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Robeyns R, Sisto A, Iturrospe E, da Silva KM, van de Lavoir M, Timmerman V, Covaci A, Stroobants S, van Nuijs ALN. The Metabolic and Lipidomic Fingerprint of Torin1 Exposure in Mouse Embryonic Fibroblasts Using Untargeted Metabolomics. Metabolites 2024; 14:248. [PMID: 38786725 PMCID: PMC11123261 DOI: 10.3390/metabo14050248] [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: 04/04/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Torin1, a selective kinase inhibitor targeting the mammalian target of rapamycin (mTOR), remains widely used in autophagy research due to its potent autophagy-inducing abilities, regardless of its unspecific properties. Recognizing the impact of mTOR inhibition on metabolism, our objective was to develop a reliable and thorough untargeted metabolomics workflow to study torin1-induced metabolic changes in mouse embryonic fibroblast (MEF) cells. Crucially, our quality assurance and quality control (QA/QC) protocols were designed to increase confidence in the reported findings by reducing the likelihood of false positives, including a validation experiment replicating all experimental steps from sample preparation to data analysis. This study investigated the metabolic fingerprint of torin1 exposure by using liquid chromatography-high resolution mass spectrometry (LC-HRMS)-based untargeted metabolomics platforms. Our workflow identified 67 altered metabolites after torin1 exposure, combining univariate and multivariate statistics and the implementation of a validation experiment. In particular, intracellular ceramides, diglycerides, phosphatidylcholines, phosphatidylethanolamines, glutathione, and 5'-methylthioadenosine were downregulated. Lyso-phosphatidylcholines, lyso-phosphatidylethanolamines, glycerophosphocholine, triglycerides, inosine, and hypoxanthine were upregulated. Further biochemical pathway analyses provided deeper insights into the reported changes. Ultimately, our study provides a valuable workflow that can be implemented for future investigations into the effects of other compounds, including more specific autophagy modulators.
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Affiliation(s)
- Rani Robeyns
- Toxicological Centre, University of Antwerp, 2610 Antwerp, Belgium; (E.I.); (A.C.)
| | - Angela Sisto
- Peripheral Neuropathy Research Group, University of Antwerp, 2610 Antwerp, Belgium
| | - Elias Iturrospe
- Toxicological Centre, University of Antwerp, 2610 Antwerp, Belgium; (E.I.); (A.C.)
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | | | - Maria van de Lavoir
- Toxicological Centre, University of Antwerp, 2610 Antwerp, Belgium; (E.I.); (A.C.)
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, University of Antwerp, 2610 Antwerp, Belgium
| | - Adrian Covaci
- Toxicological Centre, University of Antwerp, 2610 Antwerp, Belgium; (E.I.); (A.C.)
| | - Sigrid Stroobants
- Department of Nuclear Medicine, Antwerp University Hospital, 2650 Antwerp, Belgium
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2
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Achlaug L, Langier Goncalves I, Aronheim A. Cardioprotection and Suppression of Fibrosis by Diverse Cancer and Non-Cancer Cell Lines in a Murine Model of Duchenne Muscular Dystrophy. Int J Mol Sci 2024; 25:4273. [PMID: 38673859 PMCID: PMC11050177 DOI: 10.3390/ijms25084273] [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: 03/17/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
The dynamic relationship between heart failure and cancer poses a dual challenge. While cardiac remodeling can promote cancer growth and metastasis, tumor development can ameliorate cardiac dysfunction and suppress fibrosis. However, the precise mechanism through which cancer influences the heart and fibrosis is yet to be uncovered. To further explore the interaction between heart failure and cancer, we used the MDX mouse model, which suffers from cardiac fibrosis and cardiac dysfunction. A previous study from our lab demonstrated that tumor growth improves cardiac dysfunction and dampens fibrosis in the heart and diaphragm muscles of MDX mice. We used breast Polyoma middle T (PyMT) and Lewis lung carcinoma (LLC) cancer cell lines that developed into large tumors. To explore whether the aggressiveness of the cancer cell line is crucial for the beneficial phenotype, we employed a PyMT breast cancer cell line lacking integrin β1, representing a less aggressive cell line compared to the original PyMT cells. In addition, we examined immortalized and primary MEF cells. The injection of integrin β1 KO PyMT cancer cells and Mouse Embryo Fibroblasts cells (MEF) resulted in the improvement of cardiac function and decreased fibrosis in the heart, diaphragm, and skeletal muscles of MDX mice. Collectively, our data demonstrate that the cancer line aggressiveness as well as primary MEF cells are sufficient to impose the beneficial phenotype. These discoveries present potential novel clinical therapeutic approaches with beneficial outcome for patients with fibrotic diseases and cardiac dysfunction that do not require tumor growth.
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Affiliation(s)
| | | | - Ami Aronheim
- Department of Cell Biology and Cancer Science, Ruth and Bruce Rappaport Faculty of Medicine, Technion—Israel Institute of Technology, P.O. Box 9649, Haifa 31096, Israel; (L.A.); (I.L.G.)
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3
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Mariner BL, Rodriguez AS, Heath OC, McCormick MA. Induction of proteasomal activity in mammalian cells by lifespan-extending tRNA synthetase inhibitors. GeroScience 2024; 46:1755-1773. [PMID: 37749371 PMCID: PMC10828360 DOI: 10.1007/s11357-023-00938-8] [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: 05/08/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
We have recently shown that multiple tRNA synthetase inhibitors can greatly increase lifespan in multiple models by acting through the conserved transcription factor ATF4. Here, we show that these compounds, and several others of the same class, can greatly upregulate mammalian ATF4 in cells in vitro, in a dose dependent manner. Further, RNASeq analysis of these cells pointed toward changes in protein turnover. In subsequent experiments here we show that multiple tRNA synthetase inhibitors can greatly upregulate activity of the ubiquitin proteasome system (UPS) in cells in an ATF4-dependent manner. The UPS plays an important role in the turnover of many damaged or dysfunctional proteins in an organism. Increasing UPS activity has been shown to enhance the survival of Huntington's disease cell models, but there are few known pharmacological enhancers of the UPS. Additionally, we see separate ATF4 dependent upregulation of macroautophagy upon treatment with tRNA synthetase inhibitors. Protein degradation is an essential cellular process linked to many important human diseases of aging such as Alzheimer's disease and Huntington's disease. These drugs' ability to enhance proteostasis more broadly could have wide-ranging implications in the treatment of important age-related neurodegenerative diseases.
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Affiliation(s)
- Blaise L Mariner
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, Albuquerque, NM, 87131, USA
| | - Antonio S Rodriguez
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Olivia C Heath
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Mark A McCormick
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA.
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, Albuquerque, NM, 87131, USA.
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Bergeman MH, Hernandez MQ, Diefenderfer J, Drewes JA, Velarde K, Tierney WM, Enow JA, Glenn HL, Rahman MM, Hogue IB. Individual herpes simplex virus 1 (HSV-1) particles exit by exocytosis and accumulate at preferential egress sites. J Virol 2024; 98:e0178523. [PMID: 38193690 PMCID: PMC10883806 DOI: 10.1128/jvi.01785-23] [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: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 01/10/2024] Open
Abstract
The human pathogen herpes simplex virus 1 (HSV-1) produces a lifelong infection in the majority of the world's population. While the generalities of alpha herpesvirus assembly and egress pathways are known, the precise molecular and spatiotemporal details remain unclear. In order to study this aspect of HSV-1 infection, we engineered a recombinant HSV-1 strain expressing a pH-sensitive reporter, gM-pHluorin. Using a variety of fluorescent microscopy modalities, we can detect individual virus particles undergoing intracellular transport and exocytosis at the plasma membrane. We show that particles exit from epithelial cells individually, not bulk release of many particles at once, as has been reported for other viruses. In multiple cell types, HSV-1 particles accumulate over time at the cell periphery and cell-cell contacts. We show that this accumulation effect is the result of individual particles undergoing exocytosis at preferential sites and that these egress sites can contribute to cell-cell spread. We also show that the viral membrane proteins gE, gI, and US9, which have important functions in intracellular transport in neurons, are not required for preferential egress and clustering in non-neuronal cells. Importantly, by comparing HSV-1 to a related alpha herpesvirus, pseudorabies virus, we show that this preferential exocytosis and clustering effect are cell type dependent, not virus dependent. This preferential egress and clustering appear to be the result of the arrangement of the microtubule cytoskeleton, as virus particles co-accumulate at the same cell protrusions as an exogenous plus end-directed kinesin motor.IMPORTANCEAlpha herpesviruses produce lifelong infections in their human and animal hosts. The majority of people in the world are infected with herpes simplex virus 1 (HSV-1), which typically causes recurrent oral or genital lesions. However, HSV-1 can also spread to the central nervous system, causing severe encephalitis, and might also contribute to the development of neurodegenerative diseases. Many of the steps of how these viruses infect and replicate inside host cells are known in depth, but the final step, exiting from the infected cell, is not fully understood. In this study, we engineered a novel variant of HSV-1 that allows us to visualize how individual virus particles exit from infected cells. With this imaging assay, we investigated preferential egress site formation in certain cell types and their contribution to the cell-cell spread of HSV-1.
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Affiliation(s)
- Melissa H. Bergeman
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Michaella Q. Hernandez
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | | | - Jake A. Drewes
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Kimberly Velarde
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Wesley M. Tierney
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Junior A. Enow
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Honor L. Glenn
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Masmudur M. Rahman
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Ian B. Hogue
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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5
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Ferreira R, Hein N. Purification of Mouse Embryonic Fibroblasts (MEFs). Curr Protoc 2023; 3:e921. [PMID: 37987151 DOI: 10.1002/cpz1.921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Mouse embryonic fibroblasts (MEFs) are primary fibroblasts purified from mouse embryos at a defined time post-fertilization. MEFs have versatile applications, including use as feeder cell layers or sources of untransformed primary cells for a variety of biological assays. MEFs are most commonly isolated between embryonic day (E)12.5 and E13.5 but can be isolated from embryos as early as E8.5 and as late as E15.5. The individual embryos are harvested by carefully removing uterine tissue, yolk sac, and placenta. The embryos are euthanized, and non-mesenchymal tissues, such as the fetal liver and heart, are removed before tissue homogenization. The remaining fetal tissue is homogenized by mechanical mincing using a sterile blade, followed by enzymatic digestion and resuspension. During tissue dissociation, the duration of trypsin-EDTA/DNase digestion and enzyme concentration are critical parameters to produce high-quality MEFs with the highest rates of cell viability and proliferation potential. MEFs can be cryopreserved at passage (P) 0 if >80% confluent, passaged for further expansion before freezing down, or directly utilized for downstream applications, i.e., preparation as feeder cell layers. Primary MEFs possess a limited proliferation capacity of ∼20 cell divisions, beyond which the percentage of senescent cells rapidly increases; thus, cultures should only be expanded/passaged to a maximum of P5. Critical for cell viability during cryopreservation and thawing of MEFs is the slow decrease in temperature when freezing, the rapid increase when thawing, the use of a cryoprotective agent, and an optimal cell density. While it is critical to generate high-quality MEFs to standardize and optimize preparation procedures and utilize fresh reagents, some variability in proliferation capacity and cell viability between MEF preparations remains. Thus, MEF preparation, culture, and cryopreservation procedures are continuously being optimized. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Purification, passaging, and expansion of MEFs Supporting Protocol: Cryopreservation and thawing of MEFs.
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Affiliation(s)
- Rita Ferreira
- ACRF Department of Cancer Biology and Therapeutics and Division of Genome Sciences and Cancer, John Curtin School of Medical Research, Australian National University, Acton, Canberra, Australia
| | - Nadine Hein
- ACRF Department of Cancer Biology and Therapeutics and Division of Genome Sciences and Cancer, John Curtin School of Medical Research, Australian National University, Acton, Canberra, Australia
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6
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Yang L, Parajuli N, Wu P, Liu J, Wang X. S14-Phosphorylated RPN6 Mediates Proteasome Activation by PKA and Alleviates Proteinopathy. Circ Res 2023; 133:572-587. [PMID: 37641975 PMCID: PMC10502926 DOI: 10.1161/circresaha.123.322887] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND A better understanding of the regulation of proteasome activities can facilitate the search for new therapeutic strategies. A cell culture study shows that PKA (cAMP-dependent protein kinase or protein kinase A) activates the 26S proteasome by pS14-Rpn6 (serine14-phosphorylated Rpn6), but this discovery and its physiological significance remain to be established in vivo. METHODS Male and female mice with Ser14 of Rpn6 (regulatory particle non-ATPase 6) mutated to Ala (S14A [Rpn6/Psmd11S14A]) or Asp (S14D) to respectively block or mimic pS14-Rpn6 were created and used along with cells derived from them. cAMP/PKA were manipulated pharmacologically. Ubiquitin-proteasome system functioning was evaluated with the GFPdgn (green fluorescence protein with carboxyl fusion of the CL1 degron) reporter mouse and proteasomal activity assays. Impact of S14A and S14D on proteotoxicity was tested in mice and cardiomyocytes overexpressing the misfolded protein R120G-CryAB (R120G [arginine120 to glycine missense mutant alpha B-crystallin]). RESULTS PKA activation increased pS14-Rpn6 and 26S proteasome activities in wild-type but not S14A embryonic fibroblasts (mouse embryonic fibroblasts), adult cardiomyocytes, and mouse hearts. Basal 26S proteasome activities were significantly greater in S14D myocardium and adult mouse cardiomyocytes than in wild-type counterparts. S14D::GFPdgn mice displayed significantly lower myocardial GFPdgn protein but not mRNA levels than GFPdgn mice. In R120G mice, a classic model of cardiac proteotoxicity, basal myocardial pS14-Rpn6 was significantly lower compared with nontransgenic littermates, which was not always associated with reduction of other phosphorylated PKA substrates. Cultured S14D neonatal cardiomyocytes displayed significantly faster proteasomal degradation of R120G than wild-type neonatal cardiomyocytes. Compared with R120G mice, S14D/S14D::R120G mice showed significantly greater myocardial proteasome activities, lower levels of total and K48-linked ubiquitin conjugates, and of aberrant CryAB (alpha B-crystallin) protein aggregates, less fetal gene reactivation, and cardiac hypertrophy, and delays in cardiac malfunction. CONCLUSIONS This study establishes in animals that pS14-Rpn6 mediates the activation of 26S proteasomes by PKA and that the reduced pS14-Rpn6 is a key pathogenic factor in cardiac proteinopathy, thereby identifying a new therapeutic target to reduce cardiac proteotoxicity.
