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Wilms G, Schofield K, Maddern S, Foley C, Shaw Y, Smith B, Basantes LE, Schwandt K, Babendreyer A, Chavez T, McKee N, Gokhale V, Kallabis S, Meissner F, Rokey SN, Dunckley T, Montfort WR, Becker W, Hulme C. Discovery and Functional Characterization of a Potent, Selective, and Metabolically Stable PROTAC of the Protein Kinases DYRK1A and DYRK1B. J Med Chem 2024. [PMID: 39344427 DOI: 10.1021/acs.jmedchem.4c01130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Small-molecule-induced protein degradation has emerged as a promising pharmacological modality for inactivating disease-relevant protein kinases. DYRK1A and DYRK1B are closely related protein kinases that are involved in pathological processes such as neurodegeneration, cancer development, and adaptive immune homeostasis. Herein, we report the development of the first DYRK1 proteolysis targeting chimeras (PROTACs) that combine a new ATP-competitive DYRK1 inhibitor with ligands for the E3 ubiquitin ligase component cereblon (CRBN) to induce ubiquitination and subsequent proteasomal degradation of DYRK1A and DYRK1B. The lead compound (DYR684) promoted fast, efficient, potent, and selective degradation of DYRK1A in cell-based assays. Interestingly, an enzymatically inactive splicing variant of DYRK1B (p65) resisted degradation. Compared to competitive kinase inhibition, targeted degradation of DYRK1 by DYR684 provided improved suppression of downstream signaling. Collectively, our results identify DYRKs as viable targets for PROTAC-mediated degradation and qualify DYR684 as a useful chemical probe for DYRK1A and DYRK1B.
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Affiliation(s)
- Gerrit Wilms
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Kevin Schofield
- Division of Drug Discovery and Development, Department of Pharmacology and Toxicology, College of Pharmacy The University of Arizona, Tucson, Arizona 85721, United States
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Shayna Maddern
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Christopher Foley
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Yeng Shaw
- Division of Drug Discovery and Development, Department of Pharmacology and Toxicology, College of Pharmacy The University of Arizona, Tucson, Arizona 85721, United States
| | - Breland Smith
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - L Emilia Basantes
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Katharina Schwandt
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Aaron Babendreyer
- Institute of Molecular Pharmacology, RWTH Aachen University, Aachen 52074, Germany
| | - Timothy Chavez
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Nicholas McKee
- Division of Drug Discovery and Development, Department of Pharmacology and Toxicology, College of Pharmacy The University of Arizona, Tucson, Arizona 85721, United States
| | - Vijay Gokhale
- BIO5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
| | - Sebastian Kallabis
- Core Facility Translational Proteomics, Institute of Innate Immunity, University Hospital Bonn, Bonn 53127, Germany
| | - Felix Meissner
- Department of Systems Immunology and Proteomics, Institute of Innate Immunity, University Hospital Bonn, Bonn 53127, Germany
| | - Samantha N Rokey
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Travis Dunckley
- ASU-Banner Neurodegenerative Disease Research Center, Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - William R Montfort
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Walter Becker
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Christopher Hulme
- Division of Drug Discovery and Development, Department of Pharmacology and Toxicology, College of Pharmacy The University of Arizona, Tucson, Arizona 85721, United States
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
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Birtwistle MR, Huggins JR, Zadeh CO, Sarmah D, Srikanth S, Jones BK, Cascio LN, Dean DR. A 96-Well Polyacrylamide Gel for Electrophoresis and Western Blotting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593650. [PMID: 38765957 PMCID: PMC11100825 DOI: 10.1101/2024.05.10.593650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Western blotting is a stalwart technique for analyzing specific proteins and/or their post-translational modifications. However, it remains challenging to accommodate more than ~10 samples per experiment without substantial departure from trusted, established protocols involving accessible instrumentation. Here, we describe a 96-sample western blot that conforms to standard 96-well plate dimensional constraints and has little operational deviation from standard western blotting. The main differences are that (i) submerged polyacrylamide gel electrophoresis is operated horizontally (similar to agarose gels) as opposed to vertically, and (ii) a 6 mm thick gel is used, with 2 mm most relevant for membrane transfer (vs ~1 mm typical). Results demonstrate both wet and semi-dry transfer are compatible with this gel thickness. The major tradeoff is reduced molecular weight resolution, due primarily to less available migration distance per sample. We demonstrate proof-of-principle using gels loaded with molecular weight ladder, recombinant protein, and cell lysates. We expect the 96-well western blot will increase reproducibility, efficiency (cost and time ~8-fold), and capacity for biological characterization relative to established western blots.
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Liu S, Maruzuru Y, Takeshima K, Koyanagi N, Kato A, Kawaguchi Y. Impact of the interaction between herpes simplex virus 1 ICP22 and FACT on viral gene expression and pathogenesis. J Virol 2024; 98:e0073724. [PMID: 39016551 PMCID: PMC11338292 DOI: 10.1128/jvi.00737-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/21/2024] [Indexed: 07/18/2024] Open
Abstract
Facilitates chromatin transcription (FACT) interacts with nucleosomes to promote gene transcription by regulating the dissociation and reassembly of nucleosomes downstream and upstream of RNA polymerase II (Pol II). A previous study reported that herpes simplex virus 1 (HSV-1) regulatory protein ICP22 interacted with FACT and was required for its recruitment to the viral DNA genome in HSV-1-infected cells. However, the biological importance of interactions between ICP22 and FACT in relation to HSV-1 infection is unclear. Here, we mapped the minimal domain of ICP22 required for its efficient interaction with FACT to a cluster of five basic amino acids in ICP22. A recombinant virus harboring alanine substitutions in this identified cluster led to the decreased accumulation of viral mRNAs from UL54, UL38, and UL44 genes, reduced Pol II occupancy of these genes in MRC-5 cells, and impaired HSV-1 virulence in mice following ocular or intracranial infection. Furthermore, the treatment of mice infected with wild-type HSV-1 with CBL0137, a FACT inhibitor currently being investigated in clinical trials, significantly improved the survival rate of mice. These results suggested that the interaction between ICP22 and FACT was required for efficient HSV-1 gene expression and pathogenicity. Therefore, FACT might be a potential therapeutic target for HSV-1 infection.IMPORTANCEICP22 is a well-known regulatory factor of HSV-1 gene expression, but its mechanism(s) are poorly understood. Although the interaction of FACT with ICP22 was reported previously, its significance in HSV-1 infection is unknown. Given that FACT is involved in gene transcription, it is of interest to investigate this interaction as it relates to HSV-1 gene expression. To determine a direct link between the interaction and HSV-1 infection, we mapped a minimal domain of ICP22 required for its efficient interaction with FACT and generated a recombinant virus carrying mutations in the identified domain. Using the recombinant virus, we obtained evidence suggesting that the interaction between ICP22 and FACT promoted Pol II transcription from HSV-1 genes and viral virulence in mice. In addition, CBL0137, an inhibitor of FACT, effectively protected mice from lethal HSV-1 infection, suggesting FACT might be a potential target for the development of novel anti-HSV drugs.
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Grants
- 20H05692 MEXT | Japan Society for the Promotion of Science (JSPS)
- 22H04803 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 22H05584 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JPMJPR22R5 MEXT | Japan Science and Technology Agency (JST)
- JP20wm0125002, JP22fk0108640, JP223fa627001, JP23wm0225031, JP23wm0225035 Japan Agency for Medical Research and Development (AMED)
- JP22gm1610008 Japan Agency for Medical Research and Development (AMED)
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Affiliation(s)
- Shaocong Liu
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuhei Maruzuru
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kosuke Takeshima
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Naoto Koyanagi
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Akihisa Kato
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasushi Kawaguchi
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Pandemic Preparedness, Infection and Advanced Research Center, The University of Tokyo, Tokyo, Japan
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Kinhikar A, Hassanein M, Harman J, Soderstrom C, Honrine K, Lavelle A, Valentin MA, Mathews J. Recommendations for Development and Validation of a Fit-For-Purpose Biomarker Assays Using Western Blotting; An-AAPS Sponsored Initiative to Harmonize Industry Practices. AAPS J 2024; 26:87. [PMID: 39060472 DOI: 10.1208/s12248-024-00946-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 06/09/2024] [Indexed: 07/28/2024] Open
Abstract
Western blot (WB) assays are routinely used for detection and quantification of biomarkers. Although assay validation to measure biomarkers in complex matrices has become a mainstay process for ligand binding assays (LBA) and mass spectrometry (MS), no guidelines exist yet validate biomarker methods using WB techniques. In this cross-industry white paper, we outlined in detail the key steps for development and for validation of WB assays for protein biomarkers under different contexts of use (COU). In addition, we described how to determine the level of assay validation needed for biomarker assays using Western blotting. For simplicity, we described two paths of WB assay validation. The first path (Path 1) is for biomarkers being analyzed for exploratory research or for internal go- or no/go- decision making. The second path (Path 2) is for clinical decision making such as dose determination or drug response that need to be run in a regulated environment. This work is supported through AAPS Biomarkers and Precision Medicine subteam and represents AAPS members opinion.
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Affiliation(s)
- Arvind Kinhikar
- BioMedical Research, Novartis, 250 Massachusetts Avenue, Room 6A148, Cambridge, MA, 02139, USA.
| | - Mohamed Hassanein
- Early Clinical Development, Precision Medicine, Pfizer Inc, Cambridge, MA, USA
| | - Jake Harman
- Biomarker Services, Pharmaceutical Product Development (PPD) Laboratories, Richmond, VA, USA
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5
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Li X, Kirkpatrick RB, Wang X, Tucker CJ, Shukla A, Jessen HJ, Wang H, Shears SB, Gu C. Homeostatic coordination of cellular phosphate uptake and efflux requires an organelle-based receptor for the inositol pyrophosphate IP8. Cell Rep 2024; 43:114316. [PMID: 38833370 PMCID: PMC11284862 DOI: 10.1016/j.celrep.2024.114316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 04/16/2024] [Accepted: 05/17/2024] [Indexed: 06/06/2024] Open
Abstract
Phosphate (Pi) serves countless metabolic pathways and is involved in macromolecule synthesis, energy storage, cellular signaling, and bone maintenance. Herein, we describe the coordination of Pi uptake and efflux pathways to maintain mammalian cell Pi homeostasis. We discover that XPR1, the presumed Pi efflux transporter, separately supervises rates of Pi uptake. This direct, regulatory interplay arises from XPR1 being a binding partner for the Pi uptake transporter PiT1, involving a predicted transmembrane helix/extramembrane loop in XPR1, and its hitherto unknown localization in a subset of intracellular LAMP1-positive puncta (named "XLPVs"). A pharmacological mimic of Pi homeostatic challenge is sensed by the inositol pyrophosphate IP8, which functionalizes XPR1 to respond in a temporally hierarchal manner, initially adjusting the rate of Pi efflux, followed subsequently by independent modulation of PiT1 turnover to reset the rate of Pi uptake. These observations generate a unifying model of mammalian cellular Pi homeostasis, expanding opportunities for therapeutic intervention.
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Affiliation(s)
- Xingyao Li
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental, Health Sciences, Research Triangle Park, NC 27709, USA
| | - Regan B Kirkpatrick
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental, Health Sciences, Research Triangle Park, NC 27709, USA
| | - Xiaodong Wang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Charles J Tucker
- Fluorescence Microscopy and Imaging Center, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Anuj Shukla
- Institute of Organic Chemistry, and CIBSS - the Center for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, and CIBSS - the Center for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Huanchen Wang
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental, Health Sciences, Research Triangle Park, NC 27709, USA; Nucleolar Integrity Group, Signal Transduction Laboratory, National Institute of Environmental, Health Sciences, Research Triangle Park, NC 27709, USA
| | - Stephen B Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental, Health Sciences, Research Triangle Park, NC 27709, USA
| | - Chunfang Gu
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental, Health Sciences, Research Triangle Park, NC 27709, USA; Synaptic & Developmental Plasticity Group, Neurobiology Laboratory, National Institute of Environmental, Health Sciences, Research Triangle Park, NC 27709, USA.
