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Suvarna K, Jayabal P, Ma X, Wang H, Chen Y, Weintraub ST, Han X, Houghton PJ, Shiio Y. Ceramide-induced cleavage of GPR64 intracellular domain drives Ewing sarcoma. Cell Rep 2024; 43:114497. [PMID: 39024100 PMCID: PMC11416865 DOI: 10.1016/j.celrep.2024.114497] [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: 12/17/2023] [Revised: 05/07/2024] [Accepted: 06/27/2024] [Indexed: 07/20/2024] Open
Abstract
Ewing sarcoma is a cancer of bone and soft tissue in children and young adults primarily driven by the EWS-FLI1 fusion oncoprotein, which has been undruggable. Here, we report that Ewing sarcoma depends on secreted sphingomyelin phosphodiesterase 1 (SMPD1), a ceramide-generating enzyme, and ceramide. We find that G-protein-coupled receptor 64 (GPR64)/adhesion G-protein-coupled receptor G2 (ADGRG2) responds to ceramide and mediates critical growth signaling in Ewing sarcoma. We show that ceramide induces the cleavage of the C-terminal intracellular domain of GPR64, which translocates to the nucleus and restrains the protein levels of RIF1 in a manner dependent on SPOP, a substrate adaptor of the Cullin3-RING E3 ubiquitin ligase. We demonstrate that both SMPD1 and GPR64 are transcriptional targets of EWS-FLI1, indicating that SMPD1 and GPR64 are EWS-FLI1-induced cytokine-receptor dependencies. These results reveal the SMPD1-ceramide-GPR64 pathway, which drives Ewing sarcoma growth and is amenable to therapeutic intervention.
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Affiliation(s)
- Kruthi Suvarna
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Panneerselvam Jayabal
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Xiuye Ma
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Hu Wang
- Barshop Institute for Longevity and Aging Studies, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Population Health Sciences, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Susan T Weintraub
- Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Medicine, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Molecular Medicine, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Yuzuru Shiio
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229, USA.
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2
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Boddu PC, Gupta AK, Roy R, De La Peña Avalos B, Olazabal-Herrero A, Neuenkirchen N, Zimmer JT, Chandhok NS, King D, Nannya Y, Ogawa S, Lin H, Simon MD, Dray E, Kupfer GM, Verma A, Neugebauer KM, Pillai MM. Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape. Mol Cell 2024; 84:1475-1495.e18. [PMID: 38521065 PMCID: PMC11061666 DOI: 10.1016/j.molcel.2024.02.032] [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: 03/28/2023] [Revised: 11/26/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy.
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Affiliation(s)
- Prajwal C Boddu
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Abhishek K Gupta
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Rahul Roy
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Bárbara De La Peña Avalos
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA
| | - Anne Olazabal-Herrero
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Nils Neuenkirchen
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Joshua T Zimmer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Namrata S Chandhok
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Darren King
- Section of Hematology and Medical Oncology, Department of Internal Medicine and Rogel Cancer Center, University of Michigan Health, Ann Arbor, MI, USA
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Haifan Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA
| | - Gary M Kupfer
- Department of Oncology and Pediatrics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Amit Verma
- Division of Hemato-Oncology, Department of Medicine and Department of Developmental and Molecular Biology, Albert Einstein-Montefiore Cancer Center, New York, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University, New Haven, CT, USA
| | - Manoj M Pillai
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
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3
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Bonilla G, Morris A, Kundu S, Ducasse A, Jeffries NE, Chetal K, Yvanovich EE, Barghout R, Scadden D, Mansour MK, Kingston RE, Sykes DB, Mercier FE, Sadreyev RI. Leukemia aggressiveness is driven by chromatin remodeling and expression changes of core regulators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582846. [PMID: 38496490 PMCID: PMC10942317 DOI: 10.1101/2024.02.29.582846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Molecular mechanisms driving clonal aggressiveness in leukemia are not fully understood. We tracked and analyzed two mouse MLL-rearranged leukemic clones independently evolving towards higher aggressiveness. More aggressive subclones lost their growth differential ex vivo but restored it upon secondary transplantation, suggesting molecular memory of aggressiveness. Development of aggressiveness was associated with clone-specific gradual modulation of chromatin states and expression levels across the genome, with a surprising preferential trend of reversing the earlier changes between normal and leukemic progenitors. To focus on the core aggressiveness program, we identified genes with consistent changes of expression and chromatin marks that were maintained in vivo and ex vivo in both clones. Overexpressing selected core genes (Smad1 as aggressiveness driver, Irx5 and Plag1 as suppressors) affected leukemic progenitor growth in the predicted way and had convergent downstream effects on central transcription factors and repressive epigenetic modifiers, suggesting a broader regulatory network of leukemic aggressiveness.
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Ren AJ, Wei C, Liu YJ, Liu M, Wang P, Fan J, Wang K, Zhang S, Qin Z, Ren QX, Zheng Y, Chen YX, Xie Z, Gao L, Zhu Y, Zhang Y, Yang HT, Zhang WJ. ZBTB20 Regulates SERCA2a Activity and Myocardial Contractility Through Phospholamban. Circ Res 2024; 134:252-265. [PMID: 38166470 DOI: 10.1161/circresaha.123.323798] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/20/2023] [Indexed: 01/04/2024]
Abstract
BACKGROUND Intracellular Ca2+ cycling determines myocardial contraction and relaxation in response to physiological demands. SERCA2a (sarcoplasmic/endoplasmic reticulum Ca2+-ATPase 2a) is responsible for the sequestration of cytosolic Ca2+ into intracellular stores during cardiac relaxation, and its activity is reversibly inhibited by PLN (phospholamban). However, the regulatory hierarchy of SERCA2a activity remains unclear. METHODS Cardiomyocyte-specific ZBTB20 knockout mice were generated by crossing ZBTB20flox mice with Myh6-Cre mice. Echocardiography, blood pressure measurements, Langendorff perfusion, histological analysis and immunohistochemistry, quantitative reverse transcription-PCR, Western blot analysis, electrophysiological measurements, and chromatin immunoprecipitation assay were performed to clarify the phenotype and elucidate the molecular mechanisms. RESULTS Specific ablation of ZBTB20 in cardiomyocyte led to a significant increase in basal myocardial contractile parameters both in vivo and in vitro, accompanied by an impairment in cardiac reserve and exercise capacity. Moreover, the cardiomyocytes lacking ZBTB20 showed an increase in sarcoplasmic reticular Ca2+ content and exhibited a remarkable enhancement in both SERCA2a activity and electrically stimulated contraction. Mechanistically, PLN expression was dramatically reduced in cardiomyocytes at the mRNA and protein levels by ZBTB20 deletion or silencing, and PLN overexpression could largely restore the basal contractility in ZBTB20-deficient cardiomyocytes. CONCLUSIONS These data point to ZBTB20 as a fine-tuning modulator of PLN expression and SERCA2a activity, thereby offering new perspective on the regulation of basal contractility in the mammalian heart.
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Affiliation(s)
- An-Jing Ren
- Department of Pathophysiology, Naval Medical University, Shanghai, China (A.-J.R., C.W., M.L., P.W., K.W., Z.Q., Q.-X.R., Y.-X.C., W.J.Z.)
- Experimental Teaching Center, College of Basic Medical Sciences, Naval Medical University, Shanghai, China (A.-J.R., J.F.)
| | - Chunchun Wei
- Department of Pathophysiology, Naval Medical University, Shanghai, China (A.-J.R., C.W., M.L., P.W., K.W., Z.Q., Q.-X.R., Y.-X.C., W.J.Z.)
| | - Ya-Jin Liu
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Tianjin Institute of Endocrinology and Chu Hsien-I Memorial Hospital, Tianjin Medical University Tianjin, China (Y.-J.L., Y. Zhu, W.J.Z.)
| | - Mengna Liu
- Department of Pathophysiology, Naval Medical University, Shanghai, China (A.-J.R., C.W., M.L., P.W., K.W., Z.Q., Q.-X.R., Y.-X.C., W.J.Z.)
| | - Ping Wang
- Department of Pathophysiology, Naval Medical University, Shanghai, China (A.-J.R., C.W., M.L., P.W., K.W., Z.Q., Q.-X.R., Y.-X.C., W.J.Z.)
| | - Juan Fan
- Experimental Teaching Center, College of Basic Medical Sciences, Naval Medical University, Shanghai, China (A.-J.R., J.F.)
| | - Kai Wang
- Department of Pathophysiology, Naval Medical University, Shanghai, China (A.-J.R., C.W., M.L., P.W., K.W., Z.Q., Q.-X.R., Y.-X.C., W.J.Z.)
| | - Sha Zhang
- Department of Cardiovascular Diseases, Changhai Hospital, Naval Medical University, Shanghai, China (S.Z.)
| | - Zhenbang Qin
- Department of Pathophysiology, Naval Medical University, Shanghai, China (A.-J.R., C.W., M.L., P.W., K.W., Z.Q., Q.-X.R., Y.-X.C., W.J.Z.)
| | - Qiu-Xiao Ren
- Department of Pathophysiology, Naval Medical University, Shanghai, China (A.-J.R., C.W., M.L., P.W., K.W., Z.Q., Q.-X.R., Y.-X.C., W.J.Z.)
| | - Yanjun Zheng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China (Y. Zheng, H.-T.Y.)
| | - Yu-Xia Chen
- Department of Pathophysiology, Naval Medical University, Shanghai, China (A.-J.R., C.W., M.L., P.W., K.W., Z.Q., Q.-X.R., Y.-X.C., W.J.Z.)
| | - Zhifang Xie
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Institute of Early Life Health, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, China (Z.X.)
| | - Ling Gao
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, China (L.G.)
| | - Yi Zhu
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Tianjin Institute of Endocrinology and Chu Hsien-I Memorial Hospital, Tianjin Medical University Tianjin, China (Y.-J.L., Y. Zhu, W.J.Z.)
| | - Youyi Zhang
- Institute of Vascular Medicine, National Key Laboratory of Cardiovascular Homeostasis and Remodeling, Peking University Third Hospital, Beijing, China (Y. Zhang)
| | - Huang-Tian Yang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China (Y. Zheng, H.-T.Y.)
| | - Weiping J Zhang
- Department of Pathophysiology, Naval Medical University, Shanghai, China (A.-J.R., C.W., M.L., P.W., K.W., Z.Q., Q.-X.R., Y.-X.C., W.J.Z.)
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Tianjin Institute of Endocrinology and Chu Hsien-I Memorial Hospital, Tianjin Medical University Tianjin, China (Y.-J.L., Y. Zhu, W.J.Z.)
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5
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Dunn LEM, Birkenheuer CH, Baines JD. A Revision of Herpes Simplex Virus Type 1 Transcription: First, Repress; Then, Express. Microorganisms 2024; 12:262. [PMID: 38399666 PMCID: PMC10892140 DOI: 10.3390/microorganisms12020262] [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: 12/15/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The herpes virus genome bears more than 80 strong transcriptional promoters. Upon entry into the host cell nucleus, these genes are transcribed in an orderly manner, producing five immediate-early (IE) gene products, including ICP0, ICP4, and ICP22, while non-IE genes are mostly silent. The IE gene products are necessary for the transcription of temporal classes following sequentially as early, leaky late, and true late. A recent analysis using precision nuclear run-on followed by deep sequencing (PRO-seq) has revealed an important step preceding all HSV-1 transcription. Specifically, the immediate-early proteins ICP4 and ICP0 enter the cell with the incoming genome to help preclude the nascent antisense, intergenic, and sense transcription of all viral genes. VP16, which is also delivered into the nucleus upon entry, almost immediately reverses this repression on IE genes. The resulting de novo expression of ICP4 and ICP22 further repress antisense, intergenic, and early and late viral gene transcription through different mechanisms before the sequential de-repression of these gene classes later in infection. This early repression, termed transient immediate-early protein-mediated repression (TIEMR), precludes unproductive, antisense, intergenic, and late gene transcription early in infection to ensure the efficient and orderly progression of the viral cascade.
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Affiliation(s)
- Laura E M Dunn
- Baker Institute for Animal Health, Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850, USA
| | - Claire H Birkenheuer
- Baker Institute for Animal Health, Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850, USA
| | - Joel D Baines
- Baker Institute for Animal Health, Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850, USA
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6
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Uemura K, Ohyama T. Physical Peculiarity of Two Sites in Human Promoters: Universality and Diverse Usage in Gene Function. Int J Mol Sci 2024; 25:1487. [PMID: 38338773 PMCID: PMC10855393 DOI: 10.3390/ijms25031487] [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: 12/08/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/12/2024] Open
Abstract
Since the discovery of physical peculiarities around transcription start sites (TSSs) and a site corresponding to the TATA box, research has revealed only the average features of these sites. Unsettled enigmas include the individual genes with these features and whether they relate to gene function. Herein, using 10 physical properties of DNA, including duplex DNA free energy, base stacking energy, protein-induced deformability, and stabilizing energy of Z-DNA, we clarified for the first time that approximately 97% of the promoters of 21,056 human protein-coding genes have distinctive physical properties around the TSS and/or position -27; of these, nearly 65% exhibited such properties at both sites. Furthermore, about 55% of the 21,056 genes had a minimum value of regional duplex DNA free energy within TSS-centered ±300 bp regions. Notably, distinctive physical properties within the promoters and free energies of the surrounding regions separated human protein-coding genes into five groups; each contained specific gene ontology (GO) terms. The group represented by immune response genes differed distinctly from the other four regarding the parameter of the free energies of the surrounding regions. A vital suggestion from this study is that physical-feature-based analyses of genomes may reveal new aspects of the organization and regulation of genes.