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Affiliation(s)
- Liuqing Yang
- Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermillion, SD 57069, USA
| | - Nirmal Parajuli
- Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermillion, SD 57069, USA
| | - Penglong Wu
- Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermillion, SD 57069, USA
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Lab of Respiratory Disease, School of Basic Medical Sciences, Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jinbao Liu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Lab of Respiratory Disease, School of Basic Medical Sciences, Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xuejun Wang
- Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermillion, SD 57069, USA
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7
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Tandra V, Anderson T, Ayala JD, Weintraub NL, Singh N, Li H, Li J. Ufmylation of UFBP1 Is Dispensable for Endoplasmic Reticulum Stress Response, Embryonic Development, and Cardiac and Intestinal Homeostasis. Cells 2023; 12:1923. [PMID: 37566002 PMCID: PMC10416869 DOI: 10.3390/cells12151923] [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: 06/01/2023] [Revised: 06/20/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023] Open
Abstract
Protein modification by ubiquitin fold modifier 1 (UFM1), termed ufmylation, regulates various physiological and pathological processes. Among emerging UFM1 targets, UFM1 binding protein 1 (UFBP1) is the first identified ufmylation substrate. Recent clinical and animal studies have demonstrated the pivotal roles of UFBP1 in development, hematopoiesis, intestinal homeostasis, chondrogenesis, and neuronal development, which has been linked to its function in maintaining endoplasmic reticulum (ER) homeostasis. However, the importance of UFBP1 ufmylation in these cellular and physiological processes has yet to be determined. It has been proposed that ufmylation of lysine 268 (267 in humans) in UFBP1 plays a critical role in mediating the effects of the ufmylation pathway. In this study, we for the first time probe the pathophysiological significance of UFBP1 ufmylation in vivo by creating and characterizing a mouse UFBP1 knockin (KI) model in which the lysine 268 of UFBP1, the amino acid accepting UFM1, was mutated to arginine. Our results showed that the K268R mutation reduced the total ufmylated proteins without altering the expression levels of individual ufmylation enzymes in mouse embryonic fibroblasts. The K268R mutation did not alter ER stress-stimuli-induced ER stress signaling or cell death in mouse embryonic fibroblasts. The homozygous KI mice were viable and morphologically indistinguishable from their littermate wild-type controls up to one year of age. Serial echocardiography revealed no cardiac functional impairment of the homozygous KI mice. Furthermore, the homozygous KI mice exhibited the same susceptibility to dextran sulfate sodium (DSS) -induced colitis as wild-type mice. Taken together, these results suggest that UFBP1 K268 is dispensable for ER stress response, embryonic development, cardiac homeostasis under physiological conditions, and intestinal homeostasis under pathological conditions. Our studies call for future investigations to understand the biological function of UFBP1 ufmylation and offer a new mouse model to determine the roles of UFBP1 ufmylation in different tissues under stress conditions.
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Affiliation(s)
- Varsha Tandra
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Travis Anderson
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Juan D. Ayala
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Neal L. Weintraub
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Division of Cardiology, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Nagendra Singh
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Honglin Li
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Jie Li
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Division of Cardiology, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
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8
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Dimond A, Van de Pette M, Taylor-Bateman V, Brown K, Sardini A, Whilding C, Feytout A, Prinjha RK, Merkenschlager M, Fisher AG. Drug-induced loss of imprinting revealed using bioluminescent reporters of Cdkn1c. Sci Rep 2023; 13:5626. [PMID: 37024615 PMCID: PMC10079848 DOI: 10.1038/s41598-023-32747-6] [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: 12/15/2022] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
Genomic imprinting is an epigenetically mediated mechanism that regulates allelic expression of genes based upon parent-of-origin and provides a paradigm for studying epigenetic silencing and release. Here, bioluminescent reporters for the maternally-expressed imprinted gene Cdkn1c are used to examine the capacity of chromatin-modifying drugs to reverse paternal Cdkn1c silencing. Exposure of reporter mouse embryonic stem cells (mESCs) to 5-Azacytidine, HDAC inhibitors, BET inhibitors or GSK-J4 (KDM6A/B inhibitor) relieved repression of paternal Cdkn1c, either selectively or by inducing biallelic effects. Treatment of reporter fibroblasts with HDAC inhibitors or GSK-J4 resulted in similar paternal Cdkn1c activation, whereas BET inhibitor-induced loss of imprinting was specific to mESCs. Changes in allelic expression were generally not sustained in dividing cultures upon drug removal, indicating that the underlying epigenetic memory of silencing was maintained. In contrast, Cdkn1c de-repression by GSK-J4 was retained in both mESCs and fibroblasts following inhibitor removal, although this impact may be linked to cellular stress and DNA damage. Taken together, these data introduce bioluminescent reporter cells as tools for studying epigenetic silencing and disruption, and demonstrate that Cdkn1c imprinting requires distinct and cell-type specific chromatin features and modifying enzymes to enact and propagate a memory of silencing.
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Affiliation(s)
- Andrew Dimond
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
| | - Mathew Van de Pette
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Victoria Taylor-Bateman
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Karen Brown
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Alessandro Sardini
- Whole Animal Physiology and Imaging, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Chad Whilding
- Microscopy Facility, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Amelie Feytout
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Rab K Prinjha
- Immunology and Epigenetics Research Unit, Research, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, Herts, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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9
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Yang L, Parajuli N, Wu P, Liu J, Wang X. Ser14-RPN6 Phosphorylation Mediates the Activation of 26S Proteasomes by cAMP and Protects against Cardiac Proteotoxic Stress in Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535705. [PMID: 37066344 PMCID: PMC10104033 DOI: 10.1101/2023.04.05.535705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Background A better understanding of the regulation of proteasome activities can facilitate the search for new therapeutic strategies. A cell culture study shows that cAMP-dependent protein kinase (PKA) activates the 26S proteasome by phosphorylating Ser14 of RPN6 (pS14-RPN6), but this discovery and its physiological significance remain to be established in vivo . Methods Male and female mice with Ser14 of Rpn6 mutated to Ala (S14A) or Asp (S14D) to respectively block or mimic pS14-Rpn6 were created and used along with cells derived from them. cAMP/PKA were manipulated pharmacologically. Ubiquitin-proteasome system (UPS) functioning was evaluated with the GFPdgn reporter mouse and proteasomal activity assays. Impact of S14A and S14D on proteotoxicity was tested in mice and cardiomyocytes overexpressing the misfolded protein R120G-CryAB (R120G). Results PKA activation increased pS14-Rpn6 and 26S proteasome activities in wild-type (WT) but not S14A embryonic fibroblasts (MEFs), adult cardiomyocytes (AMCMs), and mouse hearts. Basal 26S proteasome activities were significantly greater in S14D myocardium and AMCMs than in WT counterparts. S14D::GFPdgn mice displayed significantly lower myocardial GFPdgn protein but not mRNA levels than GFPdgn mice. In R120G mice, a classic model of cardiac proteotoxicity, basal myocardial pS14-Rpn6 was significantly lower compared with non- transgenic littermates, which was not always associated with reduction of other phosphorylated PKA substrates. Cultured S14D neonatal cardiomyocytes displayed significantly faster proteasomal degradation of R120G than WT neonatal cardiomyocytes. Compared with R120G mice, S14D/S14D::R120G mice showed significantly greater myocardial proteasome activities, lower levels of total and K48-linked ubiquitin conjugates and of aberrant CryAB protein aggregates, less reactivation of fetal genes and cardiac hypertrophy, and delays in cardiac malfunction. Conclusions This study establishes in animals that pS14-Rpn6 mediates the activation of 26S proteasomes by PKA and that the reduced pS14-Rpn6 is a key pathogenic factor in cardiac proteinopathy, thereby identifies a new therapeutic target to reduce cardiac proteotoxicity.
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10
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Raja R, Khanum S, Aboulmouna L, Maurya MR, Gupta S, Subramaniam S, Ramkrishna D. Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533676. [PMID: 36993235 PMCID: PMC10055344 DOI: 10.1101/2023.03.21.533676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Quantitative understanding of cellular processes, such as cell cycle and differentiation, is impeded by various forms of complexity ranging from myriad molecular players and their multilevel regulatory interactions, cellular evolution with multiple intermediate stages, lack of elucidation of cause-effect relationships among the many system players, and the computational complexity associated with the profusion of variables and parameters. In this paper, we present an elegant modeling framework based on the cybernetic concept that biological regulation is inspired by objectives embedding entirely novel strategies for dimension reduction, process stage specification through the system dynamics, and innovative causal association of regulatory events with the ability to predict the evolution of the dynamical system. The elementary step of the modeling strategy involves stage-specific objective functions that are computationally-determined from experiments, augmented with dynamical network computations involving end point objective functions, mutual information, change point detection, and maximal clique centrality. We demonstrate the power of the method through application to the mammalian cell cycle, which involves thousands of biomolecules engaged in signaling, transcription, and regulation. Starting with a fine-grained transcriptional description obtained from RNA sequencing measurements, we develop an initial model, which is then dynamically modeled using the cybernetic-inspired method (CIM), utilizing the strategies described above. The CIM is able to distill the most significant interactions from a multitude of possibilities. In addition to capturing the complexity of regulatory processes in a mechanistically causal and stage-specific manner, we identify the functional network modules, including novel cell cycle stages. Our model is able to predict future cell cycles consistent with experimental measurements. We posit that this state-of-the-art framework has the promise to extend to the dynamics of other biological processes, with a potential to provide novel mechanistic insights. STATEMENT OF SIGNIFICANCE Cellular processes like cell cycle are overly complex, involving multiple players interacting at multiple levels, and explicit modeling of such systems is challenging. The availability of longitudinal RNA measurements provides an opportunity to "reverse-engineer" for novel regulatory models. We develop a novel framework, inspired using goal-oriented cybernetic model, to implicitly model transcriptional regulation by constraining the system using inferred temporal goals. A preliminary causal network based on information-theory is used as a starting point, and our framework is used to distill the network to temporally-based networks containing essential molecular players. The strength of this approach is its ability to dynamically model the RNA temporal measurements. The approach developed paves the way for inferring regulatory processes in many complex cellular processes.
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11
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Han W, Meißner EM, Neunteibl S, Günther M, Kahnt J, Dolga A, Xie C, Plesnila N, Zhu C, Blomgren K, Culmsee C. Dying transplanted neural stem cells mediate survival bystander effects in the injured brain. Cell Death Dis 2023; 14:173. [PMID: 36854658 PMCID: PMC9975220 DOI: 10.1038/s41419-023-05698-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/02/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023]
Abstract
Neural stem and progenitor cell (NSPC) transplants provide neuroprotection in models of acute brain injury, but the underlying mechanisms are not fully understood. Here, we provide evidence that caspase-dependent apoptotic cell death of NSPCs is required for sending survival signals to the injured brain. The secretome of dying NSPCs contains heat-stable proteins, which protect neurons against glutamate-induced toxicity and trophic factor withdrawal in vitro, and from ischemic brain damage in vivo. Our findings support a new concept suggesting a bystander effect of apoptotic NSPCs, which actively promote neuronal survival through the release of a protective "farewell" secretome. Similar protective effects by the secretome of apoptotic NSPC were also confirmed in human neural progenitor cells and neural stem cells but not in mouse embryonic fibroblasts (MEF) or human dopaminergic neurons, suggesting that the observed effects are cell type specific and exist for neural progenitor/stem cells across species.
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Affiliation(s)
- Wei Han
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Henan Key Laboratory of Child Brain Injury, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Eva-Maria Meißner
- Institute of Pharmacology and Clinical Pharmacy, University of Marburg, Marburg, Germany
| | - Stefanie Neunteibl
- Institute of Pharmacology and Clinical Pharmacy, University of Marburg, Marburg, Germany
| | - Madeline Günther
- Institute of Pharmacology and Clinical Pharmacy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), Universities of Marburg and Giessen, Marburg, Germany
| | - Jörg Kahnt
- Max-Planck-Institute for Terrestrial Microbiology, Department of Ecophysiology, Marburg, Germany
| | - Amalia Dolga
- Faculty of Science and Engineering, Molecular Pharmacology - Groningen Research Institute of Pharmacy, Groningen, The Netherlands
| | - Cuicui Xie
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Nikolaus Plesnila
- Institute for Stroke and Dementia Research (ISD), University Clinic Munich, Munich, Germany
| | - Changlian Zhu
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Henan Key Laboratory of Child Brain Injury, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Klas Blomgren
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
- Pediatric Oncology, Karolinska University Hospital, Stockholm, Sweden.
| | - Carsten Culmsee
- Institute of Pharmacology and Clinical Pharmacy, University of Marburg, Marburg, Germany.
- Center for Mind, Brain and Behavior (CMBB), Universities of Marburg and Giessen, Marburg, Germany.
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12
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Zhao XJ, Mohsen AW, Mihalik S, Solo K, Aliu E, Shi H, Basu S, Kochersperger C, Van't Land C, Karunanidhi A, Coughlan KA, Siddiqui S, Rice LM, Hillier S, Guadagnin E, Giangrande PH, Martini PGV, Vockley J. Synthetic mRNA rescues very long-chain acyl-CoA dehydrogenase deficiency in patient fibroblasts and a murine model. Mol Genet Metab 2023; 138:106982. [PMID: 36580829 PMCID: PMC9877169 DOI: 10.1016/j.ymgme.2022.106982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
Very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency is an inborn error of long chain fatty acid β-oxidation (FAO) with limited treatment options. Patients present with heterogeneous clinical phenotypes affecting predominantly heart, liver, and skeletal muscle. While VLCAD deficiency is a systemic disease, restoration of liver FAO has the potential to improve symptoms more broadly due to increased total body ATP production and reduced accumulation of potentially toxic metabolites. We explored the use of synthetic human VLCAD (hVLCAD) mRNA and lipid nanoparticle encapsulated hVLCAD mRNA (LNP-VLCAD) to generate functional VLCAD enzyme in patient fibroblasts derived from VLCAD deficient patients, mouse embryonic fibroblasts, hepatocytes isolated from VLCAD knockout (Acadvl-/-) mice, and Acadvl-/- mice to reverse the metabolic effects of the deficiency. Transfection of all cell types with hVLCAD mRNA resulted in high level expression of protein that localized to mitochondria with increased enzyme activity. Intravenous administration of LNP-VLCAD to Acadvl-/- mice produced a significant amount of VLCAD protein in liver, which declined over a week. Treated Acadvl-/- mice showed reduced hepatic steatosis, were more resistant to cold stress, and accumulated less toxic metabolites in blood than untreated animals. Results from this study support the potential for hVLCAD mRNA for treatment of VLCAD deficiency.