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6
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Welch N, Mishra S, Bellar A, Kannan P, Gopan A, Goudarzi M, King J, Luknis M, Musich R, Agrawal V, Bena J, Koch CJ, Li L, Willard B, Shah YM, Dasarathy S. Differential impact of sex on regulation of skeletal muscle mitochondrial function and protein homeostasis by hypoxia-inducible factor-1α in normoxia. J Physiol 2024; 602:2763-2806. [PMID: 38761133 PMCID: PMC11178475 DOI: 10.1113/jp285339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 04/19/2024] [Indexed: 05/20/2024] Open
Abstract
Hypoxia-inducible factor (HIF)-1α is continuously synthesized and degraded in normoxia. During hypoxia, HIF1α stabilization restricts cellular/mitochondrial oxygen utilization. Cellular stressors can stabilize HIF1α even during normoxia. However, less is known about HIF1α function(s) and sex-specific effects during normoxia in the basal state. Since skeletal muscle is the largest protein store in mammals and protein homeostasis has high energy demands, we determined HIF1α function at baseline during normoxia in skeletal muscle. Untargeted multiomics data analyses were followed by experimental validation in differentiated murine myotubes with loss/gain of function and skeletal muscle from mice without/with post-natal muscle-specific Hif1a deletion (Hif1amsd). Mitochondrial oxygen consumption studies using substrate, uncoupler, inhibitor, titration protocols; targeted metabolite quantification by gas chromatography-mass spectrometry; and post-mitotic senescence markers using biochemical assays were performed. Multiomics analyses showed enrichment in mitochondrial and cell cycle regulatory pathways in Hif1a deleted cells/tissue. Experimentally, mitochondrial oxidative functions and ATP content were higher with less mitochondrial free radical generation with Hif1a deletion. Deletion of Hif1a also resulted in higher concentrations of TCA cycle intermediates and HIF2α proteins in myotubes. Overall responses to Hif1amsd were similar in male and female mice, but changes in complex II function, maximum respiration, Sirt3 and HIF1β protein expression and muscle fibre diameter were sex-dependent. Adaptive responses to hypoxia are mediated by stabilization of constantly synthesized HIF1α. Despite rapid degradation, the presence of HIF1α during normoxia contributes to lower mitochondrial oxidative efficiency and greater post-mitotic senescence in skeletal muscle. In vivo responses to HIF1α in skeletal muscle were differentially impacted by sex. KEY POINTS: Hypoxia-inducible factor -1α (HIF1α), a critical transcription factor, undergoes continuous synthesis and proteolysis, enabling rapid adaptive responses to hypoxia by reducing mitochondrial oxygen consumption. In mammals, skeletal muscle is the largest protein store which is determined by a balance between protein synthesis and breakdown and is sensitive to mitochondrial oxidative function. To investigate the functional consequences of transient HIF1α expression during normoxia in the basal state, myotubes and skeletal muscle from male and female mice with HIF1α knockout were studied using complementary multiomics, biochemical and metabolite assays. HIF1α knockout altered the electron transport chain, mitochondrial oxidative function, signalling molecules for protein homeostasis, and post-mitotic senescence markers, some of which were differentially impacted by sex. The cost of rapid adaptive responses mediated by HIF1α is lower mitochondrial oxidative efficiency and post-mitotic senescence during normoxia.
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Affiliation(s)
- Nicole Welch
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Saurabh Mishra
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Annette Bellar
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Pugazhendhi Kannan
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Amrit Gopan
- KEM Hospital, Seth GS Medical College, Mumbai, India
| | - Maryam Goudarzi
- Respiratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jasmine King
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Mathew Luknis
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Ryan Musich
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Vandana Agrawal
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - James Bena
- Quantitative Health, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Ling Li
- Proteomics and Metabolomics Core, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Belinda Willard
- Proteomics and Metabolomics Core, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yatrik M Shah
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Srinivasan Dasarathy
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
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7
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Mutalik SP, O'Shaughnessy EC, Ho CT, Gupton SL. TRIM9 controls growth cone responses to netrin through DCC and UNC5C. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593135. [PMID: 38765979 PMCID: PMC11100671 DOI: 10.1101/2024.05.08.593135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The guidance cue netrin-1 promotes both growth cone attraction and growth cone repulsion. How netrin-1 elicits these diverse axonal responses, beyond engaging the attractive receptor DCC and repulsive receptors of the UNC5 family, remains elusive. Here we demonstrate that murine netrin-1 induces biphasic axonal responses in cortical neurons: attraction at lower concentrations and repulsion at higher concentrations using both a microfluidic-based netrin-1 gradient and bath application of netrin-1. TRIM9 is a brain-enriched E3 ubiquitin ligase previously shown to bind and cluster the attractive receptor DCC at the plasma membrane and regulate netrin-dependent attractive responses. However, whether TRIM9 also regulated repulsive responses to netrin-1 remained to be seen. In this study, we show that TRIM9 localizes and interacts with both the attractive netrin receptor DCC and the repulsive netrin receptor, UNC5C, and that deletion of murine Trim9 alters both attractive and repulsive responses to murine netrin-1. TRIM9 was required for netrin-1-dependent changes in surface levels of DCC and total levels of UNC5C in the growth cone during morphogenesis. We demonstrate that DCC at the membrane regulates growth cone area and show that TRIM9 negatively regulates FAK activity in the absence of netrin-1. We investigate membrane dynamics of the UNC5C receptor using pH-mScarlet fused to the extracellular domain of UNC5C. Minutes after netrin addition, levels of UNC5C at the plasma membrane drop in a TRIM9-independent fashion, however TRIM9 regulated the mobility of UNC5C in the plasma membrane in the absence of netrin-1. Together this work demonstrates that TRIM9 interacts with and regulates both DCC and UNC5C during attractive and repulsive axonal responses to netrin-1.
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Magg V, Manetto A, Kopp K, Wu CC, Naghizadeh M, Lindner D, Eke L, Welsch J, Kallenberger SM, Schott J, Haucke V, Locker N, Stoecklin G, Ruggieri A. Turnover of PPP1R15A mRNA encoding GADD34 controls responsiveness and adaptation to cellular stress. Cell Rep 2024; 43:114069. [PMID: 38602876 DOI: 10.1016/j.celrep.2024.114069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 01/25/2024] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
The integrated stress response (ISR) is a key cellular signaling pathway activated by environmental alterations that represses protein synthesis to restore homeostasis. To prevent sustained damage, the ISR is counteracted by the upregulation of growth arrest and DNA damage-inducible 34 (GADD34), a stress-induced regulatory subunit of protein phosphatase 1 that mediates translation reactivation and stress recovery. Here, we uncover a novel ISR regulatory mechanism that post-transcriptionally controls the stability of PPP1R15A mRNA encoding GADD34. We establish that the 3' untranslated region of PPP1R15A mRNA contains an active AU-rich element (ARE) recognized by proteins of the ZFP36 family, promoting its rapid decay under normal conditions and stabilization for efficient expression of GADD34 in response to stress. We identify the tight temporal control of PPP1R15A mRNA turnover as a component of the transient ISR memory, which sets the threshold for cellular responsiveness and mediates adaptation to repeated stress conditions.
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Affiliation(s)
- Vera Magg
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Alessandro Manetto
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Katja Kopp
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Chia Ching Wu
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Mohsen Naghizadeh
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany
| | - Doris Lindner
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany
| | - Lucy Eke
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Julia Welsch
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Stefan M Kallenberger
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, 10178 Berlin, Germany; Medical Oncology, National Center for Tumor Diseases, Heidelberg University, 69120 Heidelberg, Germany
| | - Johanna Schott
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry, and Pharmacy, 14195 Berlin, Germany
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK; The Pirbright Institute, GU24 0NF Pirbright, UK
| | - Georg Stoecklin
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
| | - Alessia Ruggieri
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany.
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9
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Marques-da-Silva C, Schmidt-Silva C, Baptista RP, Kurup SP. Inherently Reduced Expression of ASC Restricts Caspase-1 Processing in Hepatocytes and Promotes Plasmodium Infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:596-606. [PMID: 38149914 PMCID: PMC10872340 DOI: 10.4049/jimmunol.2300440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/06/2023] [Indexed: 12/28/2023]
Abstract
Inflammasome-mediated caspase-1 activation facilitates innate immune control of Plasmodium in the liver, thereby limiting the incidence and severity of clinical malaria. However, caspase-1 processing occurs incompletely in both mouse and human hepatocytes and precludes the generation of mature IL-1β or IL-18, unlike in other cells. Why this is so or how it impacts Plasmodium control in the liver has remained unknown. We show that an inherently reduced expression of the inflammasome adaptor molecule apoptosis-associated specklike protein containing CARD (ASC) is responsible for the incomplete proteolytic processing of caspase-1 in murine hepatocytes. Transgenically enhancing ASC expression in hepatocytes enabled complete caspase-1 processing, enhanced pyroptotic cell death, maturation of the proinflammatory cytokines IL-1β and IL-18 that was otherwise absent, and better overall control of Plasmodium infection in the liver of mice. This, however, impeded the protection offered by live attenuated antimalarial vaccination. Tempering ASC expression in mouse macrophages, on the other hand, resulted in incomplete processing of caspase-1. Our work shows how caspase-1 activation and function in host cells are fundamentally defined by ASC expression and offers a potential new pathway to create better disease and vaccination outcomes by modifying the latter.
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Affiliation(s)
- Camila Marques-da-Silva
- Department of Cellular Biology, University of Georgia, Athens, GA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA
| | - Clyde Schmidt-Silva
- Department of Cellular Biology, University of Georgia, Athens, GA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA
| | - Rodrigo P Baptista
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA
| | - Samarchith P Kurup
- Department of Cellular Biology, University of Georgia, Athens, GA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA
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10
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Domin H, Konieczny J, Cieślik P, Pochwat B, Wyska E, Szafarz M, Lenda T, Biała D, Gąsior Ł, Śmiałowska M, Szewczyk B. The antidepressant-like and glioprotective effects of the Y2 receptor antagonist SF-11 in the astroglial degeneration model of depression in rats: Involvement of glutamatergic inhibition. Behav Brain Res 2024; 457:114729. [PMID: 37871655 DOI: 10.1016/j.bbr.2023.114729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023]
Abstract
In this study, we explored the potential antidepressant-like properties of the brain-penetrant Y2 receptor (Y2R) antagonist SF-11 [N-(4-ethoxyphenyl)- 4-(hydroxydiphenylmethyl)- 1-piperidinecarbothioamide] in the astroglial degeneration model of depression with an emphasis on checking the possible mechanisms implicated in this antidepressant-like effect. The model of depression relies on the loss of astrocytes in the medial prefrontal cortex (mPFC) in Sprague-Dawley rats after administering the gliotoxin L-alpha-aminoadipic acid (L-AAA). SF-11 was administered intraperitoneally (i.p.) once (10 mg/kg) or for three consecutive days (10 mg/kg/day), and the effects of L-AAA and SF-11 injected alone or in combination were investigated using the forced swim test (FST), sucrose intake test (SIT), Western blotting, immunohistochemical staining, and microdialysis. SF-11 produced an antidepressant-like effect after single or three-day administration in rats subjected to astrocyte impairment, as demonstrated by the FST and SIT, respectively. Immunoblotting and immunohistochemical analyses showed that SF-11 reversed the L-AAA-induced astrocyte cell death in the mPFC, suggesting it is glioprotective. Microdialysis studies showed that SF-11 decreased extracellular glutamate (Glu) levels compared to basal value when administered alone and compared to the basal value and control group in LAAA-treated rats. The results from immunoblotting analysis indicated the involvement of Y2Rs in the astrocyte ablation model of depression and the antidepressant-like effect of SF-11. In addition, we observed the participation of the caspase-3 apoptotic pathway in the mechanism of gliotoxin action induced by L-AAA. These findings demonstrate that SF-11, a Y2R antagonist, elicited a rapid antidepressant-like response, possibly linked to its ability to inhibit glutamatergic neurotransmission.
