department of Biochemistry, Cambridge University, Cambridge CB2 1GA, United Kingdom.
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Donnelly Centre, University of Toronto, Toronto, ON, Canada.
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.
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49
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Okada M, Shi YB. The balance of two opposing factors Mad and Myc regulates cell fate during tissue remodeling. Cell Biosci 2018; 8:51. [PMID: 30237868 PMCID: PMC6139171 DOI: 10.1186/s13578-018-0249-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/08/2018] [Indexed: 02/04/2023] Open
Abstract
Cell proliferation and differentiation are two distinct yet coupled processes in development in diverse organisms. Understanding the molecular mechanisms that regulate this process is a central theme in developmental biology. The intestinal epithelium is a highly complex tissue that relies on the coordination of cell proliferation within the crypts and apoptosis mainly at the tip of the villi, preservation of epithelial function through differentiation, and homeostatic cell migration along the crypt-villus axis. Small populations of adult stem cells are responsible for the self-renewal of the epithelium throughout life. Surprisingly, much less is known about the mechanisms governing the remodeling of the intestine from the embryonic to adult form. Furthermore, it remains unknown how thyroid hormone (T3) affects stem cell development during this postembryonic process, which is around birth in mammals when T3 level increase rapidly in the plasma. Tissue remodeling during amphibian metamorphosis is very similar to the maturation of the mammalian organs around birth in mammals and is regulated by T3. In particular, many unique features of Xenopus intestinal remodeling during metamorphosis has enabled us and others to elucidate how adult stem cells are formed during postembryonic development in vertebrates. In this review, we will focus on recent findings on the role of Mad1/c-Myc in cell death and proliferation during intestinal metamorphosis and discuss how a Mad1-c-Myc balance controls intestinal epithelial cell fate during this T3-dependent process.
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Affiliation(s)
- Morihiro Okada
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 18 Library Dr., Bethesda, MD 20892 USA
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 18 Library Dr., Bethesda, MD 20892 USA
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50
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Patra P, Izawa T, Pena-Castillo L. REPA: Applying Pathway Analysis to Genome-Wide Transcription Factor Binding Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1270-1283. [PMID: 27019499 DOI: 10.1109/tcbb.2015.2453948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Pathway analysis has been extensively applied to aid in the interpretation of the results of genome-wide transcription profiling studies, and has been shown to successfully find associations between the biological phenomena under study and biological pathways. There are two widely used approaches of pathway analysis: over-representation analysis, and gene set analysis. Recently genome-wide transcription factor binding data has become widely available allowing for the application of pathway analysis to this type of data. In this work, we developed regulatory enrichment pathway analysis (REPA) to apply gene set analysis to genome-wide transcription factor binding data to infer associations between transcription factors and biological pathways. We used the transcription factor binding data generated by the ENCODE project, and gene sets from the Molecular Signatures and KEGG databases. Our results showed that 54 percent of the predictions examined have literature support and that REPA's recall is roughly 54 percent. This level of precision is promising as several of REPA's predictions are expected to be novel and can be used to guide new research avenues. In addition, the results of our case studies showed that REPA enhances the interpretation of genome-wide transcription profiling studies by suggesting putative regulators behind the observed transcriptional responses.
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