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Affiliation(s)
- Xue-Jun Zhao
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ai-Walid Mohsen
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephanie Mihalik
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Keaton Solo
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ermal Aliu
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Huifang Shi
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shakuntala Basu
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Catherine Kochersperger
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Clinton Van't Land
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anuradha Karunanidhi
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kimberly A Coughlan
- Moderna Therapeutics, Inc., Rare Diseases, 200 Technology Square, Cambridge, MA, USA
| | - Summar Siddiqui
- Moderna Therapeutics, Inc., Rare Diseases, 200 Technology Square, Cambridge, MA, USA
| | - Lisa M Rice
- Moderna Therapeutics, Inc., Rare Diseases, 200 Technology Square, Cambridge, MA, USA
| | - Shawn Hillier
- Moderna Therapeutics, Inc., Rare Diseases, 200 Technology Square, Cambridge, MA, USA
| | - Eleonora Guadagnin
- Moderna Therapeutics, Inc., Rare Diseases, 200 Technology Square, Cambridge, MA, USA
| | - Paloma H Giangrande
- Moderna Therapeutics, Inc., Rare Diseases, 200 Technology Square, Cambridge, MA, USA
| | - Paolo G V Martini
- Moderna Therapeutics, Inc., Rare Diseases, 200 Technology Square, Cambridge, MA, USA
| | - Jerry Vockley
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA.
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13
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Tsitsikov EN, Hameed S, Tavakol SA, Stephens TM, Tsytsykova AV, Garman L, Bi WL, Dunn IF. Specific gene expression signatures of low grade meningiomas. Front Oncol 2023; 13:1126550. [PMID: 36937440 PMCID: PMC10016690 DOI: 10.3389/fonc.2023.1126550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/10/2023] [Indexed: 03/05/2023] Open
Abstract
Introduction Meningiomas are the most common primary central nervous system (CNS) tumors in adults, representing approximately one-third of all primary adult CNS tumors. Although several recent publications have proposed alternative grading systems of meningiomas that incorporate genomic and/or epigenomic data to better predict meningioma recurrence and progression-free survival, our understanding of driving forces of meningioma development is still limited. Objective To define gene expression signatures of the most common subtypes of meningiomas to better understand cellular processes and signaling pathways specific for each tumor genotype. Methods We used RNA sequencing (RNA-seq) to determine whole transcriptome profiles of twenty meningiomas with genomic alterations including NF2 inactivation, loss of chr1p, and missense mutations in TRAF7, AKT1 and KLF4. Results The analysis revealed that meningiomas with NF2 gene inactivation expressed higher levels of BCL2 and GLI1 compared with tumors harboring TRAF7 missense mutations. Moreover, NF2 meningiomas were subdivided into two distinct groups based on additional loss of chr1p. NF2 tumors with intact chr1p were characterized by the high expression of tumor suppressor PTCH2 compared to NF2 tumors with chr1p loss. Taken together with the high expression of BCL2 and GLI1, these results suggest that activation of Sonic Hedgehog pathway may contribute to NF2 meningioma development. In contrast, NF2 tumors with chr1p loss expressed high levels of transcription factor FOXD3 and its antisense RNA FOXD3-AS1. Examination of TRAF7 tumors demonstrated that TRAF7 regulates a number of biomechanically responsive genes (KRT6a, KRT16, IL1RL1, and AQP3 among others). Interestingly, AKT1 and KLF4 meningiomas expressed genes specific for PI3K/AKT signaling pathway, suggesting overlapping gene signatures between the two subtypes. In addition, KLF4 meningiomas had high expression of carcinoembryonic antigen family members CEACAM6 and CEACAM5. Conclusions Each group of meningiomas displayed a unique gene expression signature suggesting signaling pathways potentially implicated in tumorigenesis. These findings will improve our understanding of meningioma tumorigenesis and prognosis.
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Affiliation(s)
- Erdyni N. Tsitsikov
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Sanaa Hameed
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Sherwin A. Tavakol
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Tressie M. Stephens
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Alla V. Tsytsykova
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Lori Garman
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Ian F. Dunn
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- *Correspondence: Ian F. Dunn,
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14
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Muciño-Hernández G, Acevo-Rodríguez PS, Cabrera-Benitez S, Guerrero AO, Merchant-Larios H, Castro-Obregón S. Nucleophagy contributes to genome stability through degradation of type II topoisomerases A and B and nucleolar components. J Cell Sci 2023; 136:286548. [PMID: 36633090 PMCID: PMC10112964 DOI: 10.1242/jcs.260563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/24/2022] [Indexed: 01/13/2023] Open
Abstract
The nuclear architecture of mammalian cells can be altered as a consequence of anomalous accumulation of nuclear proteins or genomic alterations. Most of the knowledge about nuclear dynamics comes from studies on cancerous cells. How normal healthy cells maintain genome stability, avoiding accumulation of nuclear damaged material, is less understood. Here, we describe that primary mouse embryonic fibroblasts develop a basal level of nuclear buds and micronuclei, which increase after etoposide-induced DNA double-stranded breaks. Both basal and induced nuclear buds and micronuclei colocalize with the autophagic proteins BECN1 and LC3B (also known as MAP1LC3B) and with acidic vesicles, suggesting their clearance by nucleophagy. Some of the nuclear alterations also contain autophagic proteins and type II DNA topoisomerases (TOP2A and TOP2B), or the nucleolar protein fibrillarin, implying they are also targets of nucleophagy. We propose that basal nucleophagy contributes to genome and nuclear stability, as well as in response to DNA damage.
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Affiliation(s)
- Gabriel Muciño-Hernández
- Departamento de Neurodesarrollo y Fisiología, División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Mexico City, México
| | - Pilar Sarah Acevo-Rodríguez
- Departamento de Neurodesarrollo y Fisiología, División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Mexico City, México
| | - Sandra Cabrera-Benitez
- Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510 Mexico City, México
| | - Adán Oswaldo Guerrero
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Morelos, Mexico
| | - Horacio Merchant-Larios
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Susana Castro-Obregón
- Departamento de Neurodesarrollo y Fisiología, División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Mexico City, México
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15
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Wang H, Stevens T, Lu J, Airik M, Airik R, Prochownik EV. Disruption of Multiple Overlapping Functions Following Stepwise Inactivation of the Extended Myc Network. Cells 2022; 11:cells11244087. [PMID: 36552851 PMCID: PMC9777503 DOI: 10.3390/cells11244087] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Myc, a member of the "Myc Network" of bHLH-ZIP transcription factors, supervises proliferation, metabolism, and translation. It also engages in crosstalk with the related "Mlx Network" to co-regulate overlapping genes and functions. We investigated the consequences of stepwise conditional inactivation of Myc and Mlx in primary and SV40 T-antigen-immortalized murine embryonic fibroblasts (MEFs). Myc-knockout (MycKO) and Myc × Mlx "double KO" (DKO)-but not MlxKO-primary MEFs showed rapid growth arrest and displayed features of accelerated aging and senescence. However, DKO MEFs soon resumed proliferating, indicating that durable growth arrest requires an intact Mlx network. All three KO MEF groups deregulated multiple genes and functions pertaining to aging, senescence, and DNA damage recognition/repair. Immortalized KO MEFs proliferated in Myc's absence while demonstrating variable degrees of widespread genomic instability and sensitivity to genotoxic agents. Finally, compared to primary MycKO MEFs, DKO MEFs selectively downregulated numerous gene sets associated with the p53 and retinoblastoma (Rb) pathways and G2/M arrest. Thus, the reversal of primary MycKO MEF growth arrest by either Mlx loss or SV40 T-antigen immortalization appears to involve inactivation of the p53 and/or Rb pathways.
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Affiliation(s)
- Huabo Wang
- Division of Hematology/Oncology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Taylor Stevens
- Division of Hematology/Oncology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jie Lu
- Division of Hematology/Oncology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Merlin Airik
- Division of Nephrology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Rannar Airik
- Division of Nephrology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
- Department of Developmental Biology, The University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Edward V. Prochownik
- Division of Hematology/Oncology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
- The Department of Microbiology and Molecular Genetics, The University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA
- The UPMC Hillman Comprehensive Cancer Center, Pittsburgh, PA 25232, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Correspondence: ; Tel.: +1-412-692-6795
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16
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Sessions DT, Kim KB, Kashatus JA, Churchill N, Park KS, Mayo MW, Sesaki H, Kashatus DF. Opa1 and Drp1 reciprocally regulate cristae morphology, ETC function, and NAD + regeneration in KRas-mutant lung adenocarcinoma. Cell Rep 2022; 41:111818. [PMID: 36516772 DOI: 10.1016/j.celrep.2022.111818] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/28/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
Oncogenic KRas activates mitochondrial fission through Erk-mediated phosphorylation of the mitochondrial fission GTPase Drp1. Drp1 deletion inhibits tumorigenesis of KRas-driven pancreatic cancer, but the role of mitochondrial dynamics in other Ras-driven malignancies is poorly defined. Here we show that in vitro and in vivo growth of KRas-driven lung adenocarcinoma is unaffected by deletion of Drp1 but is inhibited by deletion of Opa1, the GTPase that regulates inner membrane fusion and proper cristae morphology. Mechanistically, Opa1 knockout disrupts cristae morphology and inhibits electron transport chain (ETC) assembly and activity, which inhibits tumor cell proliferation through loss of NAD+ regeneration. Simultaneous inactivation of Drp1 and Opa1 restores cristae morphology, ETC activity, and cell proliferation indicating that mitochondrial fission activity drives ETC dysfunction induced by Opa1 knockout. Our results support a model in which mitochondrial fission events disrupt cristae structure, and tumor cells with hyperactive fission activity require Opa1 activity to maintain ETC function.
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Affiliation(s)
- Dane T Sessions
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Kee-Beom Kim
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Jennifer A Kashatus
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Nikolas Churchill
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Kwon-Sik Park
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Marty W Mayo
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Hiromi Sesaki
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David F Kashatus
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia Health System, Charlottesville, VA 22908, USA.
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Bodur C, Kazyken D, Huang K, Tooley AS, Cho KW, Barnes TM, Lumeng CN, Myers MG, Fingar DC. TBK1-mTOR Signaling Attenuates Obesity-Linked Hyperglycemia and Insulin Resistance. Diabetes 2022; 71:2297-2312. [PMID: 35983955 PMCID: PMC9630091 DOI: 10.2337/db22-0256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022]
Abstract
The innate immune kinase TBK1 (TANK-binding kinase 1) responds to microbial-derived signals to initiate responses against viral and bacterial pathogens. More recent work implicates TBK1 in metabolism and tumorigenesis. The kinase mTOR (mechanistic target of rapamycin) integrates diverse environmental cues to control fundamental cellular processes. Our prior work demonstrated in cells that TBK1 phosphorylates mTOR (on S2159) to increase mTORC1 and mTORC2 catalytic activity and signaling. Here we investigate a role for TBK1-mTOR signaling in control of glucose metabolism in vivo. We find that mice with diet-induced obesity (DIO) but not lean mice bearing a whole-body "TBK1-resistant" Mtor S2159A knock-in allele (MtorA/A) display exacerbated hyperglycemia and systemic insulin resistance with no change in energy balance. Mechanistically, Mtor S2159A knock-in in DIO mice reduces mTORC1 and mTORC2 signaling in response to insulin and innate immune agonists, reduces anti-inflammatory gene expression in adipose tissue, and blunts anti-inflammatory macrophage M2 polarization, phenotypes shared by mice with tissue-specific inactivation of TBK1 or mTOR complexes. Tissues from DIO mice display elevated TBK1 activity and mTOR S2159 phosphorylation relative to lean mice. We propose a model whereby obesity-associated signals increase TBK1 activity and mTOR phosphorylation, which boost mTORC1 and mTORC2 signaling in parallel to the insulin pathway, thereby attenuating insulin resistance to improve glycemic control during diet-induced obesity.
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Affiliation(s)
- Cagri Bodur
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Dubek Kazyken
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Kezhen Huang
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Aaron Seth Tooley
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Kae Won Cho
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI
| | - Tammy M. Barnes
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan Medical School, Ann Arbor, MI
| | - Carey N. Lumeng
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI
| | - Martin G. Myers
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan Medical School, Ann Arbor, MI
| | - Diane C. Fingar
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
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18
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Universal dynamics of mitochondrial networks: a finite-size scaling analysis. Sci Rep 2022; 12:17074. [PMID: 36224243 PMCID: PMC9556628 DOI: 10.1038/s41598-022-14946-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 06/15/2022] [Indexed: 01/04/2023] Open
Abstract
Evidence from models and experiments suggests that the networked structure observed in mitochondria emerges at the critical point of a phase transition controlled by fission and fusion rates. If mitochondria are poised at criticality, the relevant network quantities should scale with the system's size. However, whether or not the expected finite-size effects take place has not been demonstrated yet. Here, we first provide a theoretical framework to interpret the scaling behavior of mitochondrial network quantities by analyzing two conceptually different models of mitochondrial dynamics. Then, we perform a finite-size scaling analysis of real mitochondrial networks extracted from microscopy images and obtain scaling exponents comparable with critical exponents from models and theory. Overall, we provide a universal description of the structural phase transition in mammalian mitochondria.
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19
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Imprinting fidelity in mouse iPSCs depends on sex of donor cell and medium formulation. Nat Commun 2022; 13:5432. [PMID: 36114205 PMCID: PMC9481624 DOI: 10.1038/s41467-022-33013-5] [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: 11/05/2020] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Reprogramming of somatic cells into induced Pluripotent Stem Cells (iPSCs) is a major leap towards personalised approaches to disease modelling and cell-replacement therapies. However, we still lack the ability to fully control the epigenetic status of iPSCs, which is a major hurdle for their downstream applications. Epigenetic fidelity can be tracked by genomic imprinting, a phenomenon dependent on DNA methylation, which is frequently perturbed in iPSCs by yet unknown reasons. To try to understand the causes underlying these defects, we conducted a thorough imprinting analysis using IMPLICON, a high-throughput method measuring DNA methylation levels, in multiple female and male murine iPSC lines generated under different experimental conditions. Our results show that imprinting defects are remarkably common in iPSCs, but their nature depends on the sex of donor cells and their response to culture conditions. Imprints in female iPSCs resist the initial genome-wide DNA demethylation wave during reprogramming, but ultimately cells accumulate hypomethylation defects irrespective of culture medium formulations. In contrast, imprinting defects on male iPSCs depends on the experimental conditions and arise during reprogramming, being mitigated by the addition of vitamin C (VitC). Our findings are fundamental to further optimise reprogramming strategies and generate iPSCs with a stable epigenome. Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) is associated with epigenetic alterations. Here the authors assess DNA methylation in detail in multiple female and male mouse iPSC lines generated with different protocols and find that defects depend on the sex of donor cells and can be partially mitigated by Vitamin C.