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Affiliation(s)
- Kohei Uemura
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan;
| | - Takashi Ohyama
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan;
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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7
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Gazdik TR, Crow JJ, Lawton T, Munroe CJ, Theriault H, Wood TM, Albig AR. Notch intracellular domains form transcriptionally active heterodimeric complexes on sequence-paired sites. Sci Rep 2024; 14:218. [PMID: 38168761 PMCID: PMC10761890 DOI: 10.1038/s41598-023-50763-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/25/2023] [Indexed: 01/05/2024] Open
Abstract
Notch signaling is universally conserved in metazoans where it is important for a wide variety of both normal and abnormal physiology. All four mammalian Notch receptors are activated by a conserved mechanism that releases Notch intracellular domains (NICDs) from the plasma membrane to translocate to the nucleus. Once there, NICDs interact through highly conserved ankyrin domains to form head-to-head homodimers on Notch sensitive promoters and stimulate transcription. Due to the highly conserved nature of these Notch ankyrin domains in all four mammalian Notch proteins, we hypothesized that NICDs may also engage in heterodimerization. Our results reveal the presence of two NICD dimerization states that can both engage in homo and heterodimerization. Using a Co-IP approach, we show that all NICD's can form non-transcriptionally active dimers and that the N4ICD appears to perform this function better than the other NICDs. Using a combination of ChIP analysis and transcriptional reporter assays, we also demonstrate the formation of transcriptionally active heterodimers that form on DNA. In particular, we demonstrate heterodimerization between the N2ICD and N4ICD and show that this heterodimer pair appears to exhibit differential activity on various Notch sensitive promoters. These results illustrate a new diversification of Notch signaling mechanisms which will help us better understand basic Notch function.
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Affiliation(s)
- Tana R Gazdik
- Biomolecular Sciences PhD Program, Boise State University, Boise, ID, 83725, USA
| | - Jacob J Crow
- Biomolecular Sciences PhD Program, Boise State University, Boise, ID, 83725, USA
| | - Tyler Lawton
- Biomolecular Sciences PhD Program, Boise State University, Boise, ID, 83725, USA
| | - Chloe J Munroe
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA
| | - Hannah Theriault
- Department of Chemistry, Boise State University, Boise, ID, 83725, USA
| | - Travis M Wood
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA
| | - Allan R Albig
- Biomolecular Sciences PhD Program, Boise State University, Boise, ID, 83725, USA.
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA.
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8
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Prabakaran AD, McFarland K, Miz K, Durumutla HB, Piczer K, El Abdellaoui Soussi F, Latimer H, Werbrich C, Blair NS, Millay DP, Prideaux B, Finck BN, Quattrocelli M. Glucocorticoid intermittence coordinates rescue of energy and mass in aging-related sarcopenia through the myocyte-autonomous PGC1alpha-Lipin1 transactivation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562573. [PMID: 37905062 PMCID: PMC10614926 DOI: 10.1101/2023.10.16.562573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Sarcopenia burdens the elderly population through loss of muscle energy and mass, yet treatments to functionally rescue both parameters are missing. The glucocorticoid prednisone remodels muscle metabolism based on frequency of intake, but its mechanisms in sarcopenia are unknown. We found that once-weekly intermittent prednisone rescued muscle quality in aged 24-month-old mice to levels comparable to young 4-month-old mice. We discovered an age- and sex-independent glucocorticoid receptor transactivation program in muscle encompassing PGC1alpha and its co-factor Lipin1. Treatment coordinately improved mitochondrial abundance through isoform 1 and muscle mass through isoform 4 of the myocyte-specific PGC1alpha, which was required for the treatment-driven increase in carbon shuttling from glucose oxidation to amino acid biogenesis. We also probed the myocyte-specific Lipin1 as non-redundant factor coaxing PGC1alpha upregulation to the stimulation of both oxidative and anabolic capacities. Our study unveils an aging-resistant druggable program in myocytes to coordinately rescue energy and mass in sarcopenia.
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Affiliation(s)
- Ashok Daniel Prabakaran
- Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children’s Hospital Medical Center and Dept. Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kevin McFarland
- Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children’s Hospital Medical Center and Dept. Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Karen Miz
- Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children’s Hospital Medical Center and Dept. Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Hima Bindu Durumutla
- Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children’s Hospital Medical Center and Dept. Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kevin Piczer
- Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children’s Hospital Medical Center and Dept. Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Fadoua El Abdellaoui Soussi
- Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children’s Hospital Medical Center and Dept. Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Hannah Latimer
- Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children’s Hospital Medical Center and Dept. Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Cole Werbrich
- Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children’s Hospital Medical Center and Dept. Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - N. Scott Blair
- Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children’s Hospital Medical Center and Dept. Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Douglas P Millay
- Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children’s Hospital Medical Center and Dept. Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Brendan Prideaux
- Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Brian N Finck
- Department of Medicine, Center for Human Nutrition, Washington University in St Louis, MO, USA
| | - Mattia Quattrocelli
- Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children’s Hospital Medical Center and Dept. Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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9
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Shao J, Shi T, Chen L, Wang X, Yu H, Feng N, Wang X. AF9 targets acetyl-modified STAT6 to diminish purine metabolism and accelerate cell apoptosis during metastasis. Cell Death Differ 2023; 30:1695-1709. [PMID: 37308587 PMCID: PMC10307824 DOI: 10.1038/s41418-023-01172-7] [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: 08/04/2022] [Revised: 04/14/2023] [Accepted: 04/25/2023] [Indexed: 06/14/2023] Open
Abstract
Cell migration and invasion are two important steps for tumour metastasis, and involved the behaviors including metabolism remodeling and anti-apoptosis. However, it's still elusive that cancer cells how to antagonize apoptosis during tumour metastasis. In this study, we observed that super elongation complex (SEC) subunit AF9 depletion exacerbated cell migration and invasion but reduced the apoptosis during invasive migration. Mechanically, AF9 targeted acetyl (Ac)-STAT6 at lysine (K) 284 and blocked STAT6 transactivation on the promoter of such genes involved in regulating purine metabolism and metastasis, in turn induced apoptosis of suspended cells. Of note, AcSTAT6-K284 was not induced by IL4 signaling but decreased by limited nutrition which triggered SIRT6 to remove acetyl group at STAT6-K284. The functional experiments proved that AcSTAT6-K284 attenuated cell migration and invasion depending on AF9 expression level. Animal metastatic study further confirmed the AF9/AcSTAT6-K284 axis existed and blocked kidney renal clear cell carcinoma (KIRC) metastasis. In clinical, both AF9 expression and AcSTAT6-K284 were decreased accompanied by the advanced tumour grade and positively correlated with KIRC patients' survival. Conclusively, we explored an inhibitory axis which not only suppressed tumour metastasis but also could be utilized for drug development to hamper KIRC metastasis.
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Affiliation(s)
- Jialiang Shao
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University, Shanghai, 200080, China
| | - Tiezhu Shi
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Lianheng Chen
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Xiang Wang
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University, Shanghai, 200080, China
| | - Hua Yu
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
| | - Ninghan Feng
- Department of Urology, The Affiliated Wuxi No.2 Hospital of Nanjing Medical University, Jiangsu, 214002, China.
| | - Xiongjun Wang
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
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10
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Chandrashekar PB, Chen H, Lee M, Ahmadinejad N, Liu L. DeepCORE: An interpretable multi-view deep neural network model to detect co-operative regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.536807. [PMID: 37131697 PMCID: PMC10153112 DOI: 10.1101/2023.04.19.536807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Gene transcription is an essential process involved in all aspects of cellular functions with significant impact on biological traits and diseases. This process is tightly regulated by multiple elements that co-operate to jointly modulate the transcription levels of target genes. To decipher the complicated regulatory network, we present a novel multi-view attention-based deep neural network that models the relationship between genetic, epigenetic, and transcriptional patterns and identifies co-operative regulatory elements (COREs). We applied this new method, named DeepCORE, to predict transcriptomes in 25 different cell lines, which outperformed the state-of-the-art algorithms. Furthermore, DeepCORE translates the attention values embedded in the neural network into interpretable information, including locations of putative regulatory elements and their correlations, which collectively implies COREs. These COREs are significantly enriched with known promoters and enhancers. Novel regulatory elements discovered by DeepCORE showed epigenetic signatures consistent with the status of histone modification marks.
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11
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Walter M, Mayr F, Hanna BMF, Cookson V, Mortusewicz O, Helleday T, Herr P. NUDT22 promotes cancer growth through pyrimidine salvage. Oncogene 2023; 42:1282-1293. [PMID: 36871087 PMCID: PMC10101856 DOI: 10.1038/s41388-023-02643-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 03/06/2023]
Abstract
The NUDIX hydrolase NUDT22 converts UDP-glucose into glucose-1-phosphate and the pyrimidine nucleotide uridine monophosphate but a biological significance for this biochemical reaction has not yet been established. Glucose-1-phosphate is an important metabolite for energy and biomass production through glycolysis and nucleotides required for DNA replication are produced through energetically expensive de novo or energy-efficient salvage pathways. Here, we describe p53-regulated pyrimidine salvage through NUDT22-dependent hydrolysis of UDP-glucose to maintain cancer cell growth and to prevent replication stress. NUDT22 expression is consistently elevated in cancer tissues and high NUDT22 expression correlates with worse survival outcomes in patients indicating an increased dependency of cancer cells to NUDT22. Furthermore, we show that NUDT22 transcription is induced after inhibition of glycolysis, MYC-mediated oncogenic stress, and DNA damage directly through p53. NUDT22-deficient cancer cells suffer from growth retardation, S-phase delay, and slower DNA replication fork speed. Uridine supplementation rescues replication fork progression and alleviates replication stress and DNA damage. Conversely, NUDT22 deficiency sensitizes cells to de novo pyrimidine synthesis inhibition in vitro and reduces cancer growth in vivo. In conclusion, NUDT22 maintains pyrimidine supply in cancer cells and depletion of NUDT22 leads to genome instability. Targeting NUDT22 therefore has high potential for therapeutic applications in cancer therapy.
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Affiliation(s)
- Melanie Walter
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - Florian Mayr
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institute, 171 76, Stockholm, Sweden
| | - Bishoy M F Hanna
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institute, 171 76, Stockholm, Sweden
| | - Victoria Cookson
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - Oliver Mortusewicz
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institute, 171 76, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institute, 171 76, Stockholm, Sweden
| | - Patrick Herr
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK.
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12
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Pramio DT, Vieceli FM, Varella-Branco E, Goes CP, Kobayashi GS, da Silva Pelegrina DV, de Moraes BC, El Allam A, De Kumar B, Jara G, Farfel JM, Bennett DA, Kundu S, Viapiano MS, Reis EM, de Oliveira PSL, Dos Santos E Passos-Bueno MR, Rothlin CV, Ghosh S, Schechtman D. DNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain-specific PKMζ. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194909. [PMID: 36682583 PMCID: PMC10037092 DOI: 10.1016/j.bbagrm.2023.194909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 01/05/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023]
Abstract
Protein kinase M zeta, PKMζ, is a brain enriched kinase with a well characterized role in Long-Term Potentiation (LTP), the activity-dependent strengthening of synapses involved in long-term memory formation. However, little is known about the molecular mechanisms that maintain the tissue specificity of this kinase. Here, we characterized the epigenetic factors, mainly DNA methylation, regulating PKMζ expression in the human brain. The PRKCZ gene has an upstream promoter regulating Protein kinase C ζ (PKCζ), and an internal promoter driving PKMζ expression. A demethylated region, including a canonical CREB binding site, situated at the internal promoter was only observed in human CNS tissues. The induction of site-specific hypermethylation of this region resulted in decreased CREB1 binding and downregulation of PKMζ expression. Noteworthy, CREB binding sites were absent in the upstream promoter of PRKCZ locus, suggesting a specific mechanism for regulating PKMζ expression. These observations were validated using a system of human neuronal differentiation from induced pluripotent stem cells (iPSCs). CREB1 binding at the internal promoter was detected only in differentiated neurons, where PKMζ is expressed. The same epigenetic mechanism in the context of CREB binding site was identified in other genes involved in neuronal differentiation and LTP. Additionally, aberrant DNA hypermethylation at the internal promoter was observed in cases of Alzheimer's disease, correlating with decreased expression of PKMζ in patient brains. Altogether, we present a conserved epigenetic mechanism regulating PKMζ expression and other genes enhanced in the CNS with possible implications in neuronal differentiation and Alzheimer's disease.
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Affiliation(s)
| | | | | | - Carolina Purcell Goes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil; Laboratory of Neuromodulation of Experimental Pain, Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo, SP, Brazil
| | | | | | | | - Aicha El Allam
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | | | - Gabriel Jara
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian National Biosciences Laboratory (LNBio) Campinas, SP, Brazil
| | - José Marcelo Farfel
- Traumatology and Orthopedy Department, Faculdade de Medicina, Universidade de São Paulo, SP, Brazil; Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Health Sciences Program, Instituto de Assistência Medica ao Servidor Público do Estado (IAMSPE), SP, Brazil
| | - David Alan Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Somanath Kundu
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Mariano S Viapiano
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Eduardo Moraes Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil
| | - Paulo Sergio Lopes de Oliveira
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian National Biosciences Laboratory (LNBio) Campinas, SP, Brazil
| | | | - Carla V Rothlin
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA; Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Sourav Ghosh
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - Deborah Schechtman
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil.