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Affiliation(s)
- Helena Domin
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Neurobiology, 12 Smętna Street, 31-343 Kraków, Poland.
| | - Jolanta Konieczny
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Neuropsychopharmacology, 12 Smętna Street, 31-343 Kraków, Poland
| | - Paulina Cieślik
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Neurobiology, 12 Smętna Street, 31-343 Kraków, Poland
| | - Bartłomiej Pochwat
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Neurobiology, 12 Smętna Street, 31-343 Kraków, Poland
| | - Elżbieta Wyska
- Jagiellonian University Medical College, Faculty of Pharmacy, Department of Pharmacokinetics and Physical Pharmacy, Medyczna 9, 30-688 Kraków, Poland
| | - Małgorzata Szafarz
- Jagiellonian University Medical College, Faculty of Pharmacy, Department of Pharmacokinetics and Physical Pharmacy, Medyczna 9, 30-688 Kraków, Poland
| | - Tomasz Lenda
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Neuropsychopharmacology, 12 Smętna Street, 31-343 Kraków, Poland
| | - Dominika Biała
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Neuropsychopharmacology, 12 Smętna Street, 31-343 Kraków, Poland
| | - Łukasz Gąsior
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Neurobiology, 12 Smętna Street, 31-343 Kraków, Poland
| | - Maria Śmiałowska
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Neurobiology, 12 Smętna Street, 31-343 Kraków, Poland
| | - Bernadeta Szewczyk
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Neurobiology, 12 Smętna Street, 31-343 Kraków, Poland
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11
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Craig NA, Scruggs AM, Berens JP, Deng F, Chen Y, Dvonch JT, Huang SK. Promotion of myofibroblast differentiation through repeated treatment of fibroblasts to low concentrations of PM 2.5. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2024; 105:104329. [PMID: 38036232 PMCID: PMC11010492 DOI: 10.1016/j.etap.2023.104329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/25/2023] [Indexed: 12/02/2023]
Abstract
Exposure to particulate matter ≤ 2.5 µm (PM2.5) is a risk factor for many lung diseases. Although the toxicologic effects of PM2.5 on airway epithelium are well-described, the effects of PM2.5 on fibroblasts in the lung are less studied. Here, we sought to examine the effects of PM2.5 on the differentiation of fibroblasts into myofibroblasts. Although a single treatment of fibroblasts did not result in a change in collagen or the myofibroblast marker α-SMA, exposing fibroblasts to sequential treatments with PM2.5 at low concentrations caused a robust increase in these proteins. Treatment of fibroblasts with IMD0354, an inhibitor to nuclear factor κB, but not with an antagonist to aryl hydrocarbon receptor, abolished the ability of PM2.5 to induce myofibroblast differentiation. These data demonstrate that potential impact of PM2.5 to fibroblast activation and fibrosis and support the importance of utilizing low concentrations and varying exposure protocols to toxicologic studies.
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Affiliation(s)
- Nathan A Craig
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Anne M Scruggs
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jack P Berens
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Furong Deng
- Department of Occupational and Environmental Health Sciences, Peking University School of Public Health, Beijing, China
| | - Yahong Chen
- Department of Respiratory Medicine, Peking University Third Hospital, Beijing, China
| | - J Timothy Dvonch
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Steven K Huang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.
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12
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Yue J, Lu Y, Sun Z, Guo Y, San León D, Pasin F, Zhao M. Methyltransferase-like (METTL) homologues participate in Nicotiana benthamiana antiviral responses. PLANT SIGNALING & BEHAVIOR 2023; 18:2214760. [PMID: 37210738 DOI: 10.1080/15592324.2023.2214760] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/23/2023]
Abstract
Methyltransferase (MTase) enzymes catalyze the addition of a methyl group to a variety of biological substrates. MTase-like (METTL) proteins are Class I MTases whose enzymatic activities contribute to the epigenetic and epitranscriptomic regulation of multiple cellular processes. N6-adenosine methylation (m6A) is a common chemical modification of eukaryotic and viral RNA whose abundance is jointly regulated by MTases and METTLs, demethylases, and m6A binding proteins. m6A affects various cellular processes including RNA degradation, post-transcriptional processing, and antiviral immunity. Here, we used Nicotiana benthamiana and plum pox virus (PPV), an RNA virus of the Potyviridae family, to investigated the roles of MTases in plant-virus interaction. RNA sequencing analysis identified MTase transcripts that are differentially expressed during PPV infection; among these, accumulation of a METTL gene was significantly downregulated. Two N. benthamiana METTL transcripts (NbMETTL1 and NbMETTL2) were cloned and further characterized. Sequence and structural analyses of the two encoded proteins identified a conserved S-adenosyl methionine (SAM) binding domain, showing they are SAM-dependent MTases phylogenetically related to human METTL16 and Arabidopsis thaliana FIONA1. Overexpression of NbMETTL1 and NbMETTL2 caused a decrease of PPV accumulation. In sum, our results indicate that METTL homologues participate in plant antiviral responses.
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Affiliation(s)
- Jianying Yue
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yan Lu
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhenqi Sun
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuqing Guo
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - David San León
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Fabio Pasin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València (CSIC-UPV), Valencia, Spain
| | - Mingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
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13
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Lyu Z, Genereux JC. Quantitative Measurement of Transthyretin Mistargeting by Proximity Labeling and Parallel Reaction Monitoring. FRONTIERS IN CHEMICAL BIOLOGY 2023; 2:1288188. [PMID: 38173467 PMCID: PMC10764115 DOI: 10.3389/fchbi.2023.1288188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Proximity labeling is a powerful approach for characterizing subcellular proteomes. We recently demonstrated that proximity labeling can be used to identify mistrafficking of secretory proteins, such as occurs during pre-emptive quality control (pre-QC) following endoplasmic reticulum (ER) stress. This assay depends on protein quantification by immunoblotting and densitometry, which sometimes suffers from poor sensitivity. Here, we integrate parallel reaction monitoring (PRM) mass spectrometry to enable a more quantitative platform, and assess how chemical ER stressors impact pre-QC of the model secretory protein transthyretin in HEK293T cells. We find that some drug treatments affect labeling efficiency, which can be controlled for by normalizing to APEX2 auto-labeling. While some chemical ER stress inducers including Brefeldin A and thapsigargin induce pre-QC, tunicamycin and dithiothreitol do not, indicating ER stress alone is not sufficient. This finding contrasts with the canonical model of pre-QC induction, and establishes the utility of our platform.
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Affiliation(s)
- Ziqi Lyu
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Joseph C. Genereux
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
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14
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Lyu Z, Genereux JC. Quantitative Measurement of Secretory Protein Mistargeting by Proximity Labeling and Parallel Reaction Monitoring. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.19.549095. [PMID: 37503147 PMCID: PMC10370094 DOI: 10.1101/2023.07.19.549095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Proximity labeling is a powerful approach for characterizing subcellular proteomes. We recently demonstrated that proximity labeling can be used to identify mistrafficking of secretory proteins, such as occurs during pre-emptive quality control (pre-QC) following endoplasmic reticulum (ER) stress. This assay depends on protein quantification by immunoblotting and densitometry, which is only semi-quantitative and suffers from poor sensitivity. Here, we integrate parallel reaction monitoring mass spectrometry to enable a more quantitative platform for ER import. PRM as opposed to densitometry improves quantification of transthyretin mistargeting while also achieving at least a ten-fold gain in sensitivity. The multiplexing of PRM also enabled us to evaluate a series of normalization approaches, revealing that normalization to auto-labeled APEX2 peroxidase is necessary to account for drug treatment-dependent changes in labeling efficiency. We apply this approach to systematically characterize the relationship between chemical ER stressors and ER pre-QC induction in HEK293T cells. Using dual-FLAG-tagged transthyretin (FLAGTTR) as a model secretory protein, we find that Brefeldin A treatment as well as ER calcium depletion cause pre-QC, while tunicamycin and dithiothreitol do not, indicating ER stress alone is not sufficient. This finding contrasts with the canonical model of pre-QC induction, and establishes the utility of our platform.
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Affiliation(s)
- Ziqi Lyu
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521
| | - Joseph C. Genereux
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521
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15
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Abe JI, Imanishi M, Li S, Zhang A, Ae Ko K, Samanthapudi VSK, Lee LL, Bojorges AP, Gi YJ, Hobbs BP, Deswal A, Herrmann J, Lin SH, Chini EN, Shen YH, Schadler KL, Nguyen THM, Gupte AA, Reyes-Gibby C, Yeung SCJ, Abe RJ, Olmsted-Davis EA, Krishnan S, Dantzer R, Palaskas NL, Cooke JP, Pownall HJ, Yoshimoto M, Fujiwara K, Hamilton DJ, Burks JK, Wang G, Le NT, Kotla S. An ERK5-NRF2 Axis Mediates Senescence-Associated Stemness and Atherosclerosis. Circ Res 2023; 133:25-44. [PMID: 37264926 PMCID: PMC10357365 DOI: 10.1161/circresaha.122.322017] [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: 09/20/2022] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND ERK5 (extracellular signal-regulated kinase 5) is a dual kinase transcription factor containing an N-terminal kinase domain and a C-terminal transcriptional activation domain. Many ERK5 kinase inhibitors have been developed and tested to treat cancer and inflammatory diseases. However, recent data have raised questions about the role of the catalytic activity of ERK5 in proliferation and inflammation. We aimed to investigate how ERK5 reprograms myeloid cells to the proinflammatory senescent phenotype, subsequently leading to atherosclerosis. METHODS A ERK5 S496A (dephosphorylation mimic) knock in (KI) mouse model was generated using CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeat-associated 9), and atherosclerosis was characterized by hypercholesterolemia induction. The plaque phenotyping in homozygous ERK5 S496A KI and wild type (WT) mice was studied using imaging mass cytometry. Bone marrow-derived macrophages were isolated from hypercholesterolemic mice and characterized using RNA sequencing and functional in vitro approaches, including senescence, mitochondria reactive oxygen species, and inflammation assays, as well as by metabolic extracellular flux analysis. RESULTS We show that atherosclerosis was inhibited in ERK5 S496A KI mice. Furthermore, ERK5 S496 phosphorylation mediates both senescence-associated secretory phenotype and senescence-associated stemness by upregulating AHR (aryl hydrocarbon receptor) in plaque and bone marrow-derived macrophages isolated from hypercholesterolemic mice. We also discovered that ERK5 S496 phosphorylation could induce NRF2 (NFE2-related factor 2) SUMOylation at a novel K518 site to inhibit NRF2 transcriptional activity without altering ERK5 catalytic activity and mediates oxidized LDL (low-density lipoprotein)-induced senescence-associated secretory phenotype. Specific ERK5 kinase inhibitors (AX15836 and XMD8-92) also inhibited ERK5 S496 phosphorylation, suggesting the involvement of ERK5 S496 phosphorylation in the anti-inflammatory effects of these ERK5 kinase inhibitors. CONCLUSIONS We discovered a novel mechanism by which the macrophage ERK5-NRF2 axis develops a unique senescence-associated secretory phenotype/stemness phenotype by upregulating AHR to engender atherogenesis. The finding of senescence-associated stemness phenotype provides a molecular explanation to resolve the paradox of senescence in proliferative plaque by permitting myeloid cells to escape the senescence-induced cell cycle arrest during atherosclerosis formation.