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20
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Suppression of annexin A1 and its receptor reduces herpes simplex virus 1 lethality in mice. PLoS Pathog 2022; 18:e1010692. [PMID: 35939498 PMCID: PMC9359538 DOI: 10.1371/journal.ppat.1010692] [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: 12/06/2021] [Accepted: 06/20/2022] [Indexed: 11/27/2022] Open
Abstract
Herpes simplex virus 1 (HSV-1)-induced encephalitis is the most common cause of sporadic, fatal encephalitis in humans. HSV-1 has at least 10 different envelope glycoproteins, which can promote virus infection. The ligands for most of the envelope glycoproteins and the significance of these ligands in virus-induced encephalitis remain elusive. Here, we show that glycoprotein E (gE) binds to the cellular protein, annexin A1 (Anx-A1) to enhance infection. Anx-A1 can be detected on the surface of cells permissive for HSV-1 before infection and on virions. Suppression of Anx-A1 or its receptor, formyl peptide receptor 2 (FPR2), on the cell surface and gE or Anx-A1 on HSV-1 envelopes reduced virus binding to cells. Importantly, Anx-A1 knockout, Anx-A1 knockdown, or treatments with the FPR2 antagonist reduced the mortality and tissue viral loads of infected mice. Our results show that Anx-A1 is a novel enhancing factor of HSV-1 infection. Anx-A1-deficient mice displayed no evident physiology and behavior changes. Hence, targeting Anx-A1 and FPR2 could be a promising prophylaxis or adjuvant therapy to decrease HSV-1 lethality. Herpes simplex virus 1 (HSV-1)-induced encephalitis is the most devastating consequence of HSV-1 infection, even in patients treated with anti-HSV-1 drugs. Moreover, encephalitis induced by drug-resistant HSV-1 has been reported in immunocompromised patients. Identifying the cellular factors in promoting HSV-1 replication, especially those increasing virus attachment and entry, could facilitate the development of alternative or adjuvant therapy. Here, we identified annexin A1 (Anx-A1) and its receptor, formyl peptide receptor 2 (FPR2), facilitating HSV-1 attachment to the cell surface. Suppression of Anx-A1 or blockage of FPR2 impaired HSV-1 attachment to cells, viral yields in cells, and HSV-1 lethality in mice. Moreover, blocking FPR2 decreased the replication of drug-resistant HSV-1 in BABL/c nude mice. Hence, targeting Anx-A1 and FPR2 could be alternative or adjuvant therapy for HSV-1 infection.
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21
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Liu C, Peng Q, Wei L, Li Z, Zhang X, Wu Y, Wang J, Zheng X, Wen Y, Zheng R, Yan Q, Ye Q, Ma J. Deficiency of Lactoferrin aggravates lipopolysaccharide-induced acute inflammation via recruitment macrophage in mice. Biometals 2022; 36:549-562. [PMID: 35650365 PMCID: PMC9159647 DOI: 10.1007/s10534-022-00398-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/14/2022] [Indexed: 11/26/2022]
Abstract
Lactoferrin (Lf), a multiple functional natural immune protein, is widely distributed in mammalian milk and glandular secretions (bile, saliva, tears and nasal mucosal secretions, etc.). In the previous study, we found that Lf plays an anti-inflammatory and anti-tumorigenesis role in AOM/DSS (azoxymethane/dextran sulfate sodium) induced mouse colitis-associated colon cancer model.
Although we found that Lf has anti-inflammatory effects in chronic inflammation, its specific role and mechanisms in acute inflammation have not been clarified. Here, we reported that the expression levels of Lf were significantly increased when the organism was infected by Gram-negative bacteria. We then explored the role and potential mechanism of Lf in lipopolysaccharide (LPS)-induced acute inflammation. In the LPS-induced acute abdominal inflammation model, Lf deficiency aggravated inflammatory response and promoted macrophage chemotaxis to the inflammation site. Lf inhibited macrophage chemotaxis by suppressing the expression of macrophage-associated chemokines Ccl2 and Ccl5. Highly activated NF-κB signaling in Lf−/− mice was responsible for the high expression of Ccl2 and Ccl5. Our results suggested that the anti-inflammatory effect of Lf offers a new potential treatment for acute inflammatory diseases.
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Affiliation(s)
- Can Liu
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, China
| | - Qiu Peng
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, China
| | - Lingyu Wei
- Department of Pathology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Zhengshuo Li
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, China
| | - Xiaoyue Zhang
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, China
| | - Yangge Wu
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, China
| | - Jia Wang
- Department of Immunology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Xiang Zheng
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Yuqing Wen
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, China
| | - Run Zheng
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, China
| | - Qun Yan
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Qiurong Ye
- Department of Pathology, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China.
| | - Jian Ma
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, China.
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22
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Phan TP, Boatwright CA, Drown CG, Skinner MW, Strong MA, Jordan PW, Holland AJ. Upstream open reading frames control PLK4 translation and centriole duplication in primordial germ cells. Genes Dev 2022; 36:718-736. [PMID: 35772791 PMCID: PMC9296005 DOI: 10.1101/gad.349604.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022]
Abstract
Centrosomes are microtubule-organizing centers comprised of a pair of centrioles and the surrounding pericentriolar material. Abnormalities in centriole number are associated with cell division errors and can contribute to diseases such as cancer. Centriole duplication is limited to once per cell cycle and is controlled by the dosage-sensitive Polo-like kinase 4 (PLK4). Here, we show that PLK4 abundance is translationally controlled through conserved upstream open reading frames (uORFs) in the 5' UTR of the mRNA. Plk4 uORFs suppress Plk4 translation and prevent excess protein synthesis. Mice with homozygous knockout of Plk4 uORFs (Plk4 Δu/Δu ) are viable but display dramatically reduced fertility because of a significant depletion of primordial germ cells (PGCs). The remaining PGCs in Plk4 Δu/Δu mice contain extra centrioles and display evidence of increased mitotic errors. PGCs undergo hypertranscription and have substantially more Plk4 mRNA than somatic cells. Reducing Plk4 mRNA levels in mice lacking Plk4 uORFs restored PGC numbers and fully rescued fertility. Together, our data uncover a specific requirement for uORF-dependent control of PLK4 translation in counterbalancing the increased Plk4 transcription in PGCs. Thus, uORF-mediated translational suppression of PLK4 has a critical role in preventing centriole amplification and preserving the genomic integrity of future gametes.
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Affiliation(s)
- Thao P Phan
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Christina A Boatwright
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Chelsea G Drown
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Marnie W Skinner
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
| | - Margaret A Strong
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Philip W Jordan
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
| | - Andrew J Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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23
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Madelaire CB, Klink AC, Israelsen WJ, Hindle AG. Fibroblasts as an experimental model system for the study of comparative physiology. Comp Biochem Physiol B Biochem Mol Biol 2022; 260:110735. [PMID: 35321853 DOI: 10.1016/j.cbpb.2022.110735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 10/18/2022]
Abstract
Mechanistic evaluations of processes that underlie organism-level physiology often require reductionist approaches. Dermal fibroblasts offer one such approach. These cells are easily obtained from minimally invasive skin biopsy, making them appropriate for the study of protected and/or logistically challenging species. Cell culture approaches permit extensive and fine-scale sampling regimes as well as gene manipulation techniques that are not feasible in vivo. Fibroblast isolation and culture protocols are outlined here for primary cells, and the benefits and drawbacks of immortalization are discussed. We show examples of physiological metrics that can be used to characterize primary cells (oxygen consumption, translation, proliferation) and readouts that can be informative in understanding cell-level responses to environmental stress (lactate production, heat shock protein induction). Importantly, fibroblasts may display fidelity to whole animal physiological phenotypes, facilitating their study. Fibroblasts from Antarctic Weddell seals show greater resilience to low temperatures and hypoxia exposure than fibroblasts from humans or rats. Fibroblast oxygen consumption rates are not affected by temperature stress in the heat-tolerant camel, whereas similar temperature exposures depress mitochondrial metabolism in fibroblasts from rhinoceros. Finally, dermal fibroblasts from a hibernator, the meadow jumping mouse, better resist experimental cooling than a fibroblast line from the laboratory mouse, with the hibernator demonstrating a greater maintenance of homeostatic processes such as protein translation. These results exemplify the parallels that can be drawn between fibroblast physiology and expectations in vivo, and provide evidence for the power of fibroblasts as a model system to understand comparative physiology and biomedicine.
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Affiliation(s)
- Carla B Madelaire
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Amy C Klink
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - William J Israelsen
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA; Skroot Laboratory, Inc., Ames, IA, USA
| | - Allyson G Hindle
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA.
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24
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Fort PE, Losiewicz MK, Elghazi L, Kong D, Cras-Méneur C, Fingar DC, Kimball SR, Rajala RVS, Smith AJ, Ali RR, Abcouwer SF, Gardner TW. mTORC1 regulates high levels of protein synthesis in retinal ganglion cells of adult mice. J Biol Chem 2022; 298:101944. [PMID: 35447116 PMCID: PMC9117545 DOI: 10.1016/j.jbc.2022.101944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 02/02/2023] Open
Abstract
Mechanistic target of rapamycin (mTOR) and mTOR complex 1 (mTORC1), linchpins of the nutrient sensing and protein synthesis pathways, are present at relatively high levels in the ganglion cell layer (GCL) and retinal ganglion cells (RGCs) of rodent and human retinas. However, the role of mTORCs in the control of protein synthesis in RGC is unknown. Here, we applied the SUrface SEnsing of Translation (SUnSET) method of nascent protein labeling to localize and quantify protein synthesis in the retinas of adult mice. We also used intravitreal injection of an adeno-associated virus 2 vector encoding Cre recombinase in the eyes of mtor- or rptor-floxed mice to conditionally knockout either both mTORCs or only mTORC1, respectively, in cells within the GCL. A novel vector encoding an inactive Cre mutant (CreΔC) served as control. We found that retinal protein synthesis was highest in the GCL, particularly in RGC. Negation of both complexes or only mTORC1 significantly reduced protein synthesis in RGC. In addition, loss of mTORC1 function caused a significant reduction in the pan-RGC marker, RNA-binding protein with multiple splicing, with little decrease of the total number of cells in the RGC layer, even at 25 weeks after adeno-associated virus-Cre injection. These findings reveal that mTORC1 signaling is necessary for maintaining the high rate of protein synthesis in RGCs of adult rodents, but it may not be essential to maintain RGC viability. These findings may also be relevant to understanding the pathophysiology of RGC disorders, including glaucoma, diabetic retinopathy, and optic neuropathies.
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Affiliation(s)
- Patrice E Fort
- Ophthalmology & Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA; Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mandy K Losiewicz
- Ophthalmology & Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lynda Elghazi
- Ophthalmology & Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Dejuan Kong
- Ophthalmology & Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Corentin Cras-Méneur
- Internal Medicine (MEND Division), University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Diane C Fingar
- Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Scot R Kimball
- Cellular & Molecular Physiology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Raju V S Rajala
- Departments of Ophthalmology and Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Alexander J Smith
- Centre for Gene Therapy and Regenerative Medicine, King's College London, England, United Kingdom
| | - Robin R Ali
- Ophthalmology & Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA; Centre for Gene Therapy and Regenerative Medicine, King's College London, England, United Kingdom
| | - Steven F Abcouwer
- Ophthalmology & Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA.
| | - Thomas W Gardner
- Ophthalmology & Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA; Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Internal Medicine (MEND Division), University of Michigan Medical School, Ann Arbor, Michigan, USA
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25
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Song T, Yang Y, Zhou P, Ran J, Zhang L, Wu X, Xie W, Zhong T, Liu H, Liu M, Li D, Zhao H, Zhou J. ENKD1 promotes CP110 removal through competing with CEP97 to initiate ciliogenesis. EMBO Rep 2022; 23:e54090. [PMID: 35301795 PMCID: PMC9066061 DOI: 10.15252/embr.202154090] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/23/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
Despite the importance of cilia in cell signaling and motility, the molecular mechanisms regulating cilium formation remain incompletely understood. Herein, we characterize enkurin domain-containing protein 1 (ENKD1) as a novel centrosomal protein that mediates the removal of centriolar coiled-coil protein 110 (CP110) from the mother centriole to promote ciliogenesis. We show that Enkd1 knockout mice possess ciliogenesis defects in multiple organs. Super-resolution microscopy reveals that ENKD1 is a stable component of the centrosome throughout the ciliogenesis process. Simultaneous knockdown of ENKD1 and CP110 significantly reverses the ciliogenesis defects induced by ENKD1 depletion. Protein interaction analysis shows that ENKD1 competes with centrosomal protein 97 (CEP97) in binding to CP110. Depletion of ENKD1 enhances the CP110-CEP97 interaction and detains CP110 at the mother centriole. These findings thus identify ENKD1 as a centrosomal protein and uncover a novel mechanism controlling CP110 removal from the mother centriole for the initiation of ciliogenesis.