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13
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Boddu PC, Gupta A, Roy R, De La Pena Avalos B, Herrero AO, Neuenkirchen N, Zimmer J, Chandhok N, King D, Nannya Y, Ogawa S, Lin H, Simon M, Dray E, Kupfer G, Verma AK, Neugebauer KM, Pillai MM. Transcription elongation defects link oncogenic splicing factor mutations to targetable alterations in chromatin landscape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.530019. [PMID: 36891287 PMCID: PMC9994134 DOI: 10.1101/2023.02.25.530019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human disease remains unexplored. Here, we investigated the impact of non-synonymous mutations in SF3B1 and U2AF1, two commonly mutated splicing factors in cancer, on transcription. We find that the mutations impair RNA Polymerase II (RNAPII) transcription elongation along gene bodies leading to transcription-replication conflicts, replication stress and altered chromatin organization. This elongation defect is linked to disrupted pre-spliceosome assembly due to impaired association of HTATSF1 with mutant SF3B1. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC complex, which, when modulated, normalize transcription defects and their downstream effects. Our findings shed light on the mechanisms by which oncogenic mutant spliceosomes impact chromatin organization through their effects on RNAPII transcription elongation and present a rationale for targeting the Sin3/HDAC complex as a potential therapeutic strategy. GRAPHICAL ABSTRACT HIGHLIGHTS Oncogenic mutations of SF3B1 and U2AF1 cause a gene-body RNAPII elongation defectRNAPII transcription elongation defect leads to transcription replication conflicts, DNA damage response, and changes to chromatin organization and H3K4me3 marksThe transcription elongation defect is linked to disruption of the early spliceosome formation through impaired interaction of HTATSF1 with mutant SF3B1.Changes to chromatin organization reveal potential therapeutic strategies by targeting the Sin3/HDAC pathway.
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14
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Suvarna K, Jayabal P, Ma X, Shiio Y. Slit2 signaling stimulates Ewing sarcoma growth. Genes Cancer 2022; 13:88-99. [PMID: 36533189 PMCID: PMC9753566 DOI: 10.18632/genesandcancer.227] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
Ewing sarcoma is a cancer of bone and soft tissue in children driven by EWS::ETS fusion, most commonly EWS::FLI1. Because current cytotoxic chemotherapies are not improving the survival of those with metastatic or recurrent Ewing sarcoma cases, there is a need for novel and more effective targeted therapies. While EWS::FLI1 is the major driver of Ewing sarcoma, EWS::FLI1 has been difficult to target. A promising alternative approach is to identify and target the molecular vulnerabilities created by EWS::FLI1. Here we report that EWS::FLI1 induces the expression of Slit2, the ligand of Roundabout (Robo) receptors implicated in axon guidance and multiple other developmental processes. EWS::FLI1 binds to the Slit2 gene promoter and stimulates the expression of Slit2. Slit2 inactivates cdc42 and stabilizes the BAF chromatin remodeling complexes, enhancing EWS::FLI1 transcriptional output. Silencing of Slit2 strongly inhibited anchorage-dependent and anchorage-independent growth of Ewing sarcoma cells. Silencing of Slit2 receptors, Robo1 and Robo2, inhibited Ewing sarcoma growth as well. These results uncover a new role for Slit2 signaling in stimulating Ewing sarcoma growth and suggest that this pathway can be targeted therapeutically.
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Affiliation(s)
- Kruthi Suvarna
- 1Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
| | - Panneerselvam Jayabal
- 1Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
| | - Xiuye Ma
- 1Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
| | - Yuzuru Shiio
- 1Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA,2Cancer Therapy and Research Center, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA,3Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA,Correspondence to:Yuzuru Shiio, email:
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15
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Dahal S, Siddiqua H, Sharma S, Babu RK, Rathore D, Sharma S, Raghavan SC. Unleashing a novel function of Endonuclease G in mitochondrial genome instability. eLife 2022; 11:e69916. [PMID: 36394256 PMCID: PMC9711528 DOI: 10.7554/elife.69916] [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: 04/29/2021] [Accepted: 11/16/2022] [Indexed: 11/18/2022] Open
Abstract
Having its genome makes the mitochondrion a unique and semiautonomous organelle within cells. Mammalian mitochondrial DNA (mtDNA) is a double-stranded closed circular molecule of about 16 kb coding for 37 genes. Mutations, including deletions in the mitochondrial genome, can culminate in different human diseases. Mapping the deletion junctions suggests that the breakpoints are generally seen at hotspots. '9 bp deletion' (8271-8281), seen in the intergenic region of cytochrome c oxidase II/tRNALys, is the most common mitochondrial deletion. While it is associated with several diseases like myopathy, dystonia, and hepatocellular carcinoma, it has also been used as an evolutionary marker. However, the mechanism responsible for its fragility is unclear. In the current study, we show that Endonuclease G, a mitochondrial nuclease responsible for nonspecific cleavage of nuclear DNA during apoptosis, can induce breaks at sequences associated with '9 bp deletion' when it is present on a plasmid or in the mitochondrial genome. Through a series of in vitro and intracellular studies, we show that Endonuclease G binds to G-quadruplex structures formed at the hotspot and induces DNA breaks. Therefore, we uncover a new role for Endonuclease G in generating mtDNA deletions, which depends on the formation of G4 DNA within the mitochondrial genome. In summary, we identify a novel property of Endonuclease G, besides its role in apoptosis and the recently described 'elimination of paternal mitochondria during fertilisation.
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Affiliation(s)
- Sumedha Dahal
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Humaira Siddiqua
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Shivangi Sharma
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Ravi K Babu
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Diksha Rathore
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Sheetal Sharma
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
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16
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Karoussiotis C, Sotiriou A, Polissidis A, Symeonof A, Papavranoussi-Daponte D, Nikoletopoulou V, Georgoussi Z. The κ-opioid receptor-induced autophagy is implicated in stress-driven synaptic alterations. Front Mol Neurosci 2022; 15:1039135. [PMID: 36466809 PMCID: PMC9709411 DOI: 10.3389/fnmol.2022.1039135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/26/2022] [Indexed: 08/29/2023] Open
Abstract
Recent evidence has shown that G protein-coupled receptors (GPCRs) are direct sensors of the autophagic machinery and opioid receptors regulate neuronal plasticity and neurotransmission with an as yet unclarified mechanism. Using in vitro and in vivo experimental approaches, this study aims to clarify the potential role of autophagy and κ-opioid receptor (κ-OR) signaling in synaptic alterations. We hereby demonstrate that the selective κ-OR agonist U50,488H, induces autophagy in a time-and dose-dependent manner in Neuro-2A cells stably expressing the human κ-OR by upregulating microtubule-associated protein Light Chain 3-II (LC3-II), Beclin 1 and Autophagy Related Gene 5 (ATG5). Pretreatment of neuronal cells with pertussis toxin blocked the above κ-OR-mediated cellular responses. Our molecular analysis also revealed a κ-OR-driven upregulation of becn1 gene through ERK1,2-dependent activation of the transcription factor CREB in Neuro-2A cells. Moreover, our studies demonstrated that sub-chronic U50,488H administration in mice causes profound increases of specific autophagic markers in the hippocampus with a concomitant decrease of several pre-and post-synaptic proteins, such as spinophilin, postsynaptic density protein 95 (PSD-95) and synaptosomal associated protein 25 (SNAP25). Finally, using acute stress, a stimulus known to increase the levels of the endogenous κ-OR ligand dynorphin, we are demonstrating that administration of the κ-ΟR selective antagonist, nor-binaltorphimine (norBNI), blocks the induction of autophagy and the stress-evoked reduction of synaptic proteins in the hippocampus. These findings provide novel insights about the essential role of autophagic machinery into the mechanisms through which κ-OR signaling regulates brain plasticity.
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Affiliation(s)
- Christos Karoussiotis
- Laboratory of Cellular Signaling and Molecular Pharmacology, Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
| | - Aggeliki Sotiriou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Alexia Polissidis
- Center for Clinical Research, Experimental Surgery, and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Alexandra Symeonof
- Laboratory of Cellular Signaling and Molecular Pharmacology, Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
| | - Danae Papavranoussi-Daponte
- Laboratory of Cellular Signaling and Molecular Pharmacology, Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
| | | | - Zafiroula Georgoussi
- Laboratory of Cellular Signaling and Molecular Pharmacology, Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
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17
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Paranjape AM, Desai SS, Nishana M, Roy U, Nilavar NM, Mondal A, Kumari R, Radha G, Katapadi VK, Choudhary B, Raghavan SC. Nonamer dependent RAG cleavage at CpGs can explain mechanism of chromosomal translocations associated to lymphoid cancers. PLoS Genet 2022; 18:e1010421. [PMID: 36228010 PMCID: PMC9595545 DOI: 10.1371/journal.pgen.1010421] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/25/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022] Open
Abstract
Chromosomal translocations are considered as one of the major causes of lymphoid cancers. RAG complex, which is responsible for V(D)J recombination, can also cleave non-B DNA structures and cryptic RSSs in the genome leading to chromosomal translocations. The mechanism and factors regulating the illegitimate function of RAGs resulting in oncogenesis are largely unknown. Upon in silico analysis of 3760 chromosomal translocations from lymphoid cancer patients, we find that 93% of the translocation breakpoints possess adjacent cryptic nonamers (RAG binding sequences), of which 77% had CpGs in proximity. As a proof of principle, we show that RAGs can efficiently bind to cryptic nonamers present at multiple fragile regions and cleave at adjacent mismatches generated to mimic the deamination of CpGs. ChIP studies reveal that RAGs can indeed recognize these fragile sites on a chromatin context inside the cell. Finally, we show that AID, the cytidine deaminase, plays a significant role during the generation of mismatches at CpGs and reconstitute the process of RAG-dependent generation of DNA breaks both in vitro and inside the cells. Thus, we propose a novel mechanism for generation of chromosomal translocation, where RAGs bind to the cryptic nonamer sequences and direct cleavage at adjacent mismatch generated due to deamination of meCpGs or cytosines.
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Affiliation(s)
- Amita M. Paranjape
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sagar S. Desai
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Mayilaadumveettil Nishana
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
- Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Urbi Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Namrata M. Nilavar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Amrita Mondal
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Rupa Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Gudapureddy Radha
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India
- * E-mail: (BC); (SCR)
| | - Sathees C. Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
- * E-mail: (BC); (SCR)
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18
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Barajas-Mendiola MA, Salgado-Lora MG, López-Meza JE, Ochoa-Zarzosa A. Prolactin regulates H3K9ac and H3K9me2 epigenetic marks and miRNAs expression in bovine mammary epithelial cells challenged with Staphylococcus aureus. Front Microbiol 2022; 13:990478. [PMID: 36212825 PMCID: PMC9539446 DOI: 10.3389/fmicb.2022.990478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Epigenetic mechanisms are essential in the regulation of immune response during infections. Changes in the levels of reproductive hormones, such as prolactin, compromise the mammary gland’s innate immune response (IIR); however, its effect on epigenetic marks is poorly known. This work explored the epigenetic regulation induced by bovine prolactin (bPRL) on bovine mammary epithelial cells (bMECs) challenged with Staphylococcus aureus. In this work, bMECs were treated as follows: (1) control cells without any treatment, (2) bMECs treated with bPRL (5 ng/ml) at different times (12 or 24 h), (3) bMECs challenged with S. aureus for 2 h, and (4) bMECs treated with bPRL at different times (12 or 24 h), and then challenged with S. aureus 2 h. By western blot analyses of histones, we determined that the H3K9ac mark decreased (20%) in bMECs treated with bPRL (12 h) and challenged with S. aureus, while the H3K9me2 mark was increased (50%) in the same conditions. Also, this result coincided with an increase (2.3-fold) in HDAC activity analyzed using the cellular histone deacetylase fluorescent kit FLUOR DE LYS®. ChIP-qPCRs were performed to determine if the epigenetic marks detected in the histones correlate with enriched marks in the promoter regions of inflammatory genes associated with the S. aureus challenge. The H3K9ac mark was enriched in the promoter region of IL-1β, IL-10, and BNBD10 genes (1.5, 2.5, 7.5-fold, respectively) in bMECs treated with bPRL, but in bMECs challenged with S. aureus it was reduced. Besides, the H3K9me2 mark was enriched in the promoter region of IL-1β and IL-10 genes (3.5 and 2.5-fold, respectively) in bMECs challenged with S. aureus but was inhibited by bPRL. Additionally, the expression of several miRNAs was analyzed by qPCR. Let-7a-5p, miR-21a, miR-30b, miR-155, and miR-7863 miRNAs were up-regulated (2, 1.5, 10, 1.5, 3.9-fold, respectively) in bMECs challenged with S. aureus; however, bPRL induced a down-regulation in the expression of these miRNAs. In conclusion, bPRL induces epigenetic regulation on specific IIR elements, allowing S. aureus to persist and evade the host immune response.