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Affiliation(s)
- Jun-ichi Abe
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- These authors contributed equally to this work and were designated as co-first authors
| | - Masaki Imanishi
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- These authors contributed equally to this work and were designated as co-first authors
| | - Shengyu Li
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
- These authors contributed equally to this work and were designated as co-first authors
| | - Aijun Zhang
- Center for Bioenergetics, Houston Methodist Research Institute, Texas, and Department of Medicine, Houston Methodist, Weill Cornell Medicine Affiliate, Houston, Texas, USA
| | - Kyung Ae Ko
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Ling-Ling Lee
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Young Jin Gi
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Brian P. Hobbs
- Department of Population Health, The University of Texas at Austin, Austin, Texas, USA
| | - Anita Deswal
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Joerg Herrmann
- Cardio Oncology Clinic, Division of Preventive Cardiology, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Steven H. Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Eduardo N. Chini
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Jacksonville, Florida, USA
| | - Ying H. Shen
- Division of Cardiothoracic Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Keri L. Schadler
- Department of Pediatric Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Thi-Hong-Minh Nguyen
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
| | - Anisha A. Gupte
- Center for Bioenergetics, Houston Methodist Research Institute, Texas, and Department of Medicine, Houston Methodist, Weill Cornell Medicine Affiliate, Houston, Texas, USA
| | - Cielito Reyes-Gibby
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sai-Ching J. Yeung
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rei J. Abe
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
| | | | - Sunil Krishnan
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Robert Dantzer
- Department of Symptom Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nicolas L. Palaskas
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - John P. Cooke
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
| | - Henry J. Pownall
- Center for Bioenergetics, Houston Methodist Research Institute, Texas, and Department of Medicine, Houston Methodist, Weill Cornell Medicine Affiliate, Houston, Texas, USA
| | - Momoko Yoshimoto
- Center for Stem Cell & Regenerative Medicine, Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Keigi Fujiwara
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dale J. Hamilton
- Center for Bioenergetics, Houston Methodist Research Institute, Texas, and Department of Medicine, Houston Methodist, Weill Cornell Medicine Affiliate, Houston, Texas, USA
- These authors contributed equally to this work
| | - Jared K. Burks
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- These authors contributed equally to this work
| | - Guangyu Wang
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
- These authors were equivalent co-senior authors
| | - Nhat-Tu Le
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
- These authors were equivalent co-senior authors
| | - Sivareddy Kotla
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- These authors were equivalent co-senior authors
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16
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Rees PA, Lowy RJ. Optimizing reduction of western blotting analytical variations: Use of replicate test samples, multiple normalization methods, and sample loading positions. Anal Biochem 2023:115198. [PMID: 37302777 DOI: 10.1016/j.ab.2023.115198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 06/13/2023]
Abstract
Western blot (WB) analysis is widely used, but obtaining consistent results can be problematic, especially when using multiple gels. This study examines WB performance by explicitly applying a method commonly used to test analytical instrumentation. Test samples were lysates from RAW 264.7 murine macrophages treated with LPS to activate MAPK and NF-kB signaling targets. Samples from the pooled cell lysates placed in every lane on multiple gels were analyzed by WBs for levels of p-ERK, ERK, IkBβ and non-target protein. Different normalization methods and sample groupings were applied to the density values and the resulting coefficients of variation (CV) and ratios of maximal to minimal values (Max/Min) were compared. Ideally with identical sample replicates the CVs would be 0 and the Max/Min 1; deviation indicating introduction of variability by the WB process. Common normalizations to reduce analytical variance, total lane protein, % Control, and p-ERK/ERK ratios, did not have the lowest CVs or Max/Min values. Normalization using the sum of target protein values combined with analytical replication most effectively reduced variability, resulting CV and Max/Min values as low as 5-10% and 1.1. These methods should allow reliable interpretation of complex experiments that require samples to be placed on multiple gels.
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Affiliation(s)
- Phyllis A Rees
- Scientific Research Department, Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - R Joel Lowy
- Scientific Research Department, Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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17
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Hayward DA, Vanes L, Wissmann S, Sivapatham S, Hartweger H, Biggs O’May J, de Boer LL, Mitter R, Köchl R, Stein JV, Tybulewicz VL. B cell-intrinsic requirement for WNK1 kinase in antibody responses in mice. J Exp Med 2023; 220:e20211827. [PMID: 36662229 PMCID: PMC9872328 DOI: 10.1084/jem.20211827] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/20/2022] [Accepted: 12/23/2022] [Indexed: 01/21/2023] Open
Abstract
Migration and adhesion play critical roles in B cells, regulating recirculation between lymphoid organs, migration within lymphoid tissue, and interaction with CD4+ T cells. However, there is limited knowledge of how B cells integrate chemokine receptor and integrin signaling with B cell activation to generate efficient humoral responses. Here, we show that the WNK1 kinase, a regulator of migration and adhesion, is essential in B cells for T-dependent and -independent antibody responses. We demonstrate that WNK1 transduces signals from the BCR, CXCR5, and CD40, and using intravital imaging, we show that WNK1 regulates migration of naive and activated B cells, and their interactions with T cells. Unexpectedly, we show that WNK1 is required for BCR- and CD40-induced proliferation, acting through the OXSR1 and STK39 kinases, and for efficient B cell-T cell collaboration in vivo. Thus, WNK1 is critical for humoral immune responses, by regulating B cell migration, adhesion, and T cell-dependent activation.
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Affiliation(s)
| | | | - Stefanie Wissmann
- Department of Oncology, Microbiology and Immunology, University of Fribourg, Fribourg, Switzerland
| | - Sujana Sivapatham
- Department of Oncology, Microbiology and Immunology, University of Fribourg, Fribourg, Switzerland
| | | | | | | | | | | | - Jens V. Stein
- Department of Oncology, Microbiology and Immunology, University of Fribourg, Fribourg, Switzerland
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Redundant and Specific Roles of A-Type Lamins and Lamin B Receptor in Herpes Simplex Virus 1 Infection. J Virol 2022; 96:e0142922. [PMID: 36448808 PMCID: PMC9769381 DOI: 10.1128/jvi.01429-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
We investigated whether A-type lamins (lamin A/C) and lamin B receptor (LBR) are redundant during herpes simplex virus 1 (HSV-1) infection in HeLa cells expressing lamin A/C and LBR. Lamin A/C and LBR double knockout (KO) in HSV-1-infected HeLa cells significantly impaired expressions of HSV-1 early and late genes, maturation of replication compartments, marginalization of host chromatin to the nuclear periphery, enlargement of host cell nuclei, and viral DNA replication. Phenotypes of HSV-1-infected HeLa cells were restored by the ectopic expression of lamin A/C or LBR in lamin A/C and LBR double KO cells. Of note, lamin A/C single KO, but not LBR single KO, promoted the aberrant accumulation of virus particles outside the inner nuclear membrane (INM) and viral replication, as well as decreasing the frequency of virus particles inside the INM without affecting viral gene expression and DNA replication, time-spatial organization of replication compartments and host chromatin, and nuclear enlargement. These results indicated that lamin A/C and LBR had redundant and specific roles during HSV-1 infection. Thus, lamin A/C and LBR redundantly regulated the dynamics of the nuclear architecture, including the time-spatial organization of replication compartments and host chromatin, as well as promoting nuclear enlargement for efficient HSV-1 gene expression and DNA replication. In contrast, lamin A/C inhibited HSV-1 nuclear export through the INM during viral nuclear egress, which is a unique property of lamin A/C. IMPORTANCE This study demonstrated that lamin A/C and LBR had redundant functions associated with HSV-1 gene expression and DNA replication by regulating the dynamics of the nuclear architecture during HSV-1 infection. This is the first report to demonstrate the redundant roles of lamin A/C and LBR as well as the involvement of LBR in the regulation of these viral and cellular features in HSV-1-infected cells. These findings provide evidence for the specific property of lamin A/C to inhibit HSV-1 nuclear egress, which has long been considered but without direct proof.
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19
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Unaffected Li-Fraumeni Syndrome Carrier Parent Demonstrates Allele-Specific mRNA Stabilization of Wild-Type TP53 Compared to Affected Offspring. Genes (Basel) 2022; 13:genes13122302. [PMID: 36553570 PMCID: PMC9778056 DOI: 10.3390/genes13122302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/02/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Li-Fraumeni Syndrome (LFS) is an autosomal dominant disorder where an oncogenic TP53 germline mutation is inherited by offspring of a carrier parent. p53 is a key tumor suppressor regulating cell cycle arrest in response to DNA damage. Unexpectedly, some mutant TP53 carriers remain unaffected, while their children develop cancer early in life. To begin unravelling this paradox, the response of dermal fibroblasts (dFb) isolated from a child with LFS was compared to those from her unaffected father after UV exposure. Phospho-Chk1[S345], a key activator of cell cycle arrest, was increased by UV induction in the LFS patient compared to their unaffected parent dFb. This result, along with previous findings of reduced CDKN1A/p21 UV induction in affected dFb, suggest that cell cycle dysregulation may contribute to cancer onset in the affected LFS subject but not the unaffected parent. Mutant p53 protein and its promoter binding affinity were also higher in dFb from the LFS patient compared to their unaffected parent. These results were as predicted based on decreased mutant TP53 allele-specific mRNA expression previously found in unaffected dFb. Investigation of the potential mechanism regulating this TP53 allele-specific expression found that, while epigenetic promoter methylation was not detectable, TP53 wild-type mRNA was specifically stabilized in the unaffected dFb. Hence, the allele-specific stabilization of wild-type TP53 mRNA may allow an unaffected parent to counteract genotoxic stress by means more characteristic of homozygous wild-type TP53 individuals than their affected offspring, providing protection from the oncogenesis associated with LFS.
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20
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Bartels P, Salveson I, Coleman AM, Anderson DE, Jeng G, Estrada-Tobar ZM, Man KNM, Yu Q, Kuzmenkina E, Nieves-Cintron M, Navedo MF, Horne MC, Hell JW, Ames JB. Half-calcified calmodulin promotes basal activity and inactivation of the L-type calcium channel Ca V1.2. J Biol Chem 2022; 298:102701. [PMID: 36395884 PMCID: PMC9764201 DOI: 10.1016/j.jbc.2022.102701] [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: 07/11/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022] Open
Abstract
The L-type Ca2+ channel CaV1.2 controls gene expression, cardiac contraction, and neuronal activity. Calmodulin (CaM) governs CaV1.2 open probability (Po) and Ca2+-dependent inactivation (CDI) but the mechanisms remain unclear. Here, we present electrophysiological data that identify a half Ca2+-saturated CaM species (Ca2/CaM) with Ca2+ bound solely at the third and fourth EF-hands (EF3 and EF4) under resting Ca2+ concentrations (50-100 nM) that constitutively preassociates with CaV1.2 to promote Po and CDI. We also present an NMR structure of a complex between the CaV1.2 IQ motif (residues 1644-1665) and Ca2/CaM12', a calmodulin mutant in which Ca2+ binding to EF1 and EF2 is completely disabled. We found that the CaM12' N-lobe does not interact with the IQ motif. The CaM12' C-lobe bound two Ca2+ ions and formed close contacts with IQ residues I1654 and Y1657. I1654A and Y1657D mutations impaired CaM binding, CDI, and Po, as did disabling Ca2+ binding to EF3 and EF4 in the CaM34 mutant when compared to WT CaM. Accordingly, a previously unappreciated Ca2/CaM species promotes CaV1.2 Po and CDI, identifying Ca2/CaM as an important mediator of Ca signaling.
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Affiliation(s)
- Peter Bartels
- Department of Pharmacology, University of California, Davis, California, USA
| | - Ian Salveson
- Department of Chemistry, University of California, Davis, California, USA
| | - Andrea M Coleman
- Department of Pharmacology, University of California, Davis, California, USA; Department of Chemistry, University of California, Davis, California, USA
| | - David E Anderson
- Department of Chemistry, University of California, Davis, California, USA
| | - Grace Jeng
- Department of Pharmacology, University of California, Davis, California, USA
| | | | - Kwun Nok Mimi Man
- Department of Pharmacology, University of California, Davis, California, USA
| | - Qinhong Yu
- Department of Chemistry, University of California, Davis, California, USA
| | - Elza Kuzmenkina
- Center for Pharmacology, University of Cologne, Cologne, Germany
| | | | - Manuel F Navedo
- Department of Pharmacology, University of California, Davis, California, USA
| | - Mary C Horne
- Department of Pharmacology, University of California, Davis, California, USA.
| | - Johannes W Hell
- Department of Pharmacology, University of California, Davis, California, USA.
| | - James B Ames
- Department of Chemistry, University of California, Davis, California, USA.