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Affiliation(s)
- Ting Song
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life Sciences, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Shandong Normal University, Jinan, China
| | - Yunfan Yang
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Peng Zhou
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life Sciences, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Shandong Normal University, Jinan, China
| | - Jie Ran
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life Sciences, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Shandong Normal University, Jinan, China
| | - Liang Zhang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life Sciences, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Shandong Normal University, Jinan, China
| | - Xiaofan Wu
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecology, Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wei Xie
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life Sciences, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Shandong Normal University, Jinan, China
| | - Tao Zhong
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life Sciences, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Shandong Normal University, Jinan, China
| | - Hongbin Liu
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Min Liu
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life Sciences, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Shandong Normal University, Jinan, China
| | - Dengwen Li
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecology, Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Huijie Zhao
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life Sciences, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Shandong Normal University, Jinan, China
| | - Jun Zhou
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life Sciences, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Shandong Normal University, Jinan, China.,State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecology, Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
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26
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Chen T, Zhao Y, Zhao X, Li S, Cao J, Guo J, Bu W, Zhao H, Du J, Cao Y, Fan Y. Self-Organization of Tissue Growth by Interfacial Mechanical Interactions in Multilayered Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104301. [PMID: 35138041 PMCID: PMC9069393 DOI: 10.1002/advs.202104301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Morphogenesis is a spatially and temporally regulated process involved in various physiological and pathological transformations. In addition to the associated biochemical factors, the physical regulation of morphogenesis has attracted increasing attention. However, the driving force of morphogenesis initiation remains elusive. Here, it is shown that during the growth of multilayered tissues, a morphogenetic process can be self-organized by the progression of compression gradient stemmed from the interfacial mechanical interactions between layers. In tissues with low fluidity, the compression gradient is progressively strengthened during growth and induces stratification by triggering symmetric-to-asymmetric cell division reorientation at the critical tissue size. In tissues with high fluidity, compression gradient is dynamic and induces cell rearrangement leading to 2D in-plane morphogenesis instead of 3D deformation. Morphogenesis can be tuned by manipulating tissue fluidity, cell adhesion forces, and mechanical properties to influence the progression of compression gradient during the development of cultured cell sheets and chicken embryos. Together, the dynamics of compression gradient arising from interfacial mechanical interaction provides a conserved mechanism underlying morphogenesis initiation and size control during tissue growth.
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Affiliation(s)
- Tailin Chen
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of EducationBeijing Advanced Innovation Center for Biomedical EngineeringSchool of Biological Science and Medical EngineeringSchool of Engineering MedicineBeihang UniversityBeijing100083China
| | - Yan Zhao
- State Key Laboratory of Advanced Design and Manufacturing for Vehicle BodyCollege of Mechanical and Vehicle EngineeringHunan UniversityChangsha410082China
| | - Xinbin Zhao
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of EducationBeijing Advanced Innovation Center for Biomedical EngineeringSchool of Biological Science and Medical EngineeringSchool of Engineering MedicineBeihang UniversityBeijing100083China
| | - Shukai Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of EducationBeijing Advanced Innovation Center for Biomedical EngineeringSchool of Biological Science and Medical EngineeringSchool of Engineering MedicineBeihang UniversityBeijing100083China
| | - Jialing Cao
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of EducationBeijing Advanced Innovation Center for Biomedical EngineeringSchool of Biological Science and Medical EngineeringSchool of Engineering MedicineBeihang UniversityBeijing100083China
| | - Jun Guo
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of EducationBeijing Advanced Innovation Center for Biomedical EngineeringSchool of Biological Science and Medical EngineeringSchool of Engineering MedicineBeihang UniversityBeijing100083China
| | - Wanjuan Bu
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of EducationBeijing Advanced Innovation Center for Biomedical EngineeringSchool of Biological Science and Medical EngineeringSchool of Engineering MedicineBeihang UniversityBeijing100083China
| | - Hucheng Zhao
- Institute of Biomechanics and Medical EngineeringDepartment of Engineering MechanicsSchool of Aerospace EngineeringTsinghua UniversityBeijing100084China
| | - Jing Du
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of EducationBeijing Advanced Innovation Center for Biomedical EngineeringSchool of Biological Science and Medical EngineeringSchool of Engineering MedicineBeihang UniversityBeijing100083China
| | - Yanping Cao
- Institute of Biomechanics and Medical EngineeringDepartment of Engineering MechanicsSchool of Aerospace EngineeringTsinghua UniversityBeijing100084China
| | - Yubo Fan
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of EducationBeijing Advanced Innovation Center for Biomedical EngineeringSchool of Biological Science and Medical EngineeringSchool of Engineering MedicineBeihang UniversityBeijing100083China
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27
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Riedmayr LM, Hinrichsmeyer KS, Karguth N, Böhm S, Splith V, Michalakis S, Becirovic E. dCas9-VPR-mediated transcriptional activation of functionally equivalent genes for gene therapy. Nat Protoc 2022; 17:781-818. [PMID: 35132255 DOI: 10.1038/s41596-021-00666-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 11/18/2021] [Indexed: 12/19/2022]
Abstract
Many disease-causing genes possess functionally equivalent counterparts, which are often expressed in distinct cell types. An attractive gene therapy approach for inherited disorders caused by mutations in such genes is to transcriptionally activate the appropriate counterpart(s) to compensate for the missing gene function. This approach offers key advantages over conventional gene therapies because it is mutation- and gene size-independent. Here, we describe a protocol for the design, execution and evaluation of such gene therapies using dCas9-VPR. We offer guidelines on how to identify functionally equivalent genes, design and clone single guide RNAs and evaluate transcriptional activation in vitro. Moreover, focusing on inherited retinal diseases, we provide a detailed protocol on how to apply this strategy in mice using dual recombinant adeno-associated virus vectors and how to evaluate its functionality and off-target effects in the target tissue. This strategy is in principle applicable to all organisms that possess functionally equivalent genes suitable for transcriptional activation and addresses pivotal unmet needs in gene therapy with high translational potential. The protocol can be completed in 15-20 weeks.
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Affiliation(s)
- Lisa M Riedmayr
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Klara S Hinrichsmeyer
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nina Karguth
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sybille Böhm
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Victoria Splith
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stylianos Michalakis
- Department of Ophthalmology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Elvir Becirovic
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany.
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28
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Bryant JD, Lei Y, VanPortfliet JJ, Winters AD, West AP. Assessing Mitochondrial DNA Release into the Cytosol and Subsequent Activation of Innate Immune-related Pathways in Mammalian Cells. Curr Protoc 2022; 2:e372. [PMID: 35175686 PMCID: PMC8986093 DOI: 10.1002/cpz1.372] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Mitochondria have emerged as key drivers of mammalian innate immune responses, functioning as signaling hubs to trigger inflammation and orchestrating metabolic switches required for phagocyte activation. Mitochondria also contain damage-associated molecular patterns (DAMPs), molecules that share similarity with pathogen-associated molecular patterns (PAMPs) and can engage innate immune sensors to drive inflammation. The aberrant release of mitochondrial DAMPs during cellular stress and injury is an increasingly recognized trigger of inflammatory responses in human diseases. Mitochondrial DNA (mtDNA) is a particularly potent DAMP that engages multiple innate immune sensors, although mounting evidence suggests that cytosolic mtDNA is primarily detected via the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway. cGAS and STING are widely expressed in mammalian cells and serve as key regulators of type I interferon and cytokine expression in both infectious and inflammatory diseases. Despite growing roles for the mtDNA-cGAS-STING axis in human disease, assays to quantify mtDNA release into the cytosol and approaches to link mtDNA to cGAS-STING signaling are not standardized, which increases the possibility for experimental artifacts and misinterpretation of data. Here, we present a series of protocols for assaying the release of mtDNA into the cytosol and subsequent activation of innate immune signaling in mammalian cells. We highlight genetic and pharmacological approaches to induce and inhibit mtDNA release from mitochondria. We also describe immunofluorescence microscopy and cellular fractionation assays to visualize morphological changes in mtDNA and quantify mtDNA accumulation in the cytosol. Finally, we include protocols to examine mtDNA-dependent cGAS-STING activation by RT-qPCR and western blotting. These methods can be performed with standard laboratory equipment and are highly adaptable to a wide range of mammalian cell types. They will permit researchers working across the spectrum of biological and biomedical sciences to accurately and reproducibly measure cytosolic mtDNA release and resulting innate immune responses. © 2022 Wiley Periodicals LLC. Basic Protocol 1: siRNA-mediated knockdown of TFAM to induce mtDNA instability, cytosolic release, and activation of the cGAS-STING pathway Alternate Protocol: Pharmacological induction of mtDNA release and cGAS-STING activation using ABT-737 and Q-VD-OPH Basic Protocol 2: Isolation and quantitation of DNA from cytosolic, mitochondrial, and nuclear fractions Basic Protocol 3: Pharmacological inhibition of mtDNA replication and release.
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Affiliation(s)
- Joshua D. Bryant
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University, Bryan, TX,These authors contributed equally
| | - Yuanjiu Lei
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University, Bryan, TX,These authors contributed equally
| | - Jordyn J. VanPortfliet
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University, Bryan, TX
| | - Ashley D. Winters
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University, Bryan, TX
| | - A. Phillip West
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University, Bryan, TX,Corresponding author:
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Nollet M, Bachelier R, Joshkon A, Traboulsi W, Mahieux A, Moyon A, Muller A, Somasundaram I, Simoncini S, Peiretti F, Leroyer AS, Guillet B, Granel B, Dignat-George F, Bardin N, Foucault-Bertaud A, Blot-Chabaud M. Multiple variants of soluble CD146 are involved in Systemic Sclerosis: identification of a novel pro-fibrotic factor. Arthritis Rheumatol 2022; 74:1027-1038. [PMID: 35001552 DOI: 10.1002/art.42063] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/19/2021] [Accepted: 01/04/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Systemic sclerosis (SSc) is an autoimmune disorder characterized by excessive fibrosis, immune dysfunction and vascular damages, in which expression of many growth factors is deregulated. CD146 was recently described as a major actor in SSc. As CD146 also exists as a circulating soluble form (sCD146) acting as a growth factor in numerous angiogenic- and inflammatory-related pathologies, we sought to identify the mechanisms underlying the generation of sCD146 and characterized the regulation and functions of the different identified variants in SSc. METHODS To this end, we performed in vitro experiments, including RNA-seq and antibody arrays, and in vivo experiments using animal models of SSc induced by bleomycin and of hindlimb ischemia. RESULTS Multiple forms of sCD146, generated by both shedding and alternative splicing of the primary transcript, were discovered. The shed form of sCD146 was generated from the cleavage of both long and short membrane isoforms of membrane CD146 through Adam10 and Tace metalloproteinases, respectively. In addition, two novel sCD146 splice variants, I5-13-sCD146 and I10-sCD146 were identified. Of interest, I5-13-sCD146 was significantly increased in sera of SSc patients, in particular in patients with pulmonary fibrosis, whereas I10-sCD146 was decreased. Further experiments revealed that shed sCD146 and I10-sCD146 displayed pro-angiogenic activity through FAK and PKCε signalling pathways, respectively, whereas I5-13-sCD146 displayed pro-fibrotic effects through wint1/β-catenin/wisp1 pathway. CONCLUSION Variants of sCD146, and in particular the novel I5-13-sCD146 splice variant, could thus constitute novel biomarkers and/or molecular targets for the diagnosis and treatment of SSc, but also of other angiogenesis- or fibrosis-related pathologies.
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Affiliation(s)
- Marie Nollet
- Aix-Marseille Univ, INSERM 1263, INRAE 1260, C2VN, Marseille, France
| | - Richard Bachelier
- Aix-Marseille Univ, INSERM 1263, INRAE 1260, C2VN, Marseille, France
| | - Ahmad Joshkon
- Aix-Marseille Univ, INSERM 1263, INRAE 1260, C2VN, Marseille, France
| | - Waël Traboulsi
- Aix-Marseille Univ, INSERM 1263, INRAE 1260, C2VN, Marseille, France
| | - Amandine Mahieux
- Aix-Marseille Univ, INSERM 1263, INRAE 1260, C2VN, Marseille, France
| | - Anais Moyon
- Aix-Marseille Univ, INSERM 1263, INRAE 1260, C2VN, Marseille, France.,CERIMED, Aix-Marseille University, Marseille, France
| | - Alexandre Muller
- Aix-Marseille Univ, INSERM 1263, INRAE 1260, C2VN, Marseille, France
| | - Indumathi Somasundaram
- Department of Stem Cell and Regenerative Medicine, D.Y. Patil University, Kolhapur, India
| | | | - Franck Peiretti
- Aix-Marseille Univ, INSERM 1263, INRAE 1260, C2VN, Marseille, France
| | - Aurélie S Leroyer
- Aix-Marseille Univ, INSERM 1263, INRAE 1260, C2VN, Marseille, France
| | - Benjamin Guillet
- Aix-Marseille Univ, INSERM 1263, INRAE 1260, C2VN, Marseille, France.,CERIMED, Aix-Marseille University, Marseille, France
| | - Brigitte Granel
- Aix-Marseille Univ, INSERM 1263, INRAE 1260, C2VN, Marseille, France.,Internal Medicine Department, AP-HM, Marseille, France
| | | | - Nathalie Bardin
- Aix-Marseille Univ, INSERM 1263, INRAE 1260, C2VN, Marseille, France
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30
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Discovery of G2019S-Selective Leucine Rich Repeat Protein Kinase 2 inhibitors with in vivo efficacy. Eur J Med Chem 2021; 229:114080. [PMID: 34992038 DOI: 10.1016/j.ejmech.2021.114080] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 11/20/2022]
Abstract
Mutations in the Leucine Rich Repeat Protein Kinase 2 gene (LRRK2) are the most common genetic causes of Parkinson's Disease (PD). The G2019S mutation is the most common inherited LRRK2 mutation, occurs in the kinase domain, and results in increased kinase activity. We report the discovery and development of compound 38, an indazole-based, G2019S-selective (>2000-fold vs. WT) LRRK2 inhibitor capable of entering rodent brain (Kp = 0.5) and selectively inhibiting G2019S-LRRK2. The compounds disclosed herein present a starting point for further development of brain penetrant G2019S selective inhibitors that hopefully reduce lung phenotype side-effects and pave the way to providing a precision medicine for people with PD who carry the G2019S mutation.
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31
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Al-Sayegh M, Ali H, Jamal MH, ElGindi M, Chanyong T, Al-Awadi K, Abu-Farha M. Mouse Embryonic Fibroblast Adipogenic Potential: A Comprehensive Transcriptome Analysis. Adipocyte 2021; 10:1-20. [PMID: 33345692 PMCID: PMC7757854 DOI: 10.1080/21623945.2020.1859789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Our understanding of adipose tissue has progressed from an inert tissue for energy storage to be one of the largest endocrine organs regulating metabolic homoeostasis through its ability to synthesize and release various adipokines that regulate a myriad of pathways. The field of adipose tissue biology is growing due to this association with various chronic metabolic diseases. An important process in the regulation of adipose tissue biology is adipogenesis, which is the formation of new adipocytes. Investigating adipogenesis in vitro is currently a focus for identifying factors that might be utilized in clinically. A powerful tool for such work is high-throughput sequencing which can rapidly identify changes at gene expression level. Various cell models exist for studying adipogenesis and has been used in high-throughput studies, yet little is known about transcriptome profile that underlies adipogenesis in mouse embryonic fibroblasts. This study utilizes RNA-sequencing and computational analysis with DESeq2, gene ontology, protein–protein networks, and robust rank analysis to understand adipogenesis in mouse embryonic fibroblasts in-depth. Our analyses confirmed the requirement of mitotic clonal expansion prior to adipogenesis in this cell model and highlight the role of Cebpa and Cebpb in regulating adipogenesis through interactions of large numbers of genes.