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19
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Ma T, Gu J, Zhao Y, Li S, Zou D, Ge D. EZH2-mediated suppression of CLDN1 leads to barrier dysfunction in PPI-refractory gastroesophageal reflux disease. Dig Liver Dis 2022; 54:776-783. [PMID: 34789399 DOI: 10.1016/j.dld.2021.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/02/2021] [Accepted: 10/18/2021] [Indexed: 01/30/2023]
Abstract
BACKGROUND PPI-refractory gastroesophageal reflux disease (RGERD) is characterized as the existence of reflux symptoms resistant to optimized PPI treatment. Alleviated mucosal integrity has been regarded as one of the mechanisms of RGERD. METHODS RNA sequencing analysis and GSEA were performed. Human biopsy samples, cell lines, and rat models were recruited. Trans-epithelial electrical resistance (TEER) was tested and a FITC-dextran flux assay was performed to detect barrier permeability. Tissue morphology was evaluated using HE staining, while gene expression was measured by qRT-PCR, western blotting, flow cytometry, immunofluorescence, immunohistochemistry, and chromatin immunoprecipitation (ChIP) analysis. RESULTS The tight junction protein Claudin-1 is significantly weakened in the RGERD epithelium, while levels of EZH2-mediated H3K27me3 were increased. Forced EZH2 expression in epithelial cells led to H3K27me3 accumulation and Claudin-1 suppression, which consequently caused epithelial barrier dysfunction. Notably, studies on esophagogastroduodenal anastomosis (EGDA) rat models showed the attenuation of Claudin-1 level and barrier function could be rescued by an Ezh2 inhibitor GSK126. ChIP analysis followed by qPCR (ChIP-qPCR) revealed H3K27me3 suppressed CLDN1 via accumulating at the TSS area. CONCLUSION For the first time, we explored the attenuated tight junction of RGERD, demonstrating a potential underlying mechanism that EZH2-mediated H3K27me3 could impair esophageal epithelial barrier function by suppressing the transcription of CLDN1.
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Affiliation(s)
- Teng Ma
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jie Gu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ye Zhao
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Su Li
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Duowu Zou
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Di Ge
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
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20
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Li YJ, Fahrmann JF, Aftabizadeh M, Zhao Q, Tripathi SC, Zhang C, Yuan Y, Ann D, Hanash S, Yu H. Fatty acid oxidation protects cancer cells from apoptosis by increasing mitochondrial membrane lipids. Cell Rep 2022; 39:110870. [PMID: 35649368 DOI: 10.1016/j.celrep.2022.110870] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 03/16/2022] [Accepted: 05/04/2022] [Indexed: 12/22/2022] Open
Abstract
Overcoming resistance to chemotherapies remains a major unmet need for cancers, such as triple-negative breast cancer (TNBC). Therefore, mechanistic studies to provide insight for drug development are urgently needed to overcome TNBC therapy resistance. Recently, an important role of fatty acid β-oxidation (FAO) in chemoresistance has been shown. But how FAO might mitigate tumor cell apoptosis by chemotherapy is unclear. Here, we show that elevated FAO activates STAT3 by acetylation via elevated acetyl-coenzyme A (CoA). Acetylated STAT3 upregulates expression of long-chain acyl-CoA synthetase 4 (ACSL4), resulting in increased phospholipid synthesis. Elevating phospholipids in mitochondrial membranes leads to heightened mitochondrial integrity, which in turn overcomes chemotherapy-induced tumor cell apoptosis. Conversely, in both cultured tumor cells and xenograft tumors, enhanced cancer cell apoptosis by inhibiting ASCL4 or specifically targeting acetylated-STAT3 is associated with a reduction in phospholipids within mitochondrial membranes. This study demonstrates a critical mechanism underlying tumor cell chemoresistance.
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Affiliation(s)
- Yi-Jia Li
- Department of Immuno-Oncology, Beckman Research Institute and City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA.
| | - Johannes Francois Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Maryam Aftabizadeh
- Department of Immuno-Oncology, Beckman Research Institute and City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Qianqian Zhao
- Department of Immuno-Oncology, Beckman Research Institute and City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Satyendra C Tripathi
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Chunyan Zhang
- Department of Immuno-Oncology, Beckman Research Institute and City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Yuan Yuan
- Department of PS Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - David Ann
- Department of Diabetes Complications and Metabolism, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Samir Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Hua Yu
- Department of Immuno-Oncology, Beckman Research Institute and City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA.
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21
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Abstract
In mammals, parthenogenesis is limited because of problems arising from genomic imprinting. Here, we report live mammalian offspring derived from single unfertilized eggs. This was achieved by the targeted DNA methylation rewriting of seven imprinting control regions. By designing guide RNAs with protospacer adjacent motif (PAM) sequences matching one allele but not the other, dCas9-Dnmt3a or dCpf1-Tet1 enables targeted DNA methylation editing in an allele-specific manner. The success of parthenogenesis in mammals opens many opportunities in agriculture, research, and medicine. In mammals, a new life starts with the fusion of an oocyte and a sperm cell. Parthenogenesis, a way of generating offspring solely from female gametes, is limited because of problems arising from genomic imprinting. Here, we report live mammalian offspring derived from single unfertilized oocytes, which was achieved by targeted DNA methylation rewriting of seven imprinting control regions. Oocyte coinjection of catalytically inactive Cas9 (dCas9)-Dnmt3a or dCpf1-Tet1 messenger RNA (mRNA) with single-guide RNAs (sgRNAs) targeting specific regions induced de novo methylation or demethylation, respectively, of the targeted region. Following parthenogenetic activation, these edited regions showed maintenance of methylation as naturally established regions during early preimplantation development. The transfer of modified parthenogenetic embryos into foster mothers resulted in significantly extended development and finally in the generation of viable full-term offspring. These data demonstrate that parthenogenesis can be achieved by targeted epigenetic rewriting of multiple critical imprinting control regions.
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22
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Hossain MS, Mawatari S, Fujino T. Plasmalogens, the Vinyl Ether-Linked Glycerophospholipids, Enhance Learning and Memory by Regulating Brain-Derived Neurotrophic Factor. Front Cell Dev Biol 2022; 10:828282. [PMID: 35223852 PMCID: PMC8864319 DOI: 10.3389/fcell.2022.828282] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/17/2022] [Indexed: 01/22/2023] Open
Abstract
Plasmalogens (Pls), a kind of glycerophospholipids, have shown potent biological effects but their role in hippocampus-dependent memory remained mostly elusive. Here, we first report Pls can enhance endogenous expression of brain-derived neurotrophic factor (Bdnf) in the hippocampus and promotes neurogenesis associated with improvement of learning and memory in mice. Genomic and proteomic studies revealed that Pls enhanced recruitment of CREB transcription factor onto the murine Bdnf promoter region via upregulating ERK-Akt signaling pathways in neuronal cells. Reduction of endogenous Pls in murine hippocampus significantly reduced learning and memory associated with the reduction of memory-related protein expression, suggesting that Pls can regulate memory-related gene expression in the hippocampus.
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Affiliation(s)
| | - Shiro Mawatari
- Institute of Rheological Functions of Food, Fukuoka, Japan
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23
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Quattrocelli M, Wintzinger M, Miz K, Levine DC, Peek CB, Bass J, McNally EM. Muscle mitochondrial remodeling by intermittent glucocorticoid drugs requires an intact circadian clock and muscle PGC1α. SCIENCE ADVANCES 2022; 8:eabm1189. [PMID: 35179955 PMCID: PMC8856622 DOI: 10.1126/sciadv.abm1189] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Exogenous glucocorticoids interact with the circadian clock, but little attention is paid to the timing of intake. We recently found that intermittent once-weekly prednisone improved nutrient oxidation in dystrophic muscle. Here, we investigated whether dosage time affected prednisone effects on muscle bioenergetics. In mice treated with once-weekly prednisone, drug dosing in the light-phase promoted nicotinamide adenine dinucleotide (NAD+) levels and mitochondrial function in wild-type muscle, while this response was lost with dark-phase dosing. These effects depended on a normal circadian clock since they were disrupted in muscle from [Brain and muscle Arnt-like protein-1 (Bmal1)]-knockout mice. The light-phase prednisone pulse promoted BMAL1-dependent glucocorticoid receptor recruitment on noncanonical targets, including Nampt and Ppargc1a [peroxisome proliferator-activated receptor-γ coactivator 1α (PGC1α)]. In mice with muscle-restricted inducible PGC1α ablation, bioenergetic stimulation by light-phase prednisone required PGC1α. These results demonstrate that glucocorticoid "chronopharmacology" for muscle bioenergetics requires an intact clock and muscle PGC1α activity.
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Affiliation(s)
- Mattia Quattrocelli
- Division of Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Michelle Wintzinger
- Division of Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Karen Miz
- Division of Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Daniel C. Levine
- Division of Endocrinology, Metabolism and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Clara Bien Peek
- Division of Endocrinology, Metabolism and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Joseph Bass
- Division of Endocrinology, Metabolism and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Elizabeth M. McNally
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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24
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Rezaei-Lotfi S, Vujovic F, Simonian M, Hunter N, Farahani RM. Programmed genomic instability regulates neural transdifferentiation of human brain microvascular pericytes. Genome Biol 2021; 22:334. [PMID: 34886891 PMCID: PMC8656028 DOI: 10.1186/s13059-021-02555-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 11/22/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Transdifferentiation describes transformation in vivo of specialized cells from one lineage into another. While there is extensive literature on forced induction of lineage reprogramming in vitro, endogenous mechanisms that govern transdifferentiation remain largely unknown. The observation that human microvascular pericytes transdifferentiate into neurons provided an opportunity to explore the endogenous molecular basis for lineage reprogramming. RESULTS We show that abrupt destabilization of the higher-order chromatin topology that chaperones lineage memory of pericytes is driven by transient global transcriptional arrest. This leads within minutes to localized decompression of the repressed competing higher-order chromatin topology and expression of pro-neural genes. Transition to neural lineage is completed by probabilistic induction of R-loops in key myogenic loci upon re-initiation of RNA polymerase activity, leading to depletion of the myogenic transcriptome and emergence of the neurogenic transcriptome. CONCLUSIONS These findings suggest that the global transcriptional landscape not only shapes the functional cellular identity of pericytes, but also stabilizes lineage memory by silencing the competing neural program within a repressed chromatin state.
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Affiliation(s)
- Saba Rezaei-Lotfi
- IDR/Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006 Australia
| | - Filip Vujovic
- IDR/Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006 Australia
| | - Mary Simonian
- IDR/Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
| | - Neil Hunter
- IDR/Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
| | - Ramin M. Farahani
- IDR/Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006 Australia
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25
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Shao J, Shi T, Yu H, Ding Y, Li L, Wang X, Wang X. Cytosolic GDH1 degradation restricts protein synthesis to sustain tumor cell survival following amino acid deprivation. EMBO J 2021; 40:e107480. [PMID: 34269483 PMCID: PMC8521317 DOI: 10.15252/embj.2020107480] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 06/04/2021] [Accepted: 06/13/2021] [Indexed: 01/18/2023] Open
Abstract
The mTORC1 pathway plays key roles in regulating various biological processes, including sensing amino acid deprivation and driving expression of ribosomal protein (RP)-coding genes. In this study, we observed that depletion of glutamate dehydrogenase 1 (GDH1), an enzyme that converts glutamate to α-ketoglutarate (αKG), confers resistance to amino acid deprivation on kidney renal clear cell carcinoma (KIRC) cells. Mechanistically, under conditions of adequate nutrition, GDH1 maintains RP gene expression in a manner dependent on its enzymatic activity. Following amino acid deprivation or mTORC1 inhibition, GDH1 translocates from mitochondria to the cytoplasm, where it becomes ubiquitinated and degraded via the E3 ligase RNF213. GDH1 degradation reduces intracellular αKG levels by more than half and decreases the activity of αKG-dependent lysine demethylases (KDMs). Reduced KDM activity in turn leads to increased histone H3 lysine 9 and 27 methylation, further suppressing RP gene expression and preserving nutrition to support cell survival. In summary, our study exemplifies an economical and efficient strategy of solid tumor cells for coping with amino acid deficiency, which might in the future be targeted to block renal carcinoma progression.
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Affiliation(s)
- Jialiang Shao
- Department of UrologyShanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Tiezhu Shi
- Department of UrologyShanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Hua Yu
- CAS Key Laboratory of Tissue Microenvironment and TumorInstitute of Nutrition and Health SciencesChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
- School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Yufeng Ding
- Department of UrologyShanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Liping Li
- School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Xiang Wang
- Department of UrologyShanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Xiongjun Wang
- CAS Key Laboratory of Tissue Microenvironment and TumorInstitute of Nutrition and Health SciencesChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
- School of Life SciencesGuangzhou UniversityGuangzhouChina
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26
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Jayabal P, Zhou F, Lei X, Ma X, Blackman B, Weintraub ST, Houghton PJ, Shiio Y. NELL2-cdc42 signaling regulates BAF complexes and Ewing sarcoma cell growth. Cell Rep 2021; 36:109254. [PMID: 34233189 PMCID: PMC8312579 DOI: 10.1016/j.celrep.2021.109254] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/07/2021] [Accepted: 05/25/2021] [Indexed: 12/24/2022] Open
Abstract
BAF chromatin remodeling complexes play important roles in chromatin regulation and cancer. Here, we report that Ewing sarcoma cells are dependent on the autocrine signaling mediated by NELL2, a secreted glycoprotein that has been characterized as an axon guidance molecule. NELL2 uses Robo3 as the receptor to transmit critical growth signaling. NELL2 signaling inhibits cdc42 and upregulates BAF complexes and EWS-FLI1 transcriptional output. We demonstrate that cdc42 is a negative regulator of BAF complexes, inducing actin polymerization and complex disassembly. Furthermore, we identify NELL2highCD133highEWS-FLI1high and NELL2lowCD133lowEWS-FLI1low populations in Ewing sarcoma, which display phenotypes consistent with high and low NELL2 signaling, respectively. We show that NELL2, CD133, and EWS-FLI1 positively regulate each other and upregulate BAF complexes and cell proliferation in Ewing sarcoma. These results reveal a signaling pathway regulating critical chromatin remodeling complexes and cancer cell proliferation.