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21
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Thomaseth C, Radde NE. The effect of normalisation and error model choice on the distribution of the maximum likelihood estimator for a biochemical reaction. IET Syst Biol 2022; 17:1-13. [PMID: 36440585 PMCID: PMC9931059 DOI: 10.1049/syb2.12055] [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: 09/29/2021] [Revised: 09/13/2022] [Accepted: 11/08/2022] [Indexed: 11/29/2022] Open
Abstract
Sparse and noisy measurements make parameter estimation for biochemical reaction networks difficult and might lead to ill-posed optimisation problems. This is potentiated if the data has to be normalised, and only fold changes rather than absolute amounts are available. Here, the authors consider the propagation of measurement noise to the distribution of the maximum likelihood (ML) estimator in an in silico study. Therefore, a model of a reversible reaction is considered, for which reaction rate constants using fold changes is estimated. Noise propagation is analysed for different normalisation strategies and different error models. In particular, accuracy, precision, and asymptotic properties of the ML estimator is investigated. Results show that normalisation by the mean of a time series outperforms normalisation by a single time point in the example provided by the authors. Moreover, the error model with a heavy-tail distribution is slightly more robust to large measurement noise, but, beyond this, the choice of the error model did not have a significant impact on the estimation results provided by the authors.
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Affiliation(s)
- Caterina Thomaseth
- University of StuttgartInstitute for Systems Theory and Automatic ControlD‐70569 StuttgartGermany
| | - Nicole E. Radde
- University of StuttgartInstitute for Systems Theory and Automatic ControlD‐70569 StuttgartGermany
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22
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A critical path to producing high quality, reproducible data from quantitative western blot experiments. Sci Rep 2022; 12:17599. [PMID: 36266411 PMCID: PMC9585080 DOI: 10.1038/s41598-022-22294-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 10/12/2022] [Indexed: 01/13/2023] Open
Abstract
Western blotting experiments were initially performed to detect a target protein in a complex biological sample and more recently, to measure relative protein abundance. Chemiluminescence coupled with film-based detection was traditionally the gold standard for western blotting but accurate and reproducible quantification has been a major challenge from this methodology. The development of sensitive, camera-based detection technologies coupled with an updated technical approach permits the production of reproducible, quantitative data. Fluorescence reagent and detection solutions are the latest innovation in western blotting but there remains questions and debate concerning their relative sensitivity and dynamic range versus chemiluminescence. A methodology to optimize and produce excellent, quantitative western blot results with rigorous data analysis from membranes probed with both fluorescent and chemiluminescent antibodies is described. The data reveal when and how to apply these detection methods to achieve reproducible data with a stepwise approach to data processing for quantitative analysis.
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23
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Zhang Y, Grimwood AL, Hancox JC, Harmer SC, Dempsey CE. Evolutionary coupling analysis guides identification of mistrafficking-sensitive variants in cardiac K + channels: Validation with hERG. Front Pharmacol 2022; 13:1010119. [PMID: 36339618 PMCID: PMC9632996 DOI: 10.3389/fphar.2022.1010119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/30/2022] [Indexed: 09/27/2023] Open
Abstract
Loss of function (LOF) mutations of voltage sensitive K+ channel proteins hERG (Kv11.1) and KCNQ1 (Kv7.1) account for the majority of instances of congenital Long QT Syndrome (cLQTS) with the dominant molecular phenotype being a mistrafficking one resulting from protein misfolding. We explored the use of Evolutionary Coupling (EC) analysis, which identifies evolutionarily conserved pairwise amino acid interactions that may contribute to protein structural stability, to identify regions of the channels susceptible to misfolding mutations. Comparison with published experimental trafficking data for hERG and KCNQ1 showed that the method strongly predicts "scaffolding" regions of the channel membrane domains and has useful predictive power for trafficking phenotypes of individual variants. We identified a region in and around the cytoplasmic S2-S3 loop of the hERG Voltage Sensor Domain (VSD) as susceptible to destabilising mutation, and this was confirmed using a quantitative LI-COR ® based trafficking assay that showed severely attenuated trafficking in eight out of 10 natural hERG VSD variants selected using EC analysis. Our analysis highlights an equivalence in the scaffolding structures of the hERG and KCNQ1 membrane domains. Pathogenic variants of ion channels with an underlying mistrafficking phenotype are likely to be located within similar scaffolding structures that are identifiable by EC analysis.
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Affiliation(s)
- Yihong Zhang
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences Building, University Walk, Bristol, United Kingdom
| | - Amy L. Grimwood
- School of Biological Sciences, Life Sciences Building, Bristol, United Kingdom
| | - Jules C. Hancox
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences Building, University Walk, Bristol, United Kingdom
| | - Stephen C. Harmer
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences Building, University Walk, Bristol, United Kingdom
| | - Christopher E. Dempsey
- School of Biochemistry, Biomedical Sciences Building, University Walk, Bristol, United Kingdom
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24
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Stain-Free total-protein normalization enhances the reproducibility of Western blot data. Anal Biochem 2022; 654:114840. [PMID: 35931182 DOI: 10.1016/j.ab.2022.114840] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 12/15/2022]
Abstract
We compared the accuracy of three common methods of total protein normalization. The Stain-Free method was accurate across different types/brands of western blotting membrane and for various protein loads, unlike Ponceau S and Amido Black. Normalizing to the housekeeping proteins Actin and β-Tubulin could match the accuracy of the Stain-Free method. However, compared to Actin or β-Tubulin, normalizing to the Stain-Free signal reduced variability that led to enhanced reproducibility and a reduction in the number of samples needed to obtain statistically significant results by >50%. Stain-Free normalization can enhance the reproducibility and hence the confidence in Western Blot data.
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25
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Krchniakova M, Paukovcekova S, Chlapek P, Neradil J, Skoda J, Veselska R. Thiosemicarbazones and selected tyrosine kinase inhibitors synergize in pediatric solid tumors: NDRG1 upregulation and impaired prosurvival signaling in neuroblastoma cells. Front Pharmacol 2022; 13:976955. [PMID: 36160437 PMCID: PMC9490180 DOI: 10.3389/fphar.2022.976955] [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: 06/23/2022] [Accepted: 08/01/2022] [Indexed: 11/21/2022] Open
Abstract
Tyrosine kinase inhibitors (TKIs) are frequently used in combined therapy to enhance treatment efficacy and overcome drug resistance. The present study analyzed the effects of three inhibitors, sunitinib, gefitinib, and lapatinib, combined with iron-chelating agents, di-2-pyridylketone-4,4-dimethyl-3-thiosemicarbazone (Dp44mT) or di-2-pyridylketone-4-cyclohexyl-4-methyl-3-thiosemicarbazone (DpC). Simultaneous administration of the drugs consistently resulted in synergistic and/or additive activities against the cell lines derived from the most frequent types of pediatric solid tumors. The results of a detailed analysis of cell signaling in the neuroblastoma cell lines revealed that TKIs inhibited the phosphorylation of the corresponding receptor tyrosine kinases, and thiosemicarbazones downregulated the expression of epidermal growth factor receptor, platelet-derived growth factor receptor, and insulin-like growth factor-1 receptor, leading to a strong induction of apoptosis. Marked upregulation of the metastasis suppressor N-myc downstream regulated gene-1 (NDRG1), which is known to be activated and upregulated by thiosemicarbazones in adult cancers, was also detected in thiosemicarbazone-treated neuroblastoma cells. Importantly, these effects were more pronounced in the cells treated with drug combinations, especially with the combinations of lapatinib with thiosemicarbazones. Therefore, these results provide a rationale for novel strategies combining iron-chelating agents with TKIs in therapy of pediatric solid tumors.
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Affiliation(s)
- Maria Krchniakova
- Laboratory of Tumor Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
- International Clinical Research Center, St. Anne’s University Hospital, Brno, Czechia
| | - Silvia Paukovcekova
- Laboratory of Tumor Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Petr Chlapek
- Laboratory of Tumor Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
- International Clinical Research Center, St. Anne’s University Hospital, Brno, Czechia
| | - Jakub Neradil
- Laboratory of Tumor Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
- International Clinical Research Center, St. Anne’s University Hospital, Brno, Czechia
| | - Jan Skoda
- Laboratory of Tumor Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
- International Clinical Research Center, St. Anne’s University Hospital, Brno, Czechia
- *Correspondence: Jan Skoda, ; Renata Veselska,
| | - Renata Veselska
- Laboratory of Tumor Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
- International Clinical Research Center, St. Anne’s University Hospital, Brno, Czechia
- *Correspondence: Jan Skoda, ; Renata Veselska,
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26
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Kroon C, Breuer L, Jones L, An J, Akan A, Mohamed Ali EA, Busch F, Fislage M, Ghosh B, Hellrigel-Holderbaum M, Kazezian V, Koppold A, Moreira Restrepo CA, Riedel N, Scherschinski L, Urrutia Gonzalez FR, Weissgerber TL. Blind spots on western blots: Assessment of common problems in western blot figures and methods reporting with recommendations to improve them. PLoS Biol 2022; 20:e3001783. [PMID: 36095010 PMCID: PMC9518894 DOI: 10.1371/journal.pbio.3001783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/28/2022] [Accepted: 08/04/2022] [Indexed: 11/18/2022] Open
Abstract
Western blotting is a standard laboratory method used to detect proteins and assess their expression levels. Unfortunately, poor western blot image display practices and a lack of detailed methods reporting can limit a reader's ability to evaluate or reproduce western blot results. While several groups have studied the prevalence of image manipulation or provided recommendations for improving western blotting, data on the prevalence of common publication practices are scarce. We systematically examined 551 articles published in the top 25% of journals in neurosciences (n = 151) and cell biology (n = 400) that contained western blot images, focusing on practices that may omit important information. Our data show that most published western blots are cropped and blot source data are not made available to readers in the supplement. Publishing blots with visible molecular weight markers is rare, and many blots additionally lack molecular weight labels. Western blot methods sections often lack information on the amount of protein loaded on the gel, blocking steps, and antibody labeling protocol. Important antibody identifiers like company or supplier, catalog number, or RRID were omitted frequently for primary antibodies and regularly for secondary antibodies. We present detailed descriptions and visual examples to help scientists, peer reviewers, and editors to publish more informative western blot figures and methods. Additional resources include a toolbox to help scientists produce more reproducible western blot data, teaching slides in English and Spanish, and an antibody reporting template.
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Affiliation(s)
- Cristina Kroon
- Institute of Molecular Biology and Biochemistry, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Larissa Breuer
- German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Lydia Jones
- Berlin School of Public Health, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Jeehye An
- Berlin School of Mind and Brain, Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Experimental Neurology and Center for Stroke Research, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Ayça Akan
- Berlin School of Mind and Brain, Humboldt-Universität zu Berlin, Berlin, Germany
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | | | - Felix Busch
- Department of Radiology, Charité–Universitätsmedizin Berlin, Berlin, Germany
- Department of Anesthesiology and Intensive Care Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Marinus Fislage
- Department of Anesthesiology and Intensive Care Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Biswajit Ghosh
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Max Hellrigel-Holderbaum
- Berlin School of Mind and Brain, Humboldt-Universität zu Berlin, Berlin, Germany
- Interdisciplinary Center of Sleep Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Vartan Kazezian
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Berlin, Germany
- Department of Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Alina Koppold
- Institute for Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Nico Riedel
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Lea Scherschinski
- Department of Neurosurgery, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Fernando Raúl Urrutia Gonzalez
- Berlin School of Public Health, Charité–Universitätsmedizin Berlin, Berlin, Germany
- Institute of Public Health, Charité–Universitätsmedizin Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Tracey L. Weissgerber
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Berlin, Germany
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27
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Zadeh C, Huggins JR, Sarmah D, Westbury BC, Interiano WR, Jordan MC, Phillips SA, Dodd WB, Meredith WO, Harold NJ, Erdem C, Birtwistle MR. Mesowestern Blot: Simultaneous Analysis of Hundreds of Submicroliter Lysates. ACS OMEGA 2022; 7:28912-28923. [PMID: 36033686 PMCID: PMC9404195 DOI: 10.1021/acsomega.2c02201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Western blotting is a widely used technique for molecular-weight-resolved analysis of proteins and their posttranslational modifications, but high-throughput implementations of the standard slab gel arrangement are scarce. The previously developed Microwestern requires a piezoelectric pipetting instrument, which is not available for many labs. Here, we report the Mesowestern blot, which uses a 3D-printable gel casting mold to enable high-throughput Western blotting without piezoelectric pipetting and is compatible with the standard sample preparation and small (∼1 μL) sample sizes. The main tradeoffs are reduced molecular weight resolution and higher sample-to-sample CV, making it suitable for qualitative screening applications. The casted polyacrylamide gel contains 336, ∼0.5 μL micropipette-loadable sample wells arranged within a standard microplate footprint. Polyacrylamide % can be altered to change molecular weight resolution profiles. Proof-of-concept experiments using both infrared-fluorescent molecular weight protein ladder and cell lysate (RIPA buffer) demonstrate that the protein loaded in Mesowestern gels is amenable to the standard Western blotting steps. The main difference between Mesowestern and traditional Western is that semidry horizontal instead of immersed vertical gel electrophoresis is used. The linear range of detection is at least 32-fold, and at least ∼500 attomols of β-actin can be detected (∼29 ng of total protein from mammalian cell lysates: ∼100-300 cells). Because the gel mold is 3D-printable, users with access to additive manufacturing cores have significant design freedom for custom layouts. We expect that the technique could be easily adopted by any typical cell and molecular biology laboratory already performing Western blots.