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Affiliation(s)
- Mohamed Al-Sayegh
- New York University Abu Dhabi, Division of Biology, Abu Dhabi, United Arab Emirates
| | - Hamad Ali
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Health Sciences Center (HSC), Kuwait University, Kuwait City, State of Kuwait
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Kuwait City, State of Kuwait
| | - Mohammad H Jamal
- Department of Surgery, Faculty of Medicine, Health Sciences Center (HSC), Kuwait University, Kuwait City, State of Kuwait
| | - Mei ElGindi
- New York University Abu Dhabi, Division of Biology, Abu Dhabi, United Arab Emirates
| | - Tina Chanyong
- New York University Abu Dhabi, Division of Biology, Abu Dhabi, United Arab Emirates
| | - Khulood Al-Awadi
- New York University Abu Dhabi, Design Studio, Abu Dhabi, United Arab Emirates
| | - Mohamed Abu-Farha
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Kuwait City, State of Kuwait
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32
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The deubiquitinase USP16 functions as an oncogenic factor in K-RAS-driven lung tumorigenesis. Oncogene 2021; 40:5482-5494. [PMID: 34294846 DOI: 10.1038/s41388-021-01964-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 02/07/2023]
Abstract
K-RAS mutation and molecular alterations of its surrogates function essentially in lung tumorigenesis and malignant progression. However, it remains elusive how tumor-promoting and deleterious events downstream of K-RAS signaling are coordinated in lung tumorigenesis. Here, we show that USP16, a deubiquitinase involved in various biological processes, functions as a promoter for the development of K-RAS-driven lung tumor. Usp16 deletion significantly attenuates K-rasG12D-mutation-induced lung tumorigenesis in mice. USP16 upregulation upon RAS activation averts reactive oxygen species (ROS)-induced p38 activation that would otherwise detrimentally influence the survival and proliferation of tumor cells. In addition, USP16 interacts with and deubiquitinates JAK1, and thereby promoting lung tumor growth by augmenting JAK1 signaling. Therefore, our results reveal that USP16 functions critically in the K-RAS-driven lung tumorigenesis through modulating the strength of p38 and JAK1 signaling.
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33
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Yang Z, Xu G, Wang B, Liu Y, Zhang L, Jing T, Tang M, Xu X, Jiao K, Xiang L, Fu Y, Tang D, Zhang X, Jin W, Zhuang G, Zhao X, Liu Y. USP12 downregulation orchestrates a protumourigenic microenvironment and enhances lung tumour resistance to PD-1 blockade. Nat Commun 2021; 12:4852. [PMID: 34381028 PMCID: PMC8357983 DOI: 10.1038/s41467-021-25032-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 07/19/2021] [Indexed: 12/25/2022] Open
Abstract
Oncogenic activation of KRAS and its surrogates is essential for tumour cell proliferation and survival, as well as for the development of protumourigenic microenvironments. Here, we show that the deubiquitinase USP12 is commonly downregulated in the KrasG12D-driven mouse lung tumour and human non-small cell lung cancer owing to the activation of AKT-mTOR signalling. Downregulation of USP12 promotes lung tumour growth and fosters an immunosuppressive microenvironment with increased macrophage recruitment, hypervascularization, and reduced T cell activation. Mechanistically, USP12 downregulation creates a tumour-promoting secretome resulting from insufficient PPM1B deubiquitination that causes NF-κB hyperactivation in tumour cells. Furthermore, USP12 inhibition desensitizes mouse lung tumour cells to anti-PD-1 immunotherapy. Thus, our findings propose a critical component downstream of the oncogenic signalling pathways in the modulation of tumour-immune cell interactions and tumour response to immune checkpoint blockade therapy. The cancer cell-extrinsic roles of deubiquitinases are unclear. Here the authors show that deubiquitinase USP12 downregulation contributes to development of an immune-suppressive tumour microenvironment in KRAS-driven lung cancers and mechanistically this is through the insufficient deubiquitination of the NF-κB inhibitor, PPM1B.
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Affiliation(s)
- Zhaojuan Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guiqin Xu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Boshi Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tiantian Jing
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Tang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoli Xu
- Shanghai Jiao Tong University School of Biomedical Engineering, Shanghai, China
| | - Kun Jiao
- Shanghai Jiao Tong University School of Biomedical Engineering, Shanghai, China
| | - Lvzhu Xiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yujie Fu
- Department of Thoracic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Daoqiang Tang
- Department of Pathology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoren Zhang
- Affiliated Cancer Hospital and Institute, Guangzhou Medical University, Guangzhou, China
| | - Weilin Jin
- Institute of Cancer Neuroscience, Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Guanglei Zhuang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaojing Zhao
- Department of Thoracic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Yongzhong Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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34
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Tooley AS, Kazyken D, Bodur C, Gonzalez IE, Fingar DC. The innate immune kinase TBK1 directly increases mTORC2 activity and downstream signaling to Akt. J Biol Chem 2021; 297:100942. [PMID: 34245780 PMCID: PMC8342794 DOI: 10.1016/j.jbc.2021.100942] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/21/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
TBK1 responds to microbes to initiate cellular responses critical for host innate immune defense. We found previously that TBK1 phosphorylates mTOR (mechanistic target of rapamycin) on S2159 to increase mTOR complex 1 (mTORC1) signaling in response to the growth factor EGF and the viral dsRNA mimetic poly(I:C). mTORC1 and the less well studied mTORC2 respond to diverse cues to control cellular metabolism, proliferation, and survival. Although TBK1 has been linked to Akt phosphorylation, a direct relationship between TBK1 and mTORC2, an Akt kinase, has not been described. By studying MEFs lacking TBK1, as well as MEFs, macrophages, and mice bearing an Mtor S2159A knock-in allele (MtorA/A) using in vitro kinase assays and cell-based approaches, we demonstrate here that TBK1 activates mTOR complex 2 (mTORC2) directly to increase Akt phosphorylation. We find that TBK1 and mTOR S2159 phosphorylation promotes mTOR-dependent phosphorylation of Akt in response to several growth factors and poly(I:C). Mechanistically, TBK1 coimmunoprecipitates with mTORC2 and phosphorylates mTOR S2159 within mTORC2 in cells. Kinase assays demonstrate that TBK1 and mTOR S2159 phosphorylation increase mTORC2 intrinsic catalytic activity. Growth factors failed to activate TBK1 or increase mTOR S2159 phosphorylation in MEFs. Thus, basal TBK1 activity cooperates with growth factors in parallel to increase mTORC2 (and mTORC1) signaling. Collectively, these results reveal cross talk between TBK1 and mTOR, key regulatory nodes within two major signaling networks. As TBK1 and mTOR contribute to tumorigenesis and metabolic disorders, these kinases may work together in a direct manner in a variety of physiological and pathological settings.
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Affiliation(s)
- Aaron Seth Tooley
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Dubek Kazyken
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Cagri Bodur
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ian E Gonzalez
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Diane C Fingar
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA.
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35
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Fernández-Medarde A, Fuentes-Mateos R, García-Navas R, Juan AOS, Sánchez-López JM, Fernández-Medarde A, Santos E. Anthraquinones as Inhibitors of SOS RAS-GEF Activity. Biomolecules 2021; 11:biom11081128. [PMID: 34439794 PMCID: PMC8392861 DOI: 10.3390/biom11081128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 12/29/2022] Open
Abstract
Recent breakthroughs have reignited interest in RAS GEFs as direct therapeutic targets. To search for new inhibitors of SOS GEF activity, a repository of known/approved compounds (NIH-NACTS) and a library of new marine compounds (Biomar Microbial Technologies) were screened by means of in vitro RAS-GEF assays using purified, bacterially expressed SOS and RAS constructs. Interestingly, all inhibitors identified in our screenings (two per library) shared related chemical structures belonging to the anthraquinone family of compounds. All our anthraquinone SOS inhibitors were active against the three canonical RAS isoforms when tested in our SOS GEF assays, inhibited RAS activation in mouse embryonic fibroblasts, and were also able to inhibit the growth of different cancer cell lines harboring WT or mutant RAS genes. In contrast to the commercially available anthraquinone inhibitors, our new marine anthraquinone inhibitors did not show in vivo cardiotoxicity, thus providing a lead for future discovery of stronger, clinically useful anthraquinone SOS GEF blockers.
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Affiliation(s)
- Alberto Fernández-Medarde
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC)-Universidad de Salamanca and CIBERONC, 37007 Salamanca, Spain; (R.F.-M.); (R.G.-N.); (A.O.-S.J.)
- Correspondence: (A.F.-M.); (E.S.)
| | - Rocío Fuentes-Mateos
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC)-Universidad de Salamanca and CIBERONC, 37007 Salamanca, Spain; (R.F.-M.); (R.G.-N.); (A.O.-S.J.)
| | - Rósula García-Navas
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC)-Universidad de Salamanca and CIBERONC, 37007 Salamanca, Spain; (R.F.-M.); (R.G.-N.); (A.O.-S.J.)
| | - Andrea Olarte-San Juan
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC)-Universidad de Salamanca and CIBERONC, 37007 Salamanca, Spain; (R.F.-M.); (R.G.-N.); (A.O.-S.J.)
| | - José María Sánchez-López
- Biomar Microbial Technologies, Parque Tecnológico de León, Parcela M-10.4, Armunia, 24009 León, Spain; (J.M.S.-L.); (A.F.-M.)
| | - Antonio Fernández-Medarde
- Biomar Microbial Technologies, Parque Tecnológico de León, Parcela M-10.4, Armunia, 24009 León, Spain; (J.M.S.-L.); (A.F.-M.)
| | - Eugenio Santos
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC)-Universidad de Salamanca and CIBERONC, 37007 Salamanca, Spain; (R.F.-M.); (R.G.-N.); (A.O.-S.J.)
- Correspondence: (A.F.-M.); (E.S.)
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36
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Ramachandran A, Mehić M, Wasim L, Malinova D, Gori I, Blaszczyk BK, Carvalho DM, Shore EM, Jones C, Hyvönen M, Tolar P, Hill CS. Pathogenic ACVR1 R206H activation by Activin A-induced receptor clustering and autophosphorylation. EMBO J 2021; 40:e106317. [PMID: 34003511 PMCID: PMC8280795 DOI: 10.15252/embj.2020106317] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 11/23/2022] Open
Abstract
Fibrodysplasia ossificans progressiva (FOP) and diffuse intrinsic pontine glioma (DIPG) are debilitating diseases that share causal mutations in ACVR1, a TGF-β family type I receptor. ACVR1R206H is a frequent mutation in both diseases. Pathogenic signaling via the SMAD1/5 pathway is mediated by Activin A, but how the mutation triggers aberrant signaling is not known. We show that ACVR1 is essential for Activin A-mediated SMAD1/5 phosphorylation and is activated by two distinct mechanisms. Wild-type ACVR1 is activated by the Activin type I receptors, ACVR1B/C. In contrast, ACVR1R206H activation does not require upstream kinases, but is predominantly activated via Activin A-dependent receptor clustering, which induces its auto-activation. We use optogenetics and live-imaging approaches to demonstrate Activin A-induced receptor clustering and show it requires the type II receptors ACVR2A/B. Our data provide molecular mechanistic insight into the pathogenesis of FOP and DIPG by linking the causal activating genetic mutation to disrupted signaling.
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Affiliation(s)
- Anassuya Ramachandran
- Developmental Signalling LaboratoryThe Francis Crick InstituteLondonUK
- Present address:
Department of Molecular Medicine and PathologyUniversity of AucklandAucklandNew Zealand
| | - Merima Mehić
- Developmental Signalling LaboratoryThe Francis Crick InstituteLondonUK
| | - Laabiah Wasim
- Immune Receptor Activation LaboratoryThe Francis Crick InstituteLondonUK
| | | | - Ilaria Gori
- Developmental Signalling LaboratoryThe Francis Crick InstituteLondonUK
| | | | - Diana M Carvalho
- Division of Molecular PathologyThe Institute of Cancer ResearchSuttonUK
| | - Eileen M Shore
- Departments of Orthopaedic Surgery and GeneticsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Chris Jones
- Division of Molecular PathologyThe Institute of Cancer ResearchSuttonUK
| | - Marko Hyvönen
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Pavel Tolar
- Immune Receptor Activation LaboratoryThe Francis Crick InstituteLondonUK
- Present address:
Division of Infection and ImmunityInstitute of Immunity and TransplantationUniversity CollegeLondonUK
| | - Caroline S Hill
- Developmental Signalling LaboratoryThe Francis Crick InstituteLondonUK
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37
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Ferracchiato S, Di-Iacovo N, Scopetti D, Piobbico D, Castelli M, Pieroni S, Gargaro M, Manni G, Brancorsini S, Della-Fazia MA, Servillo G. Hops/Tmub1 Heterozygous Mouse Shows Haploinsufficiency Effect in Influencing p53-Mediated Apoptosis. Int J Mol Sci 2021; 22:ijms22137186. [PMID: 34281239 PMCID: PMC8269437 DOI: 10.3390/ijms22137186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 01/10/2023] Open
Abstract
HOPS is a ubiquitin-like protein implicated in many aspects of cellular function including the regulation of mitotic activity, proliferation, and cellular stress responses. In this study, we focused on the complex relationship between HOPS and the tumor suppressor p53, investigating both transcriptional and non-transcriptional p53 responses. Here, we demonstrated that Hops heterozygous mice and mouse embryonic fibroblasts exhibit an impaired DNA-damage response to etoposide-induced double-strand breaks when compared to wild-type genes. Specifically, alterations in HOPS levels caused significant defects in the induction of apoptosis, including a reduction in p53 protein level and percentage of apoptotic cells. We also analyzed the effect of reduced HOPS levels on the DNA-damage response by examining the transcript profiles of p53-dependent genes, showing a suggestive deregulation of the mRNA levels for a number of p53-dependent genes. Taken together, these results show an interesting haploinsufficiency effect mediated by Hops monoallelic deletion, which appears to be enough to destabilize the p53 protein and its functions. Finally, these data indicate a novel role for Hops as a tumor-suppressor gene in DNA damage repair in mammalian cells.