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Affiliation(s)
- Panneerselvam Jayabal
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Fuchun Zhou
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Xiufen Lei
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Xiuye Ma
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Barron Blackman
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Molecular Medicine, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Yuzuru Shiio
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA.
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27
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Zhou F, Elzi DJ, Jayabal P, Ma X, Chiu YC, Chen Y, Blackman B, Weintraub ST, Houghton PJ, Shiio Y. GDF6-CD99 Signaling Regulates Src and Ewing Sarcoma Growth. Cell Rep 2021; 33:108332. [PMID: 33147457 PMCID: PMC7688343 DOI: 10.1016/j.celrep.2020.108332] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/07/2020] [Accepted: 10/08/2020] [Indexed: 12/20/2022] Open
Abstract
We report here that the autocrine signaling mediated by growth and differentiation factor 6 (GDF6), a member of the bone morphogenetic protein (BMP) family of cytokines, maintains Ewing sarcoma growth by preventing Src hyperactivation. Surprisingly, Ewing sarcoma depends on the prodomain, not the BMP domain, of GDF6. We demonstrate that the GDF6 prodomain is a ligand for CD99, a transmembrane protein that has been widely used as a marker of Ewing sarcoma. The binding of the GDF6 prodomain to the CD99 extracellular domain results in recruitment of CSK (C-terminal Src kinase) to the YQKKK motif in the intracellular domain of CD99, inhibiting Src activity. GDF6 silencing causes hyperactivation of Src and p21-dependent growth arrest. We demonstrate that two GDF6 prodomain mutants linked to Klippel-Feil syndrome are hyperactive in CD99-Src signaling. These results reveal a cytokine signaling pathway that regulates the CSK-Src axis and cancer cell proliferation and suggest the gain-of-function activity for disease-causing GDF6 mutants. Ewing sarcoma is driven by the EWS-ETS fusion oncoprotein, but little is known about the extracellular signaling regulating this cancer. Zhou et al. report that the prodomain of GDF6 is a ligand for CD99, inhibiting Src through CSK and maintaining Ewing sarcoma growth in an autocrine fashion.
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Affiliation(s)
- Fuchun Zhou
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - David J Elzi
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; BioAffinity Technologies, Inc., 1 UTSA Circle, San Antonio, TX 78249, USA
| | - Panneerselvam Jayabal
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Xiuye Ma
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Yu-Chiao Chiu
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Population Health Sciences, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Barron Blackman
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Susan T Weintraub
- Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Molecular Medicine, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Yuzuru Shiio
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229, USA.
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28
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Hovenga V, Oluwadare O. CBCR: A Curriculum Based Strategy For Chromosome Reconstruction. Int J Mol Sci 2021; 22:ijms22084140. [PMID: 33923653 PMCID: PMC8073114 DOI: 10.3390/ijms22084140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/30/2022] Open
Abstract
In this paper, we introduce a novel algorithm that aims to estimate chromosomes’ structure from their Hi-C contact data, called Curriculum Based Chromosome Reconstruction (CBCR). Specifically, our method performs this three dimensional reconstruction using cis-chromosomal interactions from Hi-C data. CBCR takes intra-chromosomal Hi-C interaction frequencies as an input and outputs a set of xyz coordinates that estimate the chromosome’s three dimensional structure in the form of a .pdb file. The algorithm relies on progressively training a distance-restraint-based algorithm with a strategy we refer to as curriculum learning. Curriculum learning divides the Hi-C data into classes based on contact frequency and progressively re-trains the distance-restraint algorithm based on the assumed importance of each curriculum in predicting the underlying chromosome structure. The distance-restraint algorithm relies on a modification of a Gaussian maximum likelihood function that scales probabilities based on the importance of features. We evaluate the performance of CBCR on both simulated and actual Hi-C data and perform validation on FISH, HiChIP, and ChIA-PET data as well. We also compare the performance of CBCR to several current methods. Our analysis shows that the use of curricula affects the rate of convergence of the optimization while decreasing the computational cost of our distance-restraint algorithm. Also, CBCR is more robust to increases in data resolution and therefore yields superior reconstruction accuracy of higher resolution data than all other methods in our comparison.
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Affiliation(s)
- Van Hovenga
- Department of Mathematics, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA;
| | - Oluwatosin Oluwadare
- Department of Computer Science, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
- Correspondence:
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29
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Rashid M, Shah SG, Verma T, Chaudhary N, Rauniyar S, Patel VB, Gera PB, Smoot D, Ashaktorab H, Dalal SN, Gupta S. Tumor-specific overexpression of histone gene, H3C14 in gastric cancer is mediated through EGFR-FOXC1 axis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194703. [PMID: 33727172 DOI: 10.1016/j.bbagrm.2021.194703] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/15/2021] [Accepted: 03/07/2021] [Indexed: 02/08/2023]
Abstract
Incorporation of different H3 histone isoforms/variants have been reported to differentially regulate gene expression via alteration in chromatin organization during diverse cellular processes. However, the differential expression of highly conserved histone H3.2 genes, H3C14 and H3C13 in human cancer has not been delineated. In this study, we investigated the expression of H3.2 genes in primary human gastric, brain, breast, colon, liver, and head and neck cancer tissues and tumor cell lines. The data showed overexpression of H3.2 transcripts in tumor samples and cell lines with respect to normal counterparts. Furthermore, TCGA data of individual and TCGA PANCAN cohort also showed significant up-regulation of H3.2 genes. Further, overexpressed H3C14 gene coding for H3.2 protein was regulated by FOXC1 transcription factor and G4-cassette in gastric cancer cell lines. Elevated expression of FOXC1 protein and transcripts were also observed in human gastric cancer samples and cell lines. Further, FOXC1 protein was predominantly localized in the nuclei of neoplastic gastric cells compared to normal counterpart. In continuation, studies with EGF induction, FOXC1 knockdown, and ChIP-qPCR for the first time identified a novel axis, EGFR-FOXC1-H3C14 for regulation of H3C14 gene overexpression in gastric cancer. Therefore, the changes the epigenomic landscape due to incorporation of differential expression H3 variant contributes to change in gene expression pattern and thereby contributing to pathogenesis of cancer.
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Affiliation(s)
- Mudasir Rashid
- KS313, Epigenetics and Chromatin Biology Group, Gupta Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Sanket Girish Shah
- KS313, Epigenetics and Chromatin Biology Group, Gupta Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Tripti Verma
- KS313, Epigenetics and Chromatin Biology Group, Gupta Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Nazia Chaudhary
- KS216, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Sukanya Rauniyar
- KS313, Epigenetics and Chromatin Biology Group, Gupta Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Vidisha Bhavesh Patel
- KS313, Epigenetics and Chromatin Biology Group, Gupta Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India
| | - Poonam B Gera
- Biorepository, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India
| | - Duane Smoot
- Department of Medicine, Meharry Medical Center, Nashville, TN 37208, United States
| | - Hassan Ashaktorab
- Department of Medicine and Cancer Center, College of Medicine, Howard University, Washington DC, WA 20060, United States
| | - Sorab N Dalal
- KS216, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Sanjay Gupta
- KS313, Epigenetics and Chromatin Biology Group, Gupta Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India.
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30
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Santopolo S, Riccio A, Rossi A, Santoro MG. The proteostasis guardian HSF1 directs the transcription of its paralog and interactor HSF2 during proteasome dysfunction. Cell Mol Life Sci 2021; 78:1113-1129. [PMID: 32607595 PMCID: PMC11071745 DOI: 10.1007/s00018-020-03568-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 05/03/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023]
Abstract
Protein homeostasis is essential for life in eukaryotes. Organisms respond to proteotoxic stress by activating heat shock transcription factors (HSFs), which play important roles in cytoprotection, longevity and development. Of six human HSFs, HSF1 acts as a proteostasis guardian regulating stress-induced transcriptional responses, whereas HSF2 has a critical role in development, in particular of brain and reproductive organs. Unlike HSF1, that is a stable protein constitutively expressed, HSF2 is a labile protein and its expression varies in different tissues; however, the mechanisms regulating HSF2 expression remain poorly understood. Herein we demonstrate that the proteasome inhibitor anticancer drug bortezomib (Velcade), at clinically relevant concentrations, triggers de novo HSF2 mRNA transcription in different types of cancers via HSF1 activation. Similar results were obtained with next-generation proteasome inhibitors ixazomib and carfilzomib, indicating that induction of HSF2 expression is a general response to proteasome dysfunction. HSF2-promoter analysis, electrophoretic mobility shift assays, and chromatin immunoprecipitation studies unexpectedly revealed that HSF1 is recruited to a heat shock element located at 1.397 bp upstream from the transcription start site in the HSF2-promoter. More importantly, we found that HSF1 is critical for HSF2 gene transcription during proteasome dysfunction, representing an interesting example of transcription factor involved in controlling the expression of members of the same family. Moreover, bortezomib-induced HSF2 was found to localize in the nucleus, interact with HSF1, and participate in bortezomib-mediated control of cancer cell migration. The results shed light on HSF2-expression regulation, revealing a novel level of HSF1/HSF2 interplay that may lead to advances in pharmacological modulation of these fundamental transcription factors.
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Affiliation(s)
- Silvia Santopolo
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Anna Riccio
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Antonio Rossi
- Institute of Translational Pharmacology, CNR, Rome, Italy
| | - M Gabriella Santoro
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy.
- Institute of Translational Pharmacology, CNR, Rome, Italy.
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31
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Bartas M, Červeň J, Guziurová S, Slychko K, Pečinka P. Amino Acid Composition in Various Types of Nucleic Acid-Binding Proteins. Int J Mol Sci 2021; 22:ijms22020922. [PMID: 33477647 PMCID: PMC7831508 DOI: 10.3390/ijms22020922] [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: 12/29/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 12/20/2022] Open
Abstract
Nucleic acid-binding proteins are traditionally divided into two categories: With the ability to bind DNA or RNA. In the light of new knowledge, such categorizing should be overcome because a large proportion of proteins can bind both DNA and RNA. Another even more important features of nucleic acid-binding proteins are so-called sequence or structure specificities. Proteins able to bind nucleic acids in a sequence-specific manner usually contain one or more of the well-defined structural motifs (zinc-fingers, leucine zipper, helix-turn-helix, or helix-loop-helix). In contrast, many proteins do not recognize nucleic acid sequence but rather local DNA or RNA structures (G-quadruplexes, i-motifs, triplexes, cruciforms, left-handed DNA/RNA form, and others). Finally, there are also proteins recognizing both sequence and local structural properties of nucleic acids (e.g., famous tumor suppressor p53). In this mini-review, we aim to summarize current knowledge about the amino acid composition of various types of nucleic acid-binding proteins with a special focus on significant enrichment and/or depletion in each category.
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32
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Li W, Yan Y, Zheng Z, Zhu Q, Long Q, Sui S, Luo M, Chen M, Li Y, Hua Y, Deng W, Lai R, Li L. Targeting the NCOA3-SP1-TERT axis for tumor growth in hepatocellular carcinoma. Cell Death Dis 2020; 11:1011. [PMID: 33239622 PMCID: PMC7689448 DOI: 10.1038/s41419-020-03218-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) has a high mortality rate and lacks an effective therapeutic target. Elevated expression of human telomerase reverse transcriptase (TERT) is an important hallmark in cancers, but the mechanism by which TERT is activated differentially in cancers is poorly understood. Here, we have identified nuclear receptor coactivator-3 (NCOA3) as a new modulator of TERT expression and tumor growth in HCC. NACO3 specifically binds to the TERT promoter at the -234 to -144 region and transcriptionally activates TERT expression. NCOA3 promotes HCC cell growth and tumor progression in vitro and in vivo through upregulating the TERT signaling. Knockdown of NACO3 suppresses HCC cell viability and colony formation, whereas TERT overexpression rescues this suppression. NCOA3 interacts with and recruits SP1 binding on the TERT promoter. Knockdown of NCOA3 also inhibits the expression of the Wnt signaling-related genes but has no effect on the Notch signaling-targeting genes. Moreover, NCOA3 is positively correlated with TERT expression in HCC tumor tissues, and high expression of both NCOA3 and TERT predicts a poor prognosis in HCC patients. Our findings indicate that targeting the NCOA3-SP1-TERT signaling axis may benefit HCC patients.
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Affiliation(s)
- Wenbin Li
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, Guangzhou, China.,Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Yue Yan
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Zongheng Zheng
- The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qiaohua Zhu
- Shunde Hospital of Southern Medical University, Foshan, Guangdong, China
| | - Qian Long
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Silei Sui
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Meihua Luo
- Shunde Hospital of Southern Medical University, Foshan, Guangdong, China
| | - Miao Chen
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Yizhuo Li
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Yijun Hua
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Wuguo Deng
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, Guangzhou, China.
| | - Renchun Lai
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, Guangzhou, China.
| | - Liren Li
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, Guangzhou, China.