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Affiliation(s)
- Cameron
O. Zadeh
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Jonah R. Huggins
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Deepraj Sarmah
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Baylee C. Westbury
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - William R. Interiano
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Micah C. Jordan
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - S. Ashley Phillips
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - William B. Dodd
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Wesley O. Meredith
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Nicholas J. Harold
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Cemal Erdem
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Marc R. Birtwistle
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
- Department
of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
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28
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Tosolini AP, Sleigh JN, Surana S, Rhymes ER, Cahalan SD, Schiavo G. BDNF-dependent modulation of axonal transport is selectively impaired in ALS. Acta Neuropathol Commun 2022; 10:121. [PMID: 35996201 PMCID: PMC9396851 DOI: 10.1186/s40478-022-01418-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 02/08/2023] Open
Abstract
Axonal transport ensures long-range delivery of essential cargoes between proximal and distal compartments, and is needed for neuronal development, function, and survival. Deficits in axonal transport have been detected at pre-symptomatic stages in the SOD1G93A and TDP-43M337V mouse models of amyotrophic lateral sclerosis (ALS), suggesting that impairments in this critical process are fundamental for disease pathogenesis. Strikingly, in ALS, fast motor neurons (FMNs) degenerate first whereas slow motor neurons (SMNs) are more resistant, and this is a currently unexplained phenomenon. The main aim of this investigation was to determine the effects of brain-derived neurotrophic factor (BDNF) on in vivo axonal transport in different α-motor neuron (MN) subtypes in wild-type (WT) and SOD1G93A mice. We report that despite displaying similar basal transport speeds, stimulation of wild-type MNs with BDNF enhances in vivo trafficking of signalling endosomes specifically in FMNs. This BDNF-mediated enhancement of transport was also observed in primary ventral horn neuronal cultures. However, FMNs display selective impairment of axonal transport in vivo in symptomatic SOD1G93A mice, and are refractory to BDNF stimulation, a phenotype that was also observed in primary embryonic SOD1G93A neurons. Furthermore, symptomatic SOD1G93A mice display upregulation of the classical non-pro-survival truncated TrkB and p75NTR receptors in muscles, sciatic nerves, and Schwann cells. Altogether, these data indicate that cell- and non-cell autonomous BDNF signalling is impaired in SOD1G93A MNs, thus identifying a new key deficit in ALS.
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Affiliation(s)
- Andrew P Tosolini
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
- UCL Queen Square Motor Neuron Disease Centre, University College London, London, WC1N 3BG, UK.
| | - James N Sleigh
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- UCL Queen Square Motor Neuron Disease Centre, University College London, London, WC1N 3BG, UK
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK
| | - Sunaina Surana
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- UCL Queen Square Motor Neuron Disease Centre, University College London, London, WC1N 3BG, UK
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK
| | - Elena R Rhymes
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- UCL Queen Square Motor Neuron Disease Centre, University College London, London, WC1N 3BG, UK
| | - Stephen D Cahalan
- Comparative Neuromuscular Disease Laboratory, Department of Clinical Sciences and Services, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - Giampietro Schiavo
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
- UCL Queen Square Motor Neuron Disease Centre, University College London, London, WC1N 3BG, UK.
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK.
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29
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BlotIt—Optimal alignment of Western blot and qPCR experiments. PLoS One 2022; 17:e0264295. [PMID: 35947551 PMCID: PMC9365137 DOI: 10.1371/journal.pone.0264295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 07/04/2022] [Indexed: 11/20/2022] Open
Abstract
Biological systems are frequently analyzed by means of mechanistic mathematical models. In order to infer model parameters and provide a useful model that can be employed for systems understanding and hypothesis testing, the model is often calibrated on quantitative, time-resolved data. To do so, it is typically important to compare experimental measurements over broad time ranges and various experimental conditions, e.g. perturbations of the biological system. However, most of the established experimental techniques such as Western blot, or quantitative real-time polymerase chain reaction only provide measurements on a relative scale, since different sample volumes, experimental adjustments or varying development times of a gel lead to systematic shifts in the data. In turn, the number of measurements corresponding to the same scale enabling comparability is limited. Here, we present a new flexible method to align measurement data that obeys different scaling factors and compare it to existing normalization approaches. We propose an alignment model to estimate these scaling factors and provide the possibility to adapt this model depending on the measurement technique of interest. In addition, an error model can be specified to adequately weight the different data points and obtain scaling-model based confidence intervals of the finally scaled data points. Our approach is applicable to all sorts of relative measurements and does not need a particular experimental condition that has been measured over all available scales. An implementation of the method is provided with the R package blotIt including refined ways of visualization.
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Evaluation of Normalization Approaches for Quantitative Analysis of Bile Acids in Human Feces. Metabolites 2022; 12:metabo12080723. [PMID: 36005595 PMCID: PMC9416035 DOI: 10.3390/metabo12080723] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/29/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022] Open
Abstract
Quantitative analysis of bile acids in human feces can potentially help to better understand the influence of the gut microbiome and diet on human health. Feces is a highly heterogeneous sample matrix, mainly consisting of water and indigestible solid material (as plant fibers) that show high inter-individual variability. To compare bile acid concentrations among different individuals, a reliable normalization approach is needed. Here, we compared the impact of three normalization approaches, namely sample wet weight, dry weight, and protein concentration, on the absolute concentrations of fecal bile acids. Bile acid concentrations were determined in 70 feces samples from healthy humans. Our data show that bile acid concentrations normalized by the three different approaches are substantially different for each individual sample. Fecal bile acid concentrations normalized by wet weight show the narrowest distribution. Therefore, our analysis will provide the basis for the selection of a suitable normalization approach for the quantitative analysis of bile acids in feces.
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Development of a Dual-Fluorescent-Reporter System in Clostridioides difficile Reveals a Division of Labor between Virulence and Transmission Gene Expression. mSphere 2022; 7:e0013222. [PMID: 35638354 PMCID: PMC9241537 DOI: 10.1128/msphere.00132-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The bacterial pathogen Clostridioides difficile causes gastroenteritis by producing toxins and transmits disease by making resistant spores. Toxin and spore production are energy-expensive processes that are regulated by multiple transcription factors in response to many environmental inputs. While toxin and sporulation genes are both induced in only a subset of C. difficile cells, the relationship between these two subpopulations remains unclear. To address whether C. difficile coordinates the generation of these subpopulations, we developed a dual-transcriptional-reporter system that allows toxin and sporulation gene expression to be simultaneously visualized at the single-cell level using chromosomally encoded mScarlet and mNeonGreen fluorescent transcriptional reporters. We then adapted an automated image analysis pipeline to quantify toxin and sporulation gene expression in thousands of individual cells under different medium conditions and in different genetic backgrounds. These analyses revealed that toxin and sporulation gene expression rarely overlap during growth on agar plates, whereas broth culture increases this overlap. Our results suggest that certain growth conditions promote a “division of labor” between transmission and virulence gene expression, highlighting how environmental inputs influence these subpopulations. Our data further suggest that the RstA transcriptional regulator skews the population to activate sporulation genes rather than toxin genes. Given that recent work has revealed population-wide heterogeneity for numerous cellular processes in C. difficile, we anticipate that our dual-reporter system will be broadly useful for determining the overlap between these subpopulations. IMPORTANCEClostridioides difficile is an important nosocomial pathogen that causes severe diarrhea by producing toxins and transmits disease by producing spores. While both processes are crucial for C. difficile disease, only a subset of cells express toxins and/or undergo sporulation. Whether C. difficile coordinates the subset of cells inducing these energy-expensive processes remains unknown. To address this question, we developed a dual-fluorescent-reporter system coupled with an automated image analysis pipeline to rapidly compare the expression of two genes of interest across thousands of cells. Using this system, we discovered that certain growth conditions, particularly growth on agar plates, induce a “division of labor” between toxin and sporulation gene expression. Since C. difficile exhibits phenotypic heterogeneity for numerous vital cellular processes, this novel dual-reporter system will enable future studies aimed at understanding how C. difficile coordinates various subpopulations throughout its infectious disease cycle.
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Godin P, Tsoi MF, Morin M, Gévry N, Boerboom D. The granulosa cell response to luteinizing hormone is partly mediated by YAP1-dependent induction of amphiregulin. Cell Commun Signal 2022; 20:72. [PMID: 35619099 PMCID: PMC9137176 DOI: 10.1186/s12964-022-00843-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/08/2022] [Indexed: 12/23/2022] Open
Abstract
Background The LH surge is a pivotal event that triggers multiple key ovarian processes including oocyte maturation, cumulus expansion, follicular wall rupture and luteinization of mural granulosa and theca cells. Recently, LH-dependent activation of the Hippo signaling pathway has been shown to be required for the differentiation of granulosa cells into luteal cells. Still, the precise interactions between Hippo and LH signaling in murine granulosa cells remain to be elucidated. Methods To detect the expression of effectors of the Hippo pathway, western blot, immunohistochemical and RT-qPCR analyses were performed on granulosa cells treated with LH in vitro or isolated from immature mice treated with eCG and hCG. Cultured granulosa cells were pretreated with pharmacologic inhibitors to identify the signaling pathways involved in Hippo regulation by LH. To study the roles of Yap1 and Taz in the regulation of the LH signaling cascade, RT-qPCR and microarray analyses were done on granulosa cells from Yap1f/f;Tazf/f mice treated with an adenovirus to drive cre expression. RT-qPCR was performed to evaluate YAP1 binding to the Areg promoter following chromatin immunoprecipitation of granulosa cells collected from mice prior to or 60 min following hCG treatment. Results Granulosa cells showed a transient increase in LATS1, YAP1 and TAZ phosphorylation levels in response to the ovulatory signal. This Hippo activation by LH was mediated by protein kinase A. Furthermore, Yap1 and Taz are required for the induction of several LH target genes such as Areg, Pgr and Ptgs2, and for the activation of the ERK1/2 pathway. Consistent with these results, there was a substantial overlap between genes that are upregulated by LH and those that are downregulated following loss of Yap1/Taz, highlighting a major role for Hippo in mediating LH actions in the ovulation process. Finally, we showed that there is a marked recruitment of YAP1 to the Areg promoter of granulosa cells in response to hCG stimulation. Conclusions Overall, these results indicate that Hippo collaborates with the cAMP/PKA and ERK1/2 pathways to participate in the precise regulation of the LH cascade, and that Areg, as a direct transcriptional target of YAP1, is involved in mediating its actions in the ovary. Video Abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-022-00843-1.
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Affiliation(s)
- Philippe Godin
- Centre de Recherche en Reproduction et Fertilité (CRRF), Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Mayra F Tsoi
- Centre de Recherche en Reproduction et Fertilité (CRRF), Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Martin Morin
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Nicolas Gévry
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Derek Boerboom
- Centre de Recherche en Reproduction et Fertilité (CRRF), Université de Montréal, Saint-Hyacinthe, QC, Canada.