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38
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Genetic modifiers regulating DNA replication and double-strand break repair are associated with differences in mammary tumors in mouse models of Li-Fraumeni syndrome. Oncogene 2021; 40:5026-5037. [PMID: 34183771 PMCID: PMC8349885 DOI: 10.1038/s41388-021-01892-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/16/2021] [Accepted: 06/04/2021] [Indexed: 01/04/2023]
Abstract
Breast cancer is the most common tumor among women with inherited variants in the TP53 tumor suppressor, but onset varies widely suggesting interactions with genetic or environmental factors. Rodent models haploinsufficent for Trp53 also develop a wide variety of malignancies associated with Li-Fraumeni Syndrome, but BALB/c mice are uniquely susceptible to mammary tumors and is genetically linked to the Suprmam1 locus on chromosome 7. To define mechanisms that interact with deficiencies in p53 to alter susceptibility to mammary tumors, we fine-mapped the Suprmam1 locus in females from an N2 backcross of BALB/cMed and C57BL/6J mice. A major modifier was localized within a 10 cM interval on chromosome 7. The effect of the locus on DNA damage responses was examined in the parental strains and mice that are congenic for C57BL/6J alleles on the BALB/cMed background (SM1-Trp53+/−). The mammary epithelium of C57BL/6J-Trp53+/− females exhibited little radiation-induced apoptosis compared to BALB/cMed-Trp53+/− and SM1-Trp53+/− females indicating that the Suprmam1B6/B6 alleles could not rescue repair of radiation-induced DNA double-strand breaks mostly relying on non-homologous end joining. In contrast, the Suprmam1B6/B6 alleles in SM1-Trp53+/− mice were sufficient to confer the C57BL/6J-Trp53+/− phenotypes in homology-directed repair and replication fork progression. The Suprmam1B6/B6 alleles in SM1-Trp53+/− mice appear to act in trans to regulate a panel of DNA repair and replication genes which lie outside the locus.
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Regulation of AMPK Activity by CRBN Is Independent of the Thalidomide-CRL4 CRBN Protein Degradation Axis. Pharmaceuticals (Basel) 2021; 14:ph14060512. [PMID: 34073624 PMCID: PMC8228114 DOI: 10.3390/ph14060512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
Cereblon (CRBN), a primary target of immune-modulatory imide drugs (IMiDs), functions as a substrate receptor in the CUL4-RBX1-DDB1-CRBN (known as CRL4CRBN) E3 ubiquitin ligase complex. Binding of IMiDs to CRBN redirects the CRL4CRBN E3 ubiquitin ligase to recruit or displace its substrates. Interaction between CRBN and the AMPK α subunit leads to CRL4CRBN-dependent degradation of the γ subunit and inhibits AMPK activity. However, the effect of thalidomide on the function of CRBN as a negative regulator of AMPK through interaction with the α subunit remains unclear. Here, we show that thalidomide does not affect AMPK activation or the binding affinity between CRBN and the AMPK α subunit. Thalidomide had no effect on AMPK activity independent of CRBN expression. The N-terminal region and C-terminal tail of CRBN, which is distinct from the IMiD binding site, were critical for interaction with the AMPK α subunit. The present results suggest that CRL4CRBN negatively regulates AMPK through a pathway independent from the CRBN-IMiD binding region.
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Putker M, Wong DCS, Seinkmane E, Rzechorzek NM, Zeng A, Hoyle NP, Chesham JE, Edwards MD, Feeney KA, Fischer R, Peschel N, Chen K, Vanden Oever M, Edgar RS, Selby CP, Sancar A, O’Neill JS. CRYPTOCHROMES confer robustness, not rhythmicity, to circadian timekeeping. EMBO J 2021; 40:e106745. [PMID: 33491228 PMCID: PMC8013833 DOI: 10.15252/embj.2020106745] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/08/2020] [Accepted: 12/18/2020] [Indexed: 12/22/2022] Open
Abstract
Circadian rhythms are a pervasive property of mammalian cells, tissues and behaviour, ensuring physiological adaptation to solar time. Models of cellular timekeeping revolve around transcriptional feedback repression, whereby CLOCK and BMAL1 activate the expression of PERIOD (PER) and CRYPTOCHROME (CRY), which in turn repress CLOCK/BMAL1 activity. CRY proteins are therefore considered essential components of the cellular clock mechanism, supported by behavioural arrhythmicity of CRY-deficient (CKO) mice under constant conditions. Challenging this interpretation, we find locomotor rhythms in adult CKO mice under specific environmental conditions and circadian rhythms in cellular PER2 levels when CRY is absent. CRY-less oscillations are variable in their expression and have shorter periods than wild-type controls. Importantly, we find classic circadian hallmarks such as temperature compensation and period determination by CK1δ/ε activity to be maintained. In the absence of CRY-mediated feedback repression and rhythmic Per2 transcription, PER2 protein rhythms are sustained for several cycles, accompanied by circadian variation in protein stability. We suggest that, whereas circadian transcriptional feedback imparts robustness and functionality onto biological clocks, the core timekeeping mechanism is post-translational.
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Affiliation(s)
| | | | | | | | - Aiwei Zeng
- MRC Laboratory of Molecular BiologyCambridgeUK
| | | | | | - Mathew D Edwards
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
UCL Sainsbury Wellcome Centre for Neural Circuits and BehaviourLondonUK
| | | | | | | | - Ko‐Fan Chen
- Institute of NeurologyUniversity College LondonLondonUK
- Present address:
Department of Genetics and Genome BiologyUniversity of LeicesterLeicesterUK
| | | | | | - Christopher P Selby
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - Aziz Sancar
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNCUSA
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Targeting the 5' untranslated region of SMN2 as a therapeutic strategy for spinal muscular atrophy. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:731-742. [PMID: 33575118 PMCID: PMC7851419 DOI: 10.1016/j.omtn.2020.12.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/30/2020] [Indexed: 11/21/2022]
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disorder caused by mutations in the survival motor neuron 1 (SMN1) gene. All patients have at least one copy of a paralog, SMN2, but a C-to-T transition in this gene results in exon 7 skipping in a majority of transcripts. Approved treatment for SMA involves promoting exon 7 inclusion in the SMN2 transcript or increasing the amount of full-length SMN by gene replacement with a viral vector. Increasing the pool of SMN2 transcripts and increasing their translational efficiency can be used to enhance splice correction. We sought to determine whether the 5' untranslated region (5' UTR) of SMN2 contains a repressive feature that can be targeted to increase SMN levels. We found that antisense oligonucleotides (ASOs) complementary to the 5' end of SMN2 increase SMN mRNA and protein levels and that this effect is due to inhibition of SMN2 mRNA decay. Moreover, use of the 5' UTR ASO in combination with a splice-switching oligonucleotide (SSO) increases SMN levels above those attained with the SSO alone. Our results add to the current understanding of SMN regulation and point toward a new therapeutic target for SMA.
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Mellis AT, Roeper J, Misko AL, Kohl J, Schwarz G. Sulfite Alters the Mitochondrial Network in Molybdenum Cofactor Deficiency. Front Genet 2021; 11:594828. [PMID: 33488670 PMCID: PMC7817995 DOI: 10.3389/fgene.2020.594828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/30/2020] [Indexed: 11/25/2022] Open
Abstract
Molybdenum cofactor deficiency (MoCD) is an autosomal recessive disorder belonging to the large family of inborn errors in metabolism. Patients typically present with encephalopathy and seizures early after birth and develop severe neurodegeneration within the first few weeks of life. The main pathomechanism underlying MoCD is the loss of function of sulfite oxidase (SO), a molybdenum cofactor (Moco) dependent enzyme located in mitochondrial intermembrane space. SO catalyzes the oxidation of sulfite (SO32–) to sulfate (SO42–) in the terminal reaction of cysteine catabolism, and in the absence of its activity, sulfurous compounds such as SO32–, S-sulfocysteine, and thiosulfate accumulate in patients. Despite growing evidence that these compounds affect neuronal and mitochondrial function, the molecular basis of neuronal dysfunction and cell death in MoCD is still poorly understood. Here we show that mitochondria are severely affected by the loss of SO activity. SO-deficient mouse embryonic fibroblasts display reduced growth rates and impaired ATP production when cultured in galactose, which is an indicator of mitochondrial dysfunction. We also found that mitochondria in SO-deficient cells form a highly interconnected network compared to controls while displaying a slight decrease in motility and unchanged mitochondrial mass. Moreover, we show that the mitochondrial network is directly influenced by SO32–, as a moderate elevation of SO32– lead to the formation of an interconnected mitochondrial network, while high SO32– levels induced fragmentation. Finally, we found a highly interconnected mitochondrial network in MoCD patient-derived fibroblasts, similar to our findings in mouse-derived fibroblasts. We therefore conclude that altered mitochondrial dynamics are an important contributor to the disease phenotype and suggest that MoCD should be included among the mitochondrial disorders.
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Affiliation(s)
- Anna-Theresa Mellis
- Department of Chemistry, Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Juliane Roeper
- Department of Chemistry, Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Albert L Misko
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Joshua Kohl
- Department of Chemistry, Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Guenter Schwarz
- Department of Chemistry, Institute for Biochemistry, University of Cologne, Cologne, Germany.,Center for Molecular Medicine, University of Cologne, Cologne, Germany
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Cornish A, Roychoudhury S, Sarma K, Pramanik S, Bhakat K, Dudley A, Mishra NK, Guda C. Red panda: a novel method for detecting variants in single-cell RNA sequencing. BMC Genomics 2020; 21:830. [PMID: 33372593 PMCID: PMC7771073 DOI: 10.1186/s12864-020-07224-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/10/2020] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Single-cell sequencing enables us to better understand genetic diseases, such as cancer or autoimmune disorders, which are often affected by changes in rare cells. Currently, no existing software is aimed at identifying single nucleotide variations or micro (1-50 bp) insertions and deletions in single-cell RNA sequencing (scRNA-seq) data. Generating high-quality variant data is vital to the study of the aforementioned diseases, among others. RESULTS In this study, we report the design and implementation of Red Panda, a novel method to accurately identify variants in scRNA-seq data. Variants were called on scRNA-seq data from human articular chondrocytes, mouse embryonic fibroblasts (MEFs), and simulated data stemming from the MEF alignments. Red Panda had the highest Positive Predictive Value at 45.0%, while other tools-FreeBayes, GATK HaplotypeCaller, GATK UnifiedGenotyper, Monovar, and Platypus-ranged from 5.8-41.53%. From the simulated data, Red Panda had the highest sensitivity at 72.44%. CONCLUSIONS We show that our method provides a novel and improved mechanism to identify variants in scRNA-seq as compared to currently existing software. However, methods for identification of genomic variants using scRNA-seq data can be still improved.
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Affiliation(s)
- Adam Cornish
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Shrabasti Roychoudhury
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Krishna Sarma
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Suravi Pramanik
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Kishor Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Andrew Dudley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Nitish K Mishra
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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Bellet MM, Pieroni S, Castelli M, Piobbico D, Fallarino F, Romani L, Della-Fazia MA, Servillo G. HOPS/Tmub1 involvement in the NF-kB-mediated inflammatory response through the modulation of TRAF6. Cell Death Dis 2020; 11:865. [PMID: 33060567 PMCID: PMC7567074 DOI: 10.1038/s41419-020-03086-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 12/23/2022]
Abstract
HOPS/Tmub1 is a ubiquitously expressed transmembrane ubiquitin-like protein that shuttles between nucleus and cytoplasm during cell cycle progression. HOPS causes cell cycle arrest in G0/G1 phase, an event associated to stabilization of p19Arf, an important tumor suppressor protein. Moreover, HOPS plays an important role in driving centrosomal assembly and maintenance, mitotic spindle proper organization, and ultimately a correct cell division. Recently, HOPS has been described as an important regulator of p53, which acts as modifier, stabilizing p53 half-life and playing a key role in p53 mediating apoptosis after DNA damage. NF-κB is a transcription factor with a central role in many cellular events, including inflammation and apoptosis. Our experiments demonstrate that the transcriptional activity of the p65/RelA NF-κB subunit is regulated by HOPS. Importantly, Hops−/− cells have remarkable alterations of pro-inflammatory responses. Specifically, we found that HOPS enhances NF-κB activation leading to increase transcription of inflammatory mediators, through the reduction of IκBα stability. Notably, this effect is mediated by a direct HOPS binding to the E3 ubiquitin ligase TRAF6, which lessens TRAF6 stability ultimately leading increased IKK complex activation. These findings uncover a previously unidentified function of HOPS/Tmub1 as a novel modulator of TRAF6, regulating inflammatory responses driven by activation of the NF-κB signaling pathway. The comprehension on how HOPS/Tmub1 takes part to the inflammatory processes in vivo and whether this function is important in the control of proliferation and tumorigenesis could establish the basis for the development of novel pharmacological strategies.
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Affiliation(s)
- Marina Maria Bellet
- Department of Experimental Medicine, University of Perugia, 06132, Perugia, Italy
| | - Stefania Pieroni
- Department of Experimental Medicine, University of Perugia, 06132, Perugia, Italy
| | - Marilena Castelli
- Department of Experimental Medicine, University of Perugia, 06132, Perugia, Italy
| | - Danilo Piobbico
- Department of Experimental Medicine, University of Perugia, 06132, Perugia, Italy
| | - Francesca Fallarino
- Department of Experimental Medicine, University of Perugia, 06132, Perugia, Italy
| | - Luigina Romani
- Department of Experimental Medicine, University of Perugia, 06132, Perugia, Italy
| | | | - Giuseppe Servillo
- Department of Experimental Medicine, University of Perugia, 06132, Perugia, Italy.