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33
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Tiwari B, Jones AE, Caillet CJ, Das S, Royer SK, Abrams JM. p53 directly represses human LINE1 transposons. Genes Dev 2020; 34:1439-1451. [PMID: 33060137 PMCID: PMC7608743 DOI: 10.1101/gad.343186.120] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/14/2020] [Indexed: 12/16/2022]
Abstract
p53 is a potent tumor suppressor and commonly mutated in human cancers. Recently, we demonstrated that p53 genes act to restrict retrotransposons in germline tissues of flies and fish but whether this activity is conserved in somatic human cells is not known. Here we show that p53 constitutively restrains human LINE1s by cooperatively engaging sites in the 5'UTR and stimulating local deposition of repressive histone marks at these transposons. Consistent with this, the elimination of p53 or the removal of corresponding binding sites in LINE1s, prompted these retroelements to become hyperactive. Concurrently, p53 loss instigated chromosomal rearrangements linked to LINE sequences and also provoked inflammatory programs that were dependent on reverse transcriptase produced from LINE1s. Taken together, our observations establish that p53 continuously operates at the LINE1 promoter to restrict autonomous copies of these mobile elements in human cells. Our results further suggest that constitutive restriction of these retroelements may help to explain tumor suppression encoded by p53, since erupting LINE1s produced acute oncogenic threats when p53 was absent.
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Affiliation(s)
- Bhavana Tiwari
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Amanda E Jones
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Candace J Caillet
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Simanti Das
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Stephanie K Royer
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - John M Abrams
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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34
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Hays E, Nettleton E, Carter C, Morales M, Vo L, Passo M, Vélez-Cruz R. The SWI/SNF ATPase BRG1 stimulates DNA end resection and homologous recombination by reducing nucleosome density at DNA double strand breaks and by promoting the recruitment of the CtIP nuclease. Cell Cycle 2020; 19:3096-3114. [PMID: 33044911 PMCID: PMC7714457 DOI: 10.1080/15384101.2020.1831256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
DNA double strand breaks (DSBs) are among the most toxic DNA lesions and can be repaired accurately through homologous recombination (HR). HR requires processing of the DNA ends by nucleases (DNA end resection) in order to generate the required single-stranded DNA (ssDNA) regions. The SWI/SNF chromatin remodelers are 10–15 subunit complexes that contain one ATPase (BRG1 or BRM). Multiple subunits of these complexes have recently been identified as a novel family of tumor suppressors. These complexes are capable of remodeling chromatin by pushing nucleosomes along the DNA. More recent studies have identified these chromatin remodelers as important factors in DNA repair. Using the DR-U2OS reporter system, we show that the down regulation of BRG1 significantly reduces HR efficiency, while BRM has a minor effect. Inactivation of BRG1 impairs DSB repair and results in a defect in DNA end resection, as measured by the amount of BrdU-containing ssDNA generated after DNA damage. Inactivation of BRG1 also impairs the activation of the ATR kinase, reduces the levels of chromatin-bound RPA, and reduces the number of RPA and RAD51 foci after DNA damage. This defect in DNA end resection is explained by the defective recruitment of GFP-CtIP to laser-induced DSBs in the absence of BRG1. Importantly, we show that BRG1 reduces nucleosome density at DSBs. Finally, inactivation of BRG1 renders cells sensitive to anti-cancer drugs that induce DSBs. This study identifies BRG1 as an important factor for HR, which suggests that BRG1-mutated cancers have a DNA repair vulnerability that can be exploited therapeutically.
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Affiliation(s)
- Emily Hays
- Department of Biochemistry and Molecular Genetics, Midwestern University , Downers Grove, IL, USA.,College of Graduate Studies, Midwestern University , Downers Grove, IL, USA
| | - Elizabeth Nettleton
- Chicago College of Osteopathic Medicine, Midwestern University , Downers Grove, IL, USA
| | - Caitlin Carter
- Chicago College of Osteopathic Medicine, Midwestern University , Downers Grove, IL, USA
| | - Mariangel Morales
- College of Graduate Studies, Midwestern University , Downers Grove, IL, USA.,Biomedical Sciences Program, Midwestern University , Downers Grove, IL, USA
| | - Lynn Vo
- Chicago College of Osteopathic Medicine, Midwestern University , Downers Grove, IL, USA
| | - Max Passo
- College of Graduate Studies, Midwestern University , Downers Grove, IL, USA.,Biomedical Sciences Program, Midwestern University , Downers Grove, IL, USA
| | - Renier Vélez-Cruz
- Department of Biochemistry and Molecular Genetics, Midwestern University , Downers Grove, IL, USA.,College of Graduate Studies, Midwestern University , Downers Grove, IL, USA.,Chicago College of Optometry, Midwestern University , Downers Grove, IL, USA
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35
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Ren AJ, Chen C, Zhang S, Liu M, Wei C, Wang K, Ma X, Song Y, Wang R, Zhang H, Chen YX, Wu H, Xie Z, Zhang Y, Zhang WJ. Zbtb20 deficiency causes cardiac contractile dysfunction in mice. FASEB J 2020; 34:13862-13876. [PMID: 32844471 DOI: 10.1096/fj.202000160rr] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/15/2022]
Abstract
The zinc-finger protein ZBTB20 regulates development and metabolism in multiple systems, and is essential for postnatal survival in mice. However, its potential role in the cardiovascular system remains undefined. Here, we demonstrate that ZBTB20 is critically involved in the regulation of cardiac contractility and blood pressure in mice. At the age of 16 days, the relatively healthy Zbtb20-null mice exhibited hypotension without obvious change of heart rate or other evidence for heart failure. Moreover, Zbtb20 deletion led to a marked reduction in heart size, left ventricular wall thickness, and cell size of cardiomyocytes, which was largely proportional to the decreased body growth. Notably, echocardiographic and hemodynamic analyses showed that cardiac contractility was greatly impaired in the absence of ZBTB20. Mechanistically, ZBTB20 deficiency decreased cardiac ATP contents, and compromised the enzyme activity of mitochondrial complex I in heart as well as L-type calcium current density in cardiomyocytes. Furthermore, the developmental activation of some mitochondrial function-related genes was significantly attenuated in Zbtb20-null myocardium, which included Hspb8, Ckmt2, Cox7a1, Tfrc, and Ogdhl. Put together, these results suggest that ZBTB20 plays a crucial role in the regulation of heart development, energy metabolism, and contractility.
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Affiliation(s)
- An-Jing Ren
- Department of Pathophysiology, Naval Medical University, Shanghai, China
| | - Chao Chen
- Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
| | - Sha Zhang
- Department of Pathophysiology, Naval Medical University, Shanghai, China.,Department of Cardiovascular Diseases, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Mengna Liu
- Department of Pathophysiology, Naval Medical University, Shanghai, China
| | - Chunchun Wei
- Department of Pathophysiology, Naval Medical University, Shanghai, China
| | - Kai Wang
- Department of Pathophysiology, Naval Medical University, Shanghai, China
| | - Xianhua Ma
- Department of Pathophysiology, Naval Medical University, Shanghai, China
| | - Yao Song
- Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
| | - Rui Wang
- Department of Pathophysiology, Naval Medical University, Shanghai, China
| | - Hai Zhang
- Department of Pathophysiology, Naval Medical University, Shanghai, China
| | - Yu-Xia Chen
- Department of Pathophysiology, Naval Medical University, Shanghai, China
| | - Hong Wu
- Department of Cardiovascular Diseases, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Zhifang Xie
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Youyi Zhang
- Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
| | - Weiping J Zhang
- Department of Pathophysiology, Naval Medical University, Shanghai, China.,NHC Key Laboratory of Hormones and Development, Tianjin Institute of Endocrinology, Tianjin Medical University Chu Hsien-I Memorial Hospital, Tianjin, China
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36
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Alpha-lipoic acid protects against pressure overload-induced heart failure via ALDH2-dependent Nrf1-FUNDC1 signaling. Cell Death Dis 2020; 11:599. [PMID: 32732978 PMCID: PMC7393127 DOI: 10.1038/s41419-020-02805-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023]
Abstract
Alpha-lipoic acid (α-LA), a well-known antioxidant, was proved to active ALDH2 in nitrate tolerance and diabetic animal model. However, the therapeutic advantage of α-LA for heart failure and related signaling pathway have not been explored. This study was designed to examine the role of α-LA–ALDH2 in heart failure injury and mitochondrial damage. ALDH2 knockout (ALDH2−/−) mice and primary neonatal rat cardiomyocytes (NRCMs) were subjected to assessment of myocardial function and mitochondrial autophagy. Our data demonstrated α-LA significantly reduced the degree of TAC-induced LV hypertrophy and dysfunction in wild-type mice, not in ALDH2−/− mice. In molecular level, α-LA significantly restored ALDH2 activity and expression as well as increased the expression of a novel mitophagy receptor protein FUNDC1 in wild-type TAC mice. Besides, we confirmed that ALDH2 which was activated by α-LA governed the activation of Nrf1–FUNDC1 cascade. Our data suggest that α-LA played a positive role in protecting the heart against adverse effects of chronic pressure overload.
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37
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Moses C, Hodgetts SI, Nugent F, Ben-Ary G, Park KK, Blancafort P, Harvey AR. Transcriptional repression of PTEN in neural cells using CRISPR/dCas9 epigenetic editing. Sci Rep 2020; 10:11393. [PMID: 32647121 PMCID: PMC7347541 DOI: 10.1038/s41598-020-68257-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
After damage to the adult mammalian central nervous system (CNS), surviving neurons have limited capacity to regenerate and restore functional connectivity. Conditional genetic deletion of PTEN results in robust CNS axon regrowth, while PTEN repression with short hairpin RNA (shRNA) improves regeneration but to a lesser extent, likely due to suboptimal PTEN mRNA knockdown using this approach. Here we employed the CRISPR/dCas9 system to repress PTEN transcription in neural cells. We targeted the PTEN proximal promoter and 5' untranslated region with dCas9 fused to the repressor protein Krüppel-associated box (KRAB). dCas9-KRAB delivered in a lentiviral vector with one CRISPR guide RNA (gRNA) achieved potent and specific PTEN repression in human cell line models and neural cells derived from human iPSCs, and induced histone (H)3 methylation and deacetylation at the PTEN promoter. The dCas9-KRAB system outperformed a combination of four shRNAs targeting the PTEN transcript, a construct previously used in CNS injury models. The CRISPR system also worked more effectively than shRNAs for Pten repression in rat neural crest-derived PC-12 cells, and enhanced neurite outgrowth after nerve growth factor stimulation. PTEN silencing with CRISPR/dCas9 epigenetic editing may provide a new option for promoting axon regeneration and functional recovery after CNS trauma.
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Affiliation(s)
- C Moses
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA, 6009, Australia
| | - S I Hodgetts
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
- Perron Institute for Neurological and Translational Science, 8 Verdun Street, Nedlands, WA, 6009, Australia
| | - F Nugent
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA, 6009, Australia
- School of Molecular Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - G Ben-Ary
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - K K Park
- Department of Neurological Surgery, Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - P Blancafort
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA, 6009, Australia.
- Greehey Children's Cancer Research Institute, UT Health San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA.
| | - A R Harvey
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.
- Perron Institute for Neurological and Translational Science, 8 Verdun Street, Nedlands, WA, 6009, Australia.
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38
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Bhagat S, Biswas I, Ahmed R, Khan GA. Hypoxia induced up-regulation of tissue factor is mediated through extracellular RNA activated Toll-like receptor 3-activated protein 1 signalling. Blood Cells Mol Dis 2020; 84:102459. [PMID: 32559654 PMCID: PMC7287429 DOI: 10.1016/j.bcmd.2020.102459] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/04/2020] [Accepted: 06/07/2020] [Indexed: 12/26/2022]
Abstract
Sterile Inflammation (SI), a condition where damage associated molecular patterns (DAMPs) released from dying cells, leads to TLR (Toll-like receptor) activation and triggers hypoxemia in circulation leading to venous thrombosis (VT) through tissue factor (TF) activation, but its importance under acute hypoxia (AH) remains unexplored. Thus, we hypothesized that eRNA released from dying cells under AH activates TF via the TLR3-ERK1/2-AP1 pathway, leading to VT. Animals were exposed to stimulate hypoxia for 0–24 h at standard temperature and humidity. RNaseA and DNase1 were injected immediately before exposure. TLR3 gene silencing was performed through in vivo injection of TLR3 siRNA. 80 μg/kg BW of isolated eRNA and eDNA were injected 6 h prior to sacrifice. Antigens of TF pathway were determined by ELISA and TF activity by a chromogenic assay. AH exposure significantly induced release of SI markers i.e. eRNA, eDNA, HMGB1 and upregulated TLR3, ERK1/2 (Extracellular signal-regulated kinases), AP1 (Activator Protein-1) and TF, whereas RNaseA pre-treatment diminished the effect of AH, thus inhibiting TF expression as well as activity during AH. Hence, we propose a possible mechanism of AH-induced TF activation and thrombosis where RNaseA can become the novel focal point in ameliorating therapy for AH induced thrombosis. Acute hypoxia exposure leads to systemic Sterile Inflammation. eRNA regulates upregulation of TF by activation of TLR3 pathway. RNase A pre-treatment ameliorates effect of acute hypoxia on coagulation.