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LTBP1 promotes fibrillin incorporation into the extracellular matrix. Matrix Biol 2022; 110:60-75. [PMID: 35452817 DOI: 10.1016/j.matbio.2022.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/12/2022] [Accepted: 04/16/2022] [Indexed: 12/23/2022]
Abstract
LTBP1 is a large extracellular matrix protein and an associated ligand of fibrillin-microfibrils. Knowledge of LTBP1 functions is largely limited to its role in targeting and sequestering TGFβ growth factors within the extracellular matrix, thereby regulating their bioavailability. However, the recent description of a wide spectrum of phenotypes in multiple tissues in patients harboring LTBP1 pathogenic variants suggests a multifaceted role of the protein in the homeostasis of connective tissues. To better understand the human pathology caused by LTBP1 deficiency it is important to investigate its functional role in extracellular matrix formation. In this study, we show that LTBP1 coordinates the incorporation of fibrillin-1 and -2 into the extracellular matrix in vitro. We also demonstrate that this function is differentially exerted by the two isoforms, the short and long forms of LTBP1. Thereby our findings uncover a novel TGFβ-independent LTBP1 function potentially contributing to the development of connective tissue disorders.
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Bijata M, Bączyńska E, Müller FE, Bijata K, Masternak J, Krzystyniak A, Szewczyk B, Siwiec M, Antoniuk S, Roszkowska M, Figiel I, Magnowska M, Olszyński KH, Wardak AD, Hogendorf A, Ruszczycki B, Gorinski N, Labus J, Stępień T, Tarka S, Bojarski AJ, Tokarski K, Filipkowski RK, Ponimaskin E, Wlodarczyk J. Activation of the 5-HT7 receptor and MMP-9 signaling module in the hippocampal CA1 region is necessary for the development of depressive-like behavior. Cell Rep 2022; 38:110532. [PMID: 35294881 DOI: 10.1016/j.celrep.2022.110532] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 10/31/2021] [Accepted: 02/25/2022] [Indexed: 12/13/2022] Open
Abstract
Major depressive disorder is a complex disease resulting from aberrant synaptic plasticity that may be caused by abnormal serotonergic signaling. Using a combination of behavioral, biochemical, and imaging methods, we analyze 5-HT7R/MMP-9 signaling and dendritic spine plasticity in the hippocampus in mice treated with the selective 5-HT7R agonist (LP-211) and in a model of chronic unpredictable stress (CUS)-induced depressive-like behavior. We show that acute 5-HT7R activation induces depressive-like behavior in mice in an MMP-9-dependent manner and that post mortem brain samples from human individuals with depression reveal increased MMP-9 enzymatic activity in the hippocampus. Both pharmacological activation of 5-HT7R and modulation of its downstream effectors as a result of CUS lead to dendritic spine elongation and decreased spine density in this region. Overall, the 5-HT7R/MMP-9 pathway is specifically activated in the CA1 subregion of the hippocampus during chronic stress and is crucial for inducing depressive-like behavior.
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Affiliation(s)
- Monika Bijata
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland; Cellular Neurophysiology, Center of Physiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.
| | - Ewa Bączyńska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland; The Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Franziska E Müller
- Cellular Neurophysiology, Center of Physiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Krystian Bijata
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland; Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Julia Masternak
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland
| | - Adam Krzystyniak
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland
| | - Bernadeta Szewczyk
- Maj Institute of Pharmacology, Department of Neurobiology, Polish Academy of Sciences, Smętna 12, 31-343 Cracow, Poland
| | - Marcin Siwiec
- Maj Institute of Pharmacology, Department of Physiology, Polish Academy of Sciences, Smętna 12, 31-343 Cracow, Poland
| | - Svitlana Antoniuk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland; Cellular Neurophysiology, Center of Physiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Matylda Roszkowska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland
| | - Izabela Figiel
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland
| | - Marta Magnowska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland
| | - Krzysztof H Olszyński
- Behavior and Metabolism Research Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Agnieszka D Wardak
- Behavior and Metabolism Research Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Adam Hogendorf
- Maj Institute of Pharmacology, Department of Medicinal Chemistry, Polish Academy of Sciences, Smętna 12, 31-343 Cracow, Poland
| | - Błażej Ruszczycki
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland
| | - Nataliya Gorinski
- Cellular Neurophysiology, Center of Physiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Josephine Labus
- Cellular Neurophysiology, Center of Physiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Tomasz Stępień
- Department of Neuropathology, Institute of Psychiatry and Neurology, Jana III Sobieskiego 9, 02-957 Warsaw, Poland
| | - Sylwia Tarka
- Department of Forensic Medicine, Medical University of Warsaw, Oczki 1, 02-007 Warsaw, Poland
| | - Andrzej J Bojarski
- Maj Institute of Pharmacology, Department of Medicinal Chemistry, Polish Academy of Sciences, Smętna 12, 31-343 Cracow, Poland
| | - Krzysztof Tokarski
- Maj Institute of Pharmacology, Department of Physiology, Polish Academy of Sciences, Smętna 12, 31-343 Cracow, Poland
| | - Robert K Filipkowski
- Behavior and Metabolism Research Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Evgeni Ponimaskin
- Cellular Neurophysiology, Center of Physiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Jakub Wlodarczyk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland.
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Imoto H, Yamashiro S, Okada M. A text-based computational framework for patient -specific modeling for classification of cancers. iScience 2022; 25:103944. [PMID: 35535207 PMCID: PMC9076893 DOI: 10.1016/j.isci.2022.103944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/03/2022] [Accepted: 02/14/2022] [Indexed: 02/07/2023] Open
Abstract
Patient heterogeneity precludes cancer treatment and drug development; hence, development of methods for finding prognostic markers for individual treatment is urgently required. Here, we present Pasmopy (Patient-Specific Modeling in Python), a computational framework for stratification of patients using in silico signaling dynamics. Pasmopy converts texts and sentences on biochemical systems into an executable mathematical model. Using this framework, we built a model of the ErbB receptor signaling network, trained in cultured cell lines, and performed in silico simulation of 377 patients with breast cancer using The Cancer Genome Atlas (TCGA) transcriptome datasets. The temporal dynamics of Akt, extracellular signal-regulated kinase (ERK), and c-Myc in each patient were able to accurately predict the difference in prognosis and sensitivity to kinase inhibitors in triple-negative breast cancer (TNBC). Our model applies to any type of signaling network and facilitates the network-based use of prognostic markers and prediction of drug response. A text file describing biochemical systems is converted into an executable model Patient-specific models incorporate individual gene expression profiles In silico signaling dynamics can be utilized as prognostic biomarkers Personalized kinetic models are capable of predicting potential drug targets
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Marko DM, Finch MS, Mohammad A, MacNeil AJ, Klentrou P, MacPherson REK. Post-Exercise Serum from Humans Influences the Biological Tug of War of APP Processing in Human Neuronal Cells. Am J Physiol Cell Physiol 2022; 322:C614-C623. [PMID: 35196169 DOI: 10.1152/ajpcell.00418.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Neurodegenerative diseases such as Alzheimer's disease (AD) are becoming more prevalent in our aging society. One specific neuropathological hallmark of this disease is the accumulation of amyloid-β (Aβ) peptides, which aggregate to form extra-neuronal plaques. Increased Aβ peptides are often observed well before symptoms of AD develop, highlighting the importance of targeting Aβ producing pathways early on in disease progression. Evidence indicates that exercise has the capacity to reduce Aβ peptide production in the brain however the mechanisms remain unknown. Exercise-induced signaling mediators could be the driving force behind some of the beneficial effects observed in the brain with exercise. The purpose of this study was to examine if post-exercise serum and the factors it contains can alter neuronal APP processing. Human SH-SY5Y neuronal cells were differentiated with retinoic acid for 5 days and treated with 10% pre- or post-exercise serum from humans for 30 minutes. Cells were collected for analysis of acute (30 minutes; n=6) or adaptive (24 hours post-treatment; n=6) responses. There were no statistical differences in ADAM10 and BACE1 mRNA or protein expression with post-exercise serum treatment at either time point. However, there was an increase in the ratio of sAPPa to sAPPβ protein content (p=0.05) after 30 minutes of post-exercise serum treatment. Additionally, 30 minutes of post-exercise serum treatment increased ADAM10 (p=0.01) and BACE1 (p=0.02) activity. These findings suggest that post-exercise serum modulates important enzymes involved in APP processing, pushing the cascade towards the non-amyloidogenic arm.
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Affiliation(s)
- Daniel M Marko
- Department of Health Sciences, Brock University, St. Catharines, ON, Canada
| | - Michael S Finch
- Department of Health Sciences, Brock University, St. Catharines, ON, Canada
| | - Ahmad Mohammad
- Department of Health Sciences, Brock University, St. Catharines, ON, Canada
| | - Adam J MacNeil
- Department of Health Sciences, Brock University, St. Catharines, ON, Canada
| | - Panagiota Klentrou
- Department of Health Sciences, Brock University, St. Catharines, ON, Canada.,Department of Kinesiology, Brock University, St. Catharines, ON, Canada
| | - Rebecca E K MacPherson
- Department of Health Sciences, Brock University, St. Catharines, ON, Canada.,Centre for Neuroscience, Brock University, St. Catharines, ON, Canada
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The cell adhesion protein dystroglycan affects the structural remodeling of dendritic spines. Sci Rep 2022; 12:2506. [PMID: 35169214 PMCID: PMC8847666 DOI: 10.1038/s41598-022-06462-7] [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: 04/06/2021] [Accepted: 01/28/2022] [Indexed: 11/30/2022] Open
Abstract
Dystroglycan (DG) is a cell membrane protein that binds to the extracellular matrix in various mammalian tissues. The function of DG has been well defined in embryonic development as well as in the proper migration of differentiated neuroblasts in the central nervous system (CNS). Although DG is known to be a target for matrix metalloproteinase-9 (MMP-9), cleaved in response to enhanced synaptic activity, the role of DG in the structural remodeling of dendritic spines is still unknown. Here, we report for the first time that the deletion of DG in rat hippocampal cell cultures causes pronounced changes in the density and morphology of dendritic spines. Furthermore, we noted a decrease in laminin, one of the major extracellular partners of DG. We have also observed that the lack of DG evokes alterations in the morphological complexity of astrocytes accompanied by a decrease in the level of aquaporin 4 (AQP4), a protein located within astrocyte endfeet surrounding neuronal dendrites and synapses. Regardless of all of these changes, we did not observe any effect of DG silencing on either excitatory or inhibitory synaptic transmission. Likewise, the knockdown of DG had no effect on Psd-95 protein expression. Our results indicate that DG is involved in dendritic spine remodeling that is not functionally reflected. This may suggest the existence of unknown mechanisms that maintain proper synaptic signaling despite impaired structure of dendritic spines. Presumably, astrocytes are involved in these processes.
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Papenfuss M, Lützow S, Wilms G, Babendreyer A, Flaßhoff M, Kunick C, Becker W. Differential maturation and chaperone dependence of the paralogous protein kinases DYRK1A and DYRK1B. Sci Rep 2022; 12:2393. [PMID: 35165364 PMCID: PMC8844047 DOI: 10.1038/s41598-022-06423-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/28/2022] [Indexed: 11/16/2022] Open
Abstract
The HSP90/CDC37 chaperone system not only assists the maturation of many protein kinases but also maintains their structural integrity after folding. The interaction of mature kinases with the HSP90/CDC37 complex is governed by the conformational stability of the catalytic domain, while the initial folding of the protein kinase domain is mechanistically less well characterized. DYRK1A (Dual-specificity tyrosine (Y)-phosphorylation Regulated protein Kinase 1A) and DYRK1B are closely related protein kinases with discordant HSP90 client status. DYRK kinases stoichiometrically autophosphorylate on a tyrosine residue immediately after folding, which served us as a traceable marker of successful maturation. In the present study, we used bacterial expression systems to compare the capacity of autonomous maturation of DYRK1A and DYRK1B in the absence of eukaryotic cofactors or chaperones. Under these conditions, autophosphorylation of human DYRK1B was severely compromised when compared with DYRK1A or DYRK1B orthologs from zebrafish and Xenopus. Maturation of human DYRK1B could be restored by bacterial expression at lower temperatures, suggesting that folding was not absolutely dependent on eukaryotic chaperones. The differential folding properties of DYRK1A and DYRK1B were largely due to divergent sequences of the C-terminal lobes of the catalytic domain. Furthermore, the mature kinase domain of DYRK1B featured lower thermal stability than that of DYRK1A when exposed to heat challenge in vitro or in living cells. In summary, our study enhances the mechanistic understanding of the differential thermodynamic properties of two closely related protein kinases during initial folding and as mature kinases.