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Chi TF, Khoder-Agha F, Mennerich D, Kellokumpu S, Miinalainen II, Kietzmann T, Dimova EY. Loss of USF2 promotes proliferation, migration and mitophagy in a redox-dependent manner. Redox Biol 2020; 37:101750. [PMID: 33059314 PMCID: PMC7566946 DOI: 10.1016/j.redox.2020.101750] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/02/2020] [Accepted: 10/04/2020] [Indexed: 12/15/2022] Open
Abstract
The upstream stimulatory factor 2 (USF2) is a transcription factor implicated in several cellular processes and among them, tumor development seems to stand out. However, the data with respect to the role of USF2 in tumor development are conflicting suggesting that it acts either as tumor promoter or suppressor. Here we show that absence of USF2 promotes proliferation and migration. Thereby, we reveal a previously unknown function of USF2 in mitochondrial homeostasis. Mechanistically, we demonstrate that deficiency of USF2 promotes survival by inducing mitophagy in a ROS-sensitive manner by activating both ERK1/2 and AKT. Altogether, this study supports USF2′s function as tumor suppressor and highlights its novel role for mitochondrial function and energy homeostasis thereby linking USF2 to conditions such as insulin resistance, type-2 diabetes mellitus, and the metabolic syndrome.
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Affiliation(s)
- Tabughang Franklin Chi
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Fawzi Khoder-Agha
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Daniela Mennerich
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - IIkka Miinalainen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Elitsa Y Dimova
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.
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Abstract
Background Several long noncoding RNAs (lncRNAs) have been shown to function as components of molecular machines that play fundamental roles in biology. While the number of annotated lncRNAs in mammalian genomes has greatly expanded, studying lncRNA function has been a challenge due to their diverse biological roles and because lncRNA loci can contain multiple molecular modes that may exert function. Results We previously generated and characterized a cohort of 20 lncRNA loci knockout mice. Here, we extend this initial study and provide a more detailed analysis of the highly conserved lncRNA locus, taurine-upregulated gene 1 (Tug1). We report that Tug1-knockout male mice are sterile with underlying defects including a low number of sperm and abnormal sperm morphology. Because lncRNA loci can contain multiple modes of action, we wanted to determine which, if any, potential elements contained in the Tug1 genomic region have any activity. Using engineered mouse models and cell-based assays, we provide evidence that the Tug1 locus harbors two distinct noncoding regulatory activities, as a cis-DNA repressor that regulates neighboring genes and as a lncRNA that can regulate genes by a trans-based function. We also show that Tug1 contains an evolutionary conserved open reading frame that when overexpressed produces a stable protein which impacts mitochondrial membrane potential, suggesting a potential third coding function. Conclusions Our results reveal an essential role for the Tug1 locus in male fertility and uncover evidence for distinct molecular modes in the Tug1 locus, thus highlighting the complexity present at lncRNA loci.
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Panagiotopoulos AL, Karguth N, Pavlou M, Böhm S, Gasparoni G, Walter J, Graf A, Blum H, Biel M, Riedmayr LM, Becirovic E. Antisense Oligonucleotide- and CRISPR-Cas9-Mediated Rescue of mRNA Splicing for a Deep Intronic CLRN1 Mutation. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:1050-1061. [PMID: 32841912 PMCID: PMC7452116 DOI: 10.1016/j.omtn.2020.07.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/23/2020] [Accepted: 07/27/2020] [Indexed: 12/26/2022]
Abstract
Mutations in CLRN1 cause Usher syndrome (USH) type III (USH3A), a disease characterized by progressive hearing impairment, retinitis pigmentosa, and vestibular dysfunction. Due to the lack of appropriate disease models, no efficient therapy for retinitis pigmentosa in USH patients exists so far. In addition, given the yet undefined functional role and expression of the different CLRN1 splice isoforms in the retina, non-causative therapies such as gene supplementation are unsuitable at this stage. In this study, we focused on the recently identified deep intronic c.254-649T>G CLRN1 splicing mutation and aimed to establish two causative treatment approaches: CRISPR-Cas9-mediated excision of the mutated intronic region and antisense oligonucleotide (AON)-mediated correction of mRNA splicing. The therapeutic potential of these approaches was validated in different cell types transiently or stably expressing CLRN1 minigenes. Both approaches led to substantial correction of the splice defect. Surprisingly, however, no synergistic effect was detected when combining both methods. Finally, the injection of naked AONs into mice expressing the mutant CLRN1 minigene in the retina also led to a significant splice rescue. We propose that both AONs and CRISPR-Cas9 are suitable strategies to initiate advanced preclinical studies for treatment of USH3A patients.
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Affiliation(s)
- Anna-Lena Panagiotopoulos
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nina Karguth
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany; Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marina Pavlou
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany; Department of Ophthalmology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sybille Böhm
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany; Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gilles Gasparoni
- Department of Genetics, Saarland University, Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics, Saarland University, Saarbrücken, Germany
| | - Alexander Graf
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Blum
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin Biel
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany; Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lisa Maria Riedmayr
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany; Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Elvir Becirovic
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany; Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany.
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Vohra MS, Ahmad B, Serpell CJ, Parhar IS, Wong EH. Murine in vitro cellular models to better understand adipogenesis and its potential applications. Differentiation 2020; 115:62-84. [PMID: 32891960 DOI: 10.1016/j.diff.2020.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/08/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023]
Abstract
Adipogenesis has been extensively studied using in vitro models of cellular differentiation, enabling long-term regulation of fat cell metabolism in human adipose tissue (AT) material. Many studies promote the idea that manipulation of this process could potentially reduce the prevalence of obesity and its related diseases. It has now become essential to understand the molecular basis of fat cell development to tackle this pandemic disease, by identifying therapeutic targets and new biomarkers. This review explores murine cell models and their applications for study of the adipogenic differentiation process in vitro. We focus on the benefits and limitations of different cell line models to aid in interpreting data and selecting a good cell line model for successful understanding of adipose biology.
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Affiliation(s)
- Muhammad Sufyan Vohra
- School of Medicine, Faculty of Health and Medical Sciences, Taylor's University Lakeside Campus, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia.
| | - Bilal Ahmad
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University Lakeside Campus, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia.
| | - Christopher J Serpell
- School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH, United Kingdom.
| | - Ishwar S Parhar
- Brain Research Institute, Jeffery Cheah School of Medicine and Health Sciences, Monash University, Bandar Sunway, PJ 47500, Selangor, Malaysia.
| | - Eng Hwa Wong
- School of Medicine, Faculty of Health and Medical Sciences, Taylor's University Lakeside Campus, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia.
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Valdivia A, Cárdenas A, Brenet M, Maldonado H, Kong M, Díaz J, Burridge K, Schneider P, San Martín A, García-Mata R, Quest AFG, Leyton L. Syndecan-4/PAR-3 signaling regulates focal adhesion dynamics in mesenchymal cells. Cell Commun Signal 2020; 18:129. [PMID: 32811537 PMCID: PMC7433185 DOI: 10.1186/s12964-020-00629-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/17/2020] [Indexed: 01/04/2023] Open
Abstract
Background Syndecans regulate cell migration thus having key roles in scarring and wound healing processes. Our previous results have shown that Thy-1/CD90 can engage both αvβ3 integrin and Syndecan-4 expressed on the surface of astrocytes to induce cell migration. Despite a well-described role of Syndecan-4 during cell movement, information is scarce regarding specific Syndecan-4 partners involved in Thy-1/CD90-stimulated cell migration. Methods Mass spectrometry (MS) analysis of complexes precipitated with the Syndecan-4 cytoplasmic tail peptide was used to identify potential Syndecan-4-binding partners. The interactions found by MS were validated by immunoprecipitation and proximity ligation assays. The conducted research employed an array of genetic, biochemical and pharmacological approaches, including: PAR-3, Syndecan-4 and Tiam1 silencing, active Rac1 GEFs affinity precipitation, and video microscopy. Results We identified PAR-3 as a Syndecan-4-binding protein. Its interaction depended on the carboxy-terminal EFYA sequence present on Syndecan-4. In astrocytes where PAR-3 expression was reduced, Thy-1-induced cell migration and focal adhesion disassembly was impaired. This effect was associated with a sustained Focal Adhesion Kinase activation in the siRNA-PAR-3 treated cells. Our data also show that Thy-1/CD90 activates Tiam1, a PAR-3 effector. Additionally, we found that after Syndecan-4 silencing, Tiam1 activation was decreased and it was no longer recruited to the membrane. Syndecan-4/PAR-3 interaction and the alteration in focal adhesion dynamics were validated in mouse embryonic fibroblast (MEF) cells, thereby identifying this novel Syndecan-4/PAR-3 signaling complex as a general mechanism for mesenchymal cell migration involved in Thy-1/CD90 stimulation. Conclusions The newly identified Syndecan-4/PAR-3 signaling complex participates in Thy-1/CD90-induced focal adhesion disassembly in mesenchymal cells. The mechanism involves focal adhesion kinase dephosphorylation and Tiam1 activation downstream of Syndecan-4/PAR-3 signaling complex formation. Additionally, PAR-3 is defined here as a novel adhesome-associated component with an essential role in focal adhesion disassembly during polarized cell migration. These novel findings uncover signaling mechanisms regulating cell migration, thereby opening up new avenues for future research on Syndecan-4/PAR-3 signaling in processes such as wound healing and scarring. Graphical abstract ![]()
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Affiliation(s)
- Alejandra Valdivia
- Cellular Communication Laboratory, Program of Cellular & Molecular Biology, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, 838-0453, Santiago, Chile. .,Center for studies on Exercise, Metabolism and Cancer (CEMC) and Advanced Center for Chronic Diseases (ACCDiS), Facultad de Medicina, Universidad de Chile, 838-0453, Santiago, Chile. .,Microscopy in Medicine (MiM) Core, Emory University, Atlanta, GA, 30322, USA. .,Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. .,School of Medicine, Division of Cardiology, Emory University, Atlanta, GA, 30322, USA.
| | - Areli Cárdenas
- Cellular Communication Laboratory, Program of Cellular & Molecular Biology, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, 838-0453, Santiago, Chile.,Center for studies on Exercise, Metabolism and Cancer (CEMC) and Advanced Center for Chronic Diseases (ACCDiS), Facultad de Medicina, Universidad de Chile, 838-0453, Santiago, Chile
| | - Marianne Brenet
- Cellular Communication Laboratory, Program of Cellular & Molecular Biology, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, 838-0453, Santiago, Chile.,Center for studies on Exercise, Metabolism and Cancer (CEMC) and Advanced Center for Chronic Diseases (ACCDiS), Facultad de Medicina, Universidad de Chile, 838-0453, Santiago, Chile
| | - Horacio Maldonado
- Cellular Communication Laboratory, Program of Cellular & Molecular Biology, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, 838-0453, Santiago, Chile.,Department of Pediatrics, Pulmonology Division, Program for Rare and Interstitial Lung Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,UNC Catalyst for Rare Disease, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Milene Kong
- Cellular Communication Laboratory, Program of Cellular & Molecular Biology, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, 838-0453, Santiago, Chile.,Center for studies on Exercise, Metabolism and Cancer (CEMC) and Advanced Center for Chronic Diseases (ACCDiS), Facultad de Medicina, Universidad de Chile, 838-0453, Santiago, Chile.,Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta, Chile
| | - Jorge Díaz
- Cellular Communication Laboratory, Program of Cellular & Molecular Biology, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, 838-0453, Santiago, Chile.,Center for studies on Exercise, Metabolism and Cancer (CEMC) and Advanced Center for Chronic Diseases (ACCDiS), Facultad de Medicina, Universidad de Chile, 838-0453, Santiago, Chile
| | - Keith Burridge
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Pascal Schneider
- Department of Biochemistry, University of Lausanne, 1066, Epalinges, Switzerland
| | - Alejandra San Martín
- School of Medicine, Division of Cardiology, Emory University, Atlanta, GA, 30322, USA
| | - Rafael García-Mata
- Department of Biological Sciences, University of Toledo, Toledo, OH, 43606, USA
| | - Andrew F G Quest
- Cellular Communication Laboratory, Program of Cellular & Molecular Biology, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, 838-0453, Santiago, Chile.,Center for studies on Exercise, Metabolism and Cancer (CEMC) and Advanced Center for Chronic Diseases (ACCDiS), Facultad de Medicina, Universidad de Chile, 838-0453, Santiago, Chile
| | - Lisette Leyton
- Cellular Communication Laboratory, Program of Cellular & Molecular Biology, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, 838-0453, Santiago, Chile. .,Center for studies on Exercise, Metabolism and Cancer (CEMC) and Advanced Center for Chronic Diseases (ACCDiS), Facultad de Medicina, Universidad de Chile, 838-0453, Santiago, Chile.
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50
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Liu J, Guan D, Dong M, Yang J, Wei H, Liang Q, Song L, Xu L, Bai J, Liu C, Mao J, Zhang Q, Zhou J, Wu X, Wang M, Cong YS. UFMylation maintains tumour suppressor p53 stability by antagonizing its ubiquitination. Nat Cell Biol 2020; 22:1056-1063. [PMID: 32807901 DOI: 10.1038/s41556-020-0559-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 07/14/2020] [Indexed: 11/09/2022]
Abstract
p53 is the most intensively studied tumour suppressor1. The regulation of p53 homeostasis is essential for its tumour-suppressive function2,3. Although p53 is regulated by an array of post-translational modifications, both during normal homeostasis and in stress-induced responses2-4, how p53 maintains its homeostasis remains unclear. UFMylation is a recently identified ubiquitin-like modification with essential biological functions5-7. Deficiency in this modification leads to embryonic lethality in mice and disease in humans8-12. Here, we report that p53 can be covalently modified by UFM1 and that this modification stabilizes p53 by antagonizing its ubiquitination and proteasome degradation. Mechanistically, UFL1, the UFM1 ligase6, competes with MDM2 to bind to p53 for its stabilization. Depletion of UFL1 or DDRGK1, the critical regulator of UFMylation6,13, decreases p53 stability and in turn promotes cell growth and tumour formation in vivo. Clinically, UFL1 and DDRGK1 expression are downregulated and positively correlated with levels of p53 in a high percentage of renal cell carcinomas. Our results identify UFMylation as a crucial post-translational modification for maintenance of p53 stability and tumour-suppressive function, and point to UFMylation as a promising therapeutic target in cancer.
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Affiliation(s)
- Jiang Liu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Di Guan
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Maogong Dong
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Jingjing Yang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Haibin Wei
- Institute of Cancer and Basic Medicine, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Qian Liang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Lizhi Song
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Lu Xu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Junjie Bai
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Cui Liu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Jian Mao
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Qian Zhang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Junzhi Zhou
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Xiaoying Wu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Miao Wang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Yu-Sheng Cong
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China.
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