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Affiliation(s)
- Saumya Bhagat
- Defence Institute of Physiology and Allied Sciences, Timarpur, Delhi, India
| | - Indranil Biswas
- Defence Institute of Physiology and Allied Sciences, Timarpur, Delhi, India
| | - Rehan Ahmed
- Army Hospital Research and Referral, Delhi, India
| | - Gausal A Khan
- Defence Institute of Physiology and Allied Sciences, Timarpur, Delhi, India; Department of Physiology and Physiotherapy, CMNHS, Fiji National University, Suva, Fiji Islands.
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39
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Sodir NM, Kortlever RM, Barthet VJA, Campos T, Pellegrinet L, Kupczak S, Anastasiou P, Swigart LB, Soucek L, Arends MJ, Littlewood TD, Evan GI. MYC Instructs and Maintains Pancreatic Adenocarcinoma Phenotype. Cancer Discov 2020; 10:588-607. [PMID: 31941709 DOI: 10.1158/2159-8290.cd-19-0435] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 11/30/2019] [Accepted: 01/10/2020] [Indexed: 11/16/2022]
Abstract
The signature features of pancreatic ductal adenocarcinoma (PDAC) are its fibroinflammatory stroma, poor immune activity, and dismal prognosis. We show that acute activation of Myc in indolent pancreatic intraepithelial neoplasm (PanIN) epithelial cells in vivo is, alone, sufficient to trigger immediate release of instructive signals that together coordinate changes in multiple stromal and immune-cell types and drive transition to pancreatic adenocarcinomas that share all the characteristic stromal features of their spontaneous human counterpart. We also demonstrate that this Myc-driven PDAC switch is completely and immediately reversible: Myc deactivation/inhibition triggers meticulous disassembly of advanced PDAC tumor and stroma and concomitant death of tumor cells. Hence, both the formation and deconstruction of the complex PDAC phenotype are continuously dependent on a single, reversible Myc switch. SIGNIFICANCE: We show that Myc activation in indolent Kras G12D-induced PanIN epithelium acts as an immediate pleiotropic switch, triggering tissue-specific signals that instruct all the diverse signature stromal features of spontaneous human PDAC. Subsequent Myc deactivation or inhibition immediately triggers a program that coordinately disassembles PDAC back to PanIN.See related commentary by English and Sears, p. 495.
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Affiliation(s)
- Nicole M Sodir
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Roderik M Kortlever
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Tania Campos
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Luca Pellegrinet
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Steven Kupczak
- Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | | | - Lamorna Brown Swigart
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California
| | - Laura Soucek
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Mark J Arends
- Division of Pathology, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Trevor D Littlewood
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Gerard I Evan
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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40
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Zuo H, Yang D, Yang Q, Tang H, Fu YX, Wan Y. Differential regulation of breast cancer bone metastasis by PARP1 and PARP2. Nat Commun 2020; 11:1578. [PMID: 32221289 PMCID: PMC7101362 DOI: 10.1038/s41467-020-15429-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/11/2020] [Indexed: 11/25/2022] Open
Abstract
PARP1 and PARP2 dual inhibitors, such as olaparib, have been recently FDA approved for the treatment of advanced breast and ovarian cancers. However, their effects on bone mass and bone metastasis are unknown. Here we show that olaparib increases breast cancer bone metastasis through PARP2, but not PARP1, specifically in the myeloid lineage, but not in the cancer cells. Olaparib treatment or PARP1/2 deletion promotes osteoclast differentiation and bone loss. Intriguingly, myeloid deletion of PARP2, but not PARP1, increases the population of immature myeloid cells in bone marrow, and impairs the expression of chemokines such as CCL3 through enhancing the transcriptional repression by β-catenin. Compromised CCL3 production in turn creates an immune-suppressive milieu by altering T cell subpopulations. Our findings warrant careful examination of current PARP inhibitors on bone metastasis and bone loss, and suggest cotreatment with CCL3, β-catenin inhibitors, anti-RANKL or bisphosphonates as potential combination therapy for PARP inhibitors.
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Affiliation(s)
- Hao Zuo
- Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Dengbao Yang
- Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Qiwen Yang
- Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Haidong Tang
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yang-Xin Fu
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yihong Wan
- Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Simmons Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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41
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Fang C, Yang L, Chen W, Li L, Zhang P, Li Y, He H, Lin W. MYB57 transcriptionally regulates MAPK11 to interact with PAL2;3 and modulate rice allelopathy. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2127-2141. [PMID: 31811717 PMCID: PMC7242072 DOI: 10.1093/jxb/erz540] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/06/2019] [Indexed: 05/14/2023]
Abstract
Rice allelopathy is a natural method of weed control that is regarded as an eco-friendly practice in agroecology. The allelopathic potential of rice is regulated by various genes, including those that encode transcription factors. Our study characterized a MYB transcription factor, OsMYB57, to explore its role in the regulation of rice allelopathy. Increasing the expression of OsMYB57 in rice using the transcription activator VP64 resulted in increased inhibitory ratios against barnyardgrass. The gene expression levels of OsPAL, OsC4H, OsOMT, and OsCAD from the phenylpropanoid pathway were also up-regulated, and the content of l-phenylalanine increased. Chromatin immunoprecipitation incorporated with HiSeq demonstrated that OsMYB57 transcriptionally regulated a mitogen-activated protein kinase (OsMAPK11); in addition, OsMAPK11 interacted with OsPAL2;3. The expression of OsPAL2;3was higher in the allelopathic rice PI312777 than in the non-allelopathic rice Lemont, and OsPAL2;3 was negatively regulated by Whirly transcription factors. Moreover, microbes with weed-suppression potential, including Penicillium spp. and Bacillus spp., were assembled in the rhizosphere of the rice accession Kitaake with increased expression of OsMYB57, and were responsible for phenolic acid induction. Our findings suggest that OsMYB57 positively regulates rice allelopathy, providing an option for the improvement of rice allelopathic traits through genetic modification.
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Affiliation(s)
- Changxun Fang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Luke Yang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Weisi Chen
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Lanlan Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Pengli Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Yingzhe Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Haibin He
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
- Correspondence: ,
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42
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Lai HT, Chiang CT, Tseng WK, Chao TC, Su Y. GATA6 enhances the stemness of human colon cancer cells by creating a metabolic symbiosis through upregulating LRH-1 expression. Mol Oncol 2020; 14:1327-1347. [PMID: 32037723 PMCID: PMC7266275 DOI: 10.1002/1878-0261.12647] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/09/2020] [Accepted: 02/07/2020] [Indexed: 12/13/2022] Open
Abstract
Cancer stem cells play critical roles in tumor initiation, progression, and relapse. Since we previously found that GATA6 promotes the stemness in HCT‐116 and HT‐29 human colorectal cancer (CRC) cells, we aimed to identify the downstream mediator(s) of the stemness‐stimulating effect of GATA6 herein. LRH‐1 was found as a direct target of GATA6 and its upregulation promoted the stemness in both HCT‐116 and HT‐29 cells. Subsequently, hypoxia‐inducible factor‐1α (HIF‐1α) was identified as a direct target of LRH‐1 and its expression level and activity were significantly elevated in the LRH‐1‐overexpressing clones established from the aforementioned two CRC lines. Accordingly, the expression levels of several HIF‐1α targets were also markedly increased, resulting in a stronger glycolysis associated with dramatic elevations of the lactate levels in these cells. Strikingly, higher mitochondrial activities were also found in these clones which might be attributed to the increase of PGC‐1α stimulated by the lactate uptaken through the upregulated MCT‐1. Finally, significant increases in the self‐renewal ability, intracellular radical oxygen species levels and mitochondrial mass were detected in the CD133+/CD44+ subpopulations isolated from CRC cells regardless of their LRH‐1 expression levels. Together, our results suggest a novel metabolic symbiosis between different colorectal cancer stem cell subpopulations critical for maintaining their mutual stemness.
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Affiliation(s)
- Hung-Tzu Lai
- Institute of Biopharmaceutical Sciences, School of Pharmaceutical Sciences, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Chin-Ting Chiang
- Institute of Biopharmaceutical Sciences, School of Pharmaceutical Sciences, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Wen-Ko Tseng
- Program in Molecular Medicine, School of Life Sciences, National Yang-Ming University, Taipei, Taiwan, R.O.C.,Colorectal Surgery Department, Chung-Gung Memorial Hospital, Keelung Branch, Taiwan, R.O.C
| | - Ta-Chung Chao
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taiwan, R.O.C.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Yeu Su
- Institute of Biopharmaceutical Sciences, School of Pharmaceutical Sciences, National Yang-Ming University, Taipei, Taiwan, R.O.C
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43
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Malavika D, Shreya S, Raj Priya V, Rohini M, He Z, Partridge NC, Selvamurugan N. miR‐873‐3p targets HDAC4 to stimulate matrix metalloproteinase‐13 expression upon parathyroid hormone exposure in rat osteoblasts. J Cell Physiol 2020; 235:7996-8009. [DOI: 10.1002/jcp.29454] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/03/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Desai Malavika
- Department of Biotechnology, School of Bioengineering SRM Institute of Science and Technology Kattankulathur Tamil Nadu India
| | - Srinivasan Shreya
- Department of Biotechnology, School of Bioengineering SRM Institute of Science and Technology Kattankulathur Tamil Nadu India
| | - Vembar Raj Priya
- Department of Biotechnology, School of Bioengineering SRM Institute of Science and Technology Kattankulathur Tamil Nadu India
| | - Muthukumar Rohini
- Department of Biotechnology, School of Bioengineering SRM Institute of Science and Technology Kattankulathur Tamil Nadu India
| | - Zhiming He
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry New York University New York New York
| | - Nicola C. Partridge
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry New York University New York New York
| | - Nagarajan Selvamurugan
- Department of Biotechnology, School of Bioengineering SRM Institute of Science and Technology Kattankulathur Tamil Nadu India
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44
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Yin L, Li W, Xu A, Shi H, Wang K, Yang H, Wang R, Peng B. SH3BGRL2 inhibits growth and metastasis in clear cell renal cell carcinoma via activating hippo/TEAD1-Twist1 pathway. EBioMedicine 2020; 51:102596. [PMID: 31911271 PMCID: PMC7000347 DOI: 10.1016/j.ebiom.2019.12.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 12/12/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is one of the most prevalent malignancies in the world, and tumor metastasis is still the main reason for disease progression. Accumulating evidence shows that SH3BGRL2 may play a key role in tumor progression and metastasis. However, the role of SH3BGRL2 in ccRCC has not been systematically investigated and remains elusive. Methods The clinical significance of SH3BGRL2 was evaluated by bioinformatic analysis and tissue microarray (TMA) samples. SH3BGRL2 expression was determined by RT-PCR, western blot and immunohistochemistry staining. Tumor suppressive effect of SH3BGRL2 was determined by both in vitro and in vivo studies. Western blot, chromatin immunoprecipitation assay and luciferase report assay were applied for mechanism dissection. Findings SH3BGRL2 was crucial for epithelial-mesenchymal transition (EMT) progression and metastasis in ccRCC. Clinically, SH3BGRL2 was identified as an independent prognostic factor for ccRCC patients. Gain- and loss-of-function results suggested that SH3BGRL2 played a critical role in cell proliferation, migration and invasion. Mechanistically, we found that SH3BGRL2 acted as a tumor suppressor through Hippo/TEAD1 signaling, then TEAD1 altered Twist1 expression at the transcriptional level via directly binding to its promoter region. Interpretation Our findings established that SH3BGRL2 performed as a tumor suppressor and modulator via Hippo/TEAD1-Twist1 signaling in ccRCC, and the alteration of SH3BGRL2 could serve as a functional response biomarker of tumor progression and metastasis in ccRCC.
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Affiliation(s)
- Lei Yin
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China
| | - Wenjia Li
- Shanghai Institute of Cardiovascular Disease, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Aiming Xu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Heng Shi
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China
| | - Keyi Wang
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China
| | - Huan Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Ronghao Wang
- School of basic medical sciences, Southwest Medical University, Luzhou, China.
| | - Bo Peng
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China.
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45
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Quattrocelli M, Zelikovich AS, Jiang Z, Peek CB, Demonbreun AR, Kuntz NL, Barish GD, Haldar SM, Bass J, McNally EM. Pulsed glucocorticoids enhance dystrophic muscle performance through epigenetic-metabolic reprogramming. JCI Insight 2019; 4:132402. [PMID: 31852847 PMCID: PMC6975267 DOI: 10.1172/jci.insight.132402] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/13/2019] [Indexed: 12/23/2022] Open
Abstract
In humans, chronic glucocorticoid use is associated with side effects like muscle wasting, obesity, and metabolic syndrome. Intermittent steroid dosing has been proposed in Duchenne Muscular Dystrophy patients to mitigate the side effects seen with daily steroid intake. We evaluated biomarkers from Duchenne Muscular Dystrophy patients, finding that, compared with chronic daily steroid use, weekend steroid use was associated with reduced serum insulin, free fatty acids, and branched chain amino acids, as well as reduction in fat mass despite having similar BMIs. We reasoned that intermittent prednisone administration in dystrophic mice would alter muscle epigenomic signatures, and we identified the coordinated action of the glucocorticoid receptor, KLF15 and MEF2C as mediators of a gene expression program driving metabolic reprogramming and enhanced nutrient utilization. Muscle lacking Klf15 failed to respond to intermittent steroids. Furthermore, coadministration of the histone acetyltransferase inhibitor anacardic acid with steroids in mdx mice eliminated steroid-specific epigenetic marks and abrogated the steroid response. Together, these findings indicate that intermittent, repeated exposure to glucocorticoids promotes performance in dystrophic muscle through an epigenetic program that enhances nutrient utilization.
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MESH Headings
- Anacardic Acids/administration & dosage
- Animals
- Biomarkers/blood
- Biomarkers/metabolism
- Child
- Cross-Sectional Studies
- Disease Models, Animal
- Drug Therapy, Combination
- Epigenesis, Genetic/drug effects
- Epigenomics
- Gene Expression Regulation/drug effects
- Glucocorticoids/administration & dosage
- Histone Acetyltransferases/antagonists & inhibitors
- Histone Acetyltransferases/metabolism
- Humans
- Kruppel-Like Transcription Factors/genetics
- Kruppel-Like Transcription Factors/metabolism
- MEF2 Transcription Factors/metabolism
- Male
- Metabolomics
- Mice
- Mice, Inbred mdx
- Muscle, Skeletal/drug effects
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscular Dystrophy, Duchenne/blood
- Muscular Dystrophy, Duchenne/diagnosis
- Muscular Dystrophy, Duchenne/drug therapy
- Muscular Dystrophy, Duchenne/genetics
- Nutrients/blood
- Nutrients/metabolism
- Prednisone/administration & dosage
- Pulse Therapy, Drug
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Affiliation(s)
- Mattia Quattrocelli
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University (NU), Chicago, Illinois, USA
| | - Aaron S. Zelikovich
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University (NU), Chicago, Illinois, USA
| | - Zhen Jiang
- Gladstone Institutes, San Francisco, California, USA
- Amgen Research, South San Francisco, California, USA
| | - Clara Bien Peek
- Division of Endocrinology, Metabolism and Molecular Medicine, Feinberg School of Medicine, NU, Chicago, Illinois, USA
| | - Alexis R. Demonbreun
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University (NU), Chicago, Illinois, USA
| | - Nancy L. Kuntz
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Grant D. Barish
- Division of Endocrinology, Metabolism and Molecular Medicine, Feinberg School of Medicine, NU, Chicago, Illinois, USA
| | - Saptarsi M. Haldar
- Gladstone Institutes, San Francisco, California, USA
- Amgen Research, South San Francisco, California, USA
- Cardiology Division, Department of Medicine, UCSF School of Medicine, San Francisco, California, USA
| | - Joseph Bass
- Division of Endocrinology, Metabolism and Molecular Medicine, Feinberg School of Medicine, NU, Chicago, Illinois, USA
| | - Elizabeth M. McNally
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University (NU), Chicago, Illinois, USA
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46
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Hay EA, Cowie P, McEwan AR, Ross R, Pertwee RG, MacKenzie A. Disease-associated polymorphisms within the conserved ECR1 enhancer differentially regulate the tissue-specific activity of the cannabinoid-1 receptor gene promoter; implications for cannabinoid pharmacogenetics. Hum Mutat 2019; 41:291-298. [PMID: 31608546 PMCID: PMC6973010 DOI: 10.1002/humu.23931] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/19/2019] [Accepted: 09/26/2019] [Indexed: 12/14/2022]
Abstract
Cannabinoid receptor‐1 (CB1) represents a potential drug target against conditions that include obesity and substance abuse. However, drug trials targeting CB1 (encoded by the CNR1 gene) have been compromised by differences in patient response. Toward addressing the hypothesis that genetic changes within the regulatory regions controlling CNR1 expression contribute to these differences, we characterized the effects of disease‐associated allelic variation within a conserved regulatory sequence (ECR1) in CNR1 intron 2 that had previously been shown to modulate cannabinoid response, alcohol intake, and anxiety‐like behavior. We used primary cell analysis of reporters carrying different allelic variants of the human ECR1 and found that human‐specific C‐allele variants of ECR1 (ECR1(C)) drove higher levels of CNR1prom activity in primary hippocampal cells than did the ancestral T‐allele and demonstrated a differential response to CB1 agonism. We further demonstrate a role for the AP‐1 transcription factor in driving higher ECR1(C) activity and evidence that the ancestral t‐allele variant of ECR1 interacted with higher affinity with the insulator binding factor CTCF. The cell‐specific approaches used in our study represent an important step in gaining a mechanistic understanding of the roles of noncoding polymorphic variation in disease and in the increasingly important field of cannabinoid pharmacogenetics.
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Affiliation(s)
- Elizabeth A Hay
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen, UK
| | - Philip Cowie
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen, UK
| | - Andrew R McEwan
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen, UK
| | - Ruth Ross
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Roger G Pertwee
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen, UK
| | - Alasdair MacKenzie
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen, UK
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47
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Xiong Y, Yi Y, Wang Y, Yang N, Rudd CE, Liu H. Ubc9 Interacts with and SUMOylates the TCR Adaptor SLP-76 for NFAT Transcription in T Cells. THE JOURNAL OF IMMUNOLOGY 2019; 203:3023-3036. [PMID: 31666306 DOI: 10.4049/jimmunol.1900556] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/30/2019] [Indexed: 12/25/2022]
Abstract
Although the immune adaptor SH2 domain containing leukocyte phosphoprotein of 76 kDa (SLP-76) integrates and propagates the TCR signaling, the regulation of SLP-76 during the TCR signaling is incompletely studied. In this article, we report that SLP-76 interacts with the small ubiquitin-like modifier (SUMO) E2 conjugase Ubc9 and is a substrate for Ubc9-mediated SUMOylation in human and mouse T cells. TCR stimulation promotes SLP-76-Ubc9 binding, accompanied by an increase in SLP-76 SUMOylation. Ubc9 binds to the extreme C terminus of SLP-76 spanning residues 516-533 and SUMOylates SLP-76 at two conserved residues K266 and K284. In addition, SLP-76 and Ubc9 synergizes to augment the TCR-mediated IL-2 transcription by NFAT in a manner dependent of SUMOylation of SLP-76. Moreover, although not affecting the TCR proximal signaling events, the Ubc9-mediated SUMOylation of SLP-76 is required for TCR-induced assembly of Ubc9-NFAT complex for IL-2 transcription. Together, these results suggest that Ubc9 modulates the function of SLP-76 in T cell activation both by direct interaction and by SUMOylation of SLP-76 and that the Ubc9-SLP-76 module acts as a novel regulatory complex in the control of T cell activation.
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Affiliation(s)
- Yiwei Xiong
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province 215123, China
| | - Yulan Yi
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province 215123, China
| | - Yan Wang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province 215123, China
| | - Naiqi Yang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province 215123, China
| | - Christopher E Rudd
- Division of Immunology-Oncology Research Center, Maisonneuve-Rosemont Hospital, Montreal, Quebec H1T 2M4, Canada; and.,Département de Medicine, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Hebin Liu
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province 215123, China;
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48
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Esseltine JL, Brooks CR, Edwards NA, Subasri M, Sampson J, Séguin C, Betts DH, Laird DW. Dynamic regulation of connexins in stem cell pluripotency. Stem Cells 2019; 38:52-66. [DOI: 10.1002/stem.3092] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 07/18/2019] [Accepted: 08/08/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Jessica L. Esseltine
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry; University of Western Ontario; London Ontario Canada
- Division of BioMedical Sciences, Faculty of Medicine; Memorial University of Newfoundland; St. John's Newfoundland and Labrador Canada
| | - Courtney R. Brooks
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry; University of Western Ontario; London Ontario Canada
| | - Nicole A. Edwards
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry; University of Western Ontario; London Ontario Canada
| | - Mathushan Subasri
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry; University of Western Ontario; London Ontario Canada
| | - Jacinda Sampson
- Department of Neurology; Stanford University Medical Center; Palo Alto California
| | - Cheryle Séguin
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry; University of Western Ontario; London Ontario Canada
| | - Dean H. Betts
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry; University of Western Ontario; London Ontario Canada
| | - Dale W. Laird
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry; University of Western Ontario; London Ontario Canada
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry; University of Western Ontario; London Ontario Canada
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49
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Fahrner JA, Lin WY, Riddle RC, Boukas L, DeLeon VB, Chopra S, Lad SE, Luperchio TR, Hansen KD, Bjornsson HT. Precocious chondrocyte differentiation disrupts skeletal growth in Kabuki syndrome mice. JCI Insight 2019; 4:129380. [PMID: 31557133 DOI: 10.1172/jci.insight.129380] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 09/11/2019] [Indexed: 12/12/2022] Open
Abstract
Kabuki syndrome 1 (KS1) is a Mendelian disorder of the epigenetic machinery caused by mutations in the gene encoding KMT2D, which methylates lysine 4 on histone H3 (H3K4). KS1 is characterized by intellectual disability, postnatal growth retardation, and distinct craniofacial dysmorphisms. A mouse model (Kmt2d+/βGeo) exhibits features of the human disorder and has provided insight into other phenotypes; however, the mechanistic basis of skeletal abnormalities and growth retardation remains elusive. Using high-resolution micro-CT, we show that Kmt2d+/βGeo mice have shortened long bones and ventral bowing of skulls. In vivo expansion of growth plates within skulls and long bones suggests disrupted endochondral ossification as a common disease mechanism. Stable chondrocyte cell lines harboring inactivating mutations in Kmt2d exhibit precocious differentiation, further supporting this mechanism. A known inducer of chondrogenesis, SOX9, and its targets show markedly increased expression in Kmt2d-/- chondrocytes. By transcriptome profiling, we identify Shox2 as a putative KMT2D target. We propose that decreased KMT2D-mediated H3K4me3 at Shox2 releases Sox9 inhibition and thereby leads to enhanced chondrogenesis, providing a potentially novel and plausible explanation for precocious chondrocyte differentiation. Our findings provide insight into the pathogenesis of growth retardation in KS1 and suggest therapeutic approaches for this and related disorders.
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Affiliation(s)
- Jill A Fahrner
- McKusick-Nathans Institute of Genetic Medicine.,Department of Pediatrics
| | | | | | - Leandros Boukas
- McKusick-Nathans Institute of Genetic Medicine.,Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Valerie B DeLeon
- Department of Anthropology, University of Florida, Gainesville, Florida, USA
| | | | - Susan E Lad
- Department of Anthropology, University of Florida, Gainesville, Florida, USA
| | | | - Kasper D Hansen
- McKusick-Nathans Institute of Genetic Medicine.,Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hans T Bjornsson
- McKusick-Nathans Institute of Genetic Medicine.,Department of Pediatrics.,Landspitali University Hospital, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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50
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Gonzalez-Lopez O, DeCotiis J, Goyeneche C, Mello H, Vicente-Ortiz BA, Shin HJ, Driscoll KE, Du P, Palmeri D, Lukac DM. A herpesvirus transactivator and cellular POU proteins extensively regulate DNA binding of the host Notch signaling protein RBP-Jκ to the virus genome. J Biol Chem 2019; 294:13073-13092. [PMID: 31308175 DOI: 10.1074/jbc.ra118.007331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 07/10/2019] [Indexed: 12/11/2022] Open
Abstract
Reactivation of Kaposi's sarcoma-associated herpesvirus (KSHV) from latency requires the viral transactivator Rta to contact the host protein Jκ recombination signal-binding protein (RBP-Jκ or CSL). RBP-Jκ normally binds DNA sequence-specifically to determine the transcriptional targets of the Notch-signaling pathway, yet Notch alone cannot reactivate KSHV. We previously showed that Rta stimulates RBP-Jκ DNA binding to the viral genome. On a model viral promoter, this function requires Rta to bind to multiple copies of an Rta DNA motif (called "CANT" or Rta-c) proximal to an RBP-Jκ motif. Here, high-resolution ChIP/deep sequencing from infected primary effusion lymphoma cells revealed that RBP-Jκ binds nearly exclusively to different sets of viral genome sites during latency and reactivation. RBP-Jκ bound DNA frequently, but not exclusively, proximal to Rta bound to single, but not multiple, Rta-c motifs. To discover additional regulators of RBP-Jκ DNA binding, we used bioinformatics to identify cellular DNA-binding protein motifs adjacent to either latent or reactivation-specific RBP-Jκ-binding sites. Many of these cellular factors, including POU class homeobox (POU) proteins, have known Notch or herpesvirus phenotypes. Among a set of Rta- and RBP-Jκ-bound promoters, Rta transactivated only those that also contained POU motifs in conserved positions. On some promoters, POU factors appeared to inhibit RBP-Jκ DNA binding unless Rta bound to a proximal Rta-c motif. Moreover, POU2F1/Oct-1 expression was induced during KSHV reactivation, and POU2F1 knockdown diminished infectious virus production. Our results suggest that Rta and POU proteins broadly regulate DNA binding of RBP-Jκ during KSHV reactivation.
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Affiliation(s)
- Olga Gonzalez-Lopez
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103; Graduate School of Biomedical Sciences, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103
| | - Jennifer DeCotiis
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103; Graduate School of Biomedical Sciences, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103
| | - Corey Goyeneche
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103; Graduate School of Biomedical Sciences, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103
| | - Helena Mello
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103; Graduate School of Biomedical Sciences, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103
| | - Bryan Alexis Vicente-Ortiz
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103
| | - Hye Jin Shin
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103; Graduate School of Biomedical Sciences, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103
| | - Kyla E Driscoll
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103
| | - Peicheng Du
- High Performance and Research Computing, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103
| | - Diana Palmeri
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103
| | - David M Lukac
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103; Graduate School of Biomedical Sciences, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103.
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