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Affiliation(s)
- Marco Papenfuss
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Svenja Lützow
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Gerrit Wilms
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Aaron Babendreyer
- Institute of Molecular Pharmacology, RWTH Aachen University, 52074, Aachen, Germany
| | - Maren Flaßhoff
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Conrad Kunick
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Walter Becker
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany.
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Mahesaniya A, Williamson CR, Keyvani Chahi A, Martin CE, Mitro AE, Lu P, New LA, Watson KL, Moorehead RA, Jones N. Sex Differences in Glomerular Protein Expression and Effects of Soy-Based Diet on Podocyte Signaling. Can J Kidney Health Dis 2022; 9:20543581221121636. [PMID: 36199279 PMCID: PMC9528100 DOI: 10.1177/20543581221121636] [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: 04/07/2021] [Indexed: 12/02/2022] Open
Abstract
Background: Kidney disease is a major public health issue arising from loss of glomerular podocyte function, and there are considerable sex differences in its prognosis. Evidence suggests a renoprotective effect of estrogen and soy diet-derived phytoestrogens, although the molecular basis for this is poorly understood. Objective: Here, we aim to assess sex differences in expression of key proteins associated with podocyte survival and determine the effects of dietary soy on glomerular and podocyte signaling. Methods: Male and female FVB mice were fed control, low (1%), and high (20%) doses of isolated soy protein (ISP) in utero and until 100 days of age. Spot urine was collected to measure proteinuria and isolated glomeruli were used to quantify activated and total levels of nephrin, Akt, and ERK1/2. To investigate protective effects of specific soy phytoestrogens, cultured podocytes were treated with or without daidzein and subject to control or high glucose as a model of podocyte injury. Results: Nephrin and Akt were elevated at baseline in glomeruli from females compared to males. Both sexes that were fed 1% and 20% ISP displayed robust increases in total glomerular Akt compared to controls, and these effects were more prominent in females. A similar trend at both doses in both sexes was observed with activated Akt and total nephrin. Notably, males exclusively showed increased phosphorylation of nephrin and extracellular signal-regulated kinase (ERK) at the 1% ISP dose; however, no overt changes in urinary albumin excretion or podocin levels were observed, suggesting that the soy diets did not impair podocyte function. Finally, in cultured male and female podocytes, daidzein treatment suppressed high glucose-induced ERK activation. Conclusions: Together, our findings reveal a putative mechanism to explain the protective influence of sex on kidney disease progression, and they provide further evidence to support a beneficial role for dietary soy in preserving glomerular function.
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Affiliation(s)
- Afreeda Mahesaniya
- Department of Molecular and Cellular Biology, University of Guelph, ON, Canada
| | - Casey R. Williamson
- Department of Molecular and Cellular Biology, University of Guelph, ON, Canada
| | - Ava Keyvani Chahi
- Department of Molecular and Cellular Biology, University of Guelph, ON, Canada
- Present address: Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Claire E. Martin
- Department of Molecular and Cellular Biology, University of Guelph, ON, Canada
- Present address: Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
| | - Alexander E. Mitro
- Department of Molecular and Cellular Biology, University of Guelph, ON, Canada
| | - Peihua Lu
- Department of Molecular and Cellular Biology, University of Guelph, ON, Canada
| | - Laura A. New
- Department of Molecular and Cellular Biology, University of Guelph, ON, Canada
| | | | | | - Nina Jones
- Department of Molecular and Cellular Biology, University of Guelph, ON, Canada
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Relationship Between Dimensionality and Convergence of Optimization Algorithms: A Comparison Between Data-Driven Normalization and Scaling Factor-Based Methods Using PEPSSBI. Methods Mol Biol 2022; 2385:91-115. [PMID: 34888717 PMCID: PMC9446379 DOI: 10.1007/978-1-0716-1767-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ordinary differential equation models are used to represent intracellular signaling pathways in silico, aiding and guiding biological experiments to elucidate intracellular regulation. To construct such quantitative and predictive models of intracellular interactions, unknown parameters need to be estimated. Most of biological data are expressed in relative or arbitrary units, raising the question of how to compare model simulations with data. It has recently been shown that for models with large number of unknown parameters, fitting algorithms using a data-driven normalization of the simulations (DNS) performs best in terms of the convergence time and parameter identifiability. DNS approach compares model simulations and corresponding data both normalized by the same normalization procedure, without requiring additional parameters to be estimated, as necessary for widely used scaling factor-based methods. However, currently there is no parameter estimation software that directly supports DNS. In this chapter, we show how to apply DNS to dynamic models of systems and synthetic biology using PEPSSBI (Parameter Estimation Pipeline for Systems and Synthetic Biology). PEPSSBI is the first software that supports DNS, through algorithmically supported data normalization and objective function construction. PEPSSBI also supports model import using SBML and repeated parameter estimation runs executed in parallel either on a personal computer or a multi-CPU cluster.
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Mary S, Boder P, Rossitto G, Graham L, Scott K, Flynn A, Kipgen D, Graham D, Delles C. Salt loading decreases urinary excretion and increases intracellular accumulation of uromodulin in stroke-prone spontaneously hypertensive rats. Clin Sci (Lond) 2021; 135:2749-2761. [PMID: 34870708 PMCID: PMC8689196 DOI: 10.1042/cs20211017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/24/2021] [Accepted: 12/06/2021] [Indexed: 12/15/2022]
Abstract
Uromodulin (UMOD) is the most abundant renal protein secreted into urine by the thick ascending limb (TAL) epithelial cells of the loop of Henle. Genetic studies have demonstrated an association between UMOD risk variants and hypertension. We aimed to dissect the role of dietary salt in renal UMOD excretion in normotension and chronic hypertension. Normotensive Wistar-Kyoto rats (WKY) and stroke-prone spontaneously hypertensive rats (SHRSP) (n=8/sex/strain) were maintained on 1% NaCl for 3 weeks. A subset of salt-loaded SHRSP was treated with nifedipine. Salt-loading in SHRSP increased blood pressure (ΔSBP 35 ± 5 mmHg, P<0.0001) and kidney injury markers such as kidney injury marker-1 (KIM-1; fold change, FC 3.4; P=0.003), neutrophil gelatinase-associated lipocalin (NGAL; FC, 2.0; P=0.012) and proteinuria. After salt-loading there was a reduction in urinary UMOD excretion in WKY and SHRSP by 26 and 55% respectively, compared with baseline. Nifedipine treatment reduced blood pressure (BP) in SHRSP, however, did not prevent salt-induced reduction in urinary UMOD excretion. In all experiments, changes in urinary UMOD excretion were dissociated from kidney UMOD protein and mRNA levels. Colocalization and ex-vivo studies showed that salt-loading increased intracellular UMOD retention in both WKY and SHRSP. Our study provides novel insights into the interplay among salt, UMOD, and BP. The role of UMOD as a cardiovascular risk marker deserves mechanistic reappraisal and further investigations based on our findings.
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Affiliation(s)
- Sheon Mary
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, Scotland, U.K
| | - Philipp Boder
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, Scotland, U.K
| | - Giacomo Rossitto
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, Scotland, U.K
- Department of Medicine, University of Padua, Padua, Italy
| | - Lesley Graham
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, Scotland, U.K
| | - Kayley Scott
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, Scotland, U.K
| | - Arun Flynn
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, Scotland, U.K
| | - David Kipgen
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, Scotland, U.K
| | - Delyth Graham
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, Scotland, U.K
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, Scotland, U.K
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Corrales E, Levit-Zerdoun E, Metzger P, Kowar S, Ku M, Brummer T, Boerries M. Dynamic transcriptome analysis reveals signatures of paradoxical effect of vemurafenib on human dermal fibroblasts. Cell Commun Signal 2021; 19:123. [PMID: 34930313 PMCID: PMC8686565 DOI: 10.1186/s12964-021-00801-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 11/09/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Vemurafenib (PLX4032) is one of the most frequently used treatments for late-stage melanoma patients with the BRAFV600E mutation; however, acquired resistance to the drug poses as a major challenge. It remains to be determined whether off-target effects of vemurafenib on normal stroma components could reshape the tumor microenvironment in a way that contributes to cancer progression and drug resistance. METHODS By using temporally-resolved RNA- and ATAC-seq, we studied the early molecular changes induced by vemurafenib in human dermal fibroblast (HDF), a main stromal component in melanoma and other tumors with high prevalence of BRAFV600 mutations. RESULTS Transcriptomics analyses revealed a stepwise up-regulation of proliferation signatures, together with a down-regulation of autophagy and proteolytic processes. The gene expression changes in HDF strongly correlated in an inverse way with those in BRAFV600E mutant malignant melanoma (MaMel) cell lines, consistent with the observation of a paradoxical effect of vemurafenib, leading to hyperphosphorylation of MEK1/2 and ERK1/2. The transcriptional changes in HDF were not strongly determined by alterations in chromatin accessibility; rather, an already permissive chromatin landscape seemed to facilitate the early accessibility to MAPK/ERK-regulated transcription factor binding sites. Combinatorial treatment with the MEK inhibitor trametinib did not preclude the paradoxical activation of MAPK/ERK signaling in HDF. When administered together, vemurafenib partially compensated for the reduction of cell viability and proliferation induced by trametinib. These paradoxical changes were restrained by using the third generation BRAF inhibitor PLX8394, a so-called paradox breaker compound. However, the advantageous effects on HDF during combination therapies were also lost. CONCLUSIONS Vemurafenib induces paradoxical changes in HDF, enabled by a permissive chromatin landscape. These changes might provide an advantage during combination therapies, by compensating for the toxicity induced in stromal cells by less specific MAPK/ERK inhibitors. Our results highlight the relevance of evaluating the effects of the drugs on non-transformed stromal components, carefully considering the implications of their administration either as mono- or combination therapies. Video Abstract.
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Affiliation(s)
- Eyleen Corrales
- Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Ella Levit-Zerdoun
- Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Patrick Metzger
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
| | - Silke Kowar
- Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
| | - Manching Ku
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Mathildenstr. 1, 79106 Freiburg, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - Melanie Boerries
- Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
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Jahangiri S, Khoei S, Khoee S, Safa M, Shirvalilou S, Pirhajati Mahabadi V. Potential anti-tumor activity of 13.56 MHz alternating magnetic hyperthermia and chemotherapy on the induction of apoptosis in human colon cancer cell lines HT29 and HCT116 by up-regulation of Bax, cleaved caspase 3&9, and cleaved PARP proteins. Cancer Nanotechnol 2021. [DOI: 10.1186/s12645-021-00108-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The purpose of the present study was to evaluate the efficacy of chemo-magnetic hyperthermia (MH), a combination of alternating magnetic field (AMF) and superparamagnetic nanoparticles (SPIONs) coated with Polyethylene glycol-Poly(butyl acrylate)-Polyethylene glycol (PEG-PBA-PEG) carrying 5-Fluorouracil (5-Fu), at inducing apoptosis in the human cancer cell lines HT29 and HCT116. This process can be mediated by alterations in the expression of apoptotic effector proteins, including Bax, Bcl-2, cleaved caspase 3&9, and cleaved PARP, which are involved in the intrinsic pathway of apoptosis. For this purpose, the cells were cultured as monolayers. Then both cell lines were treated with 5-Fu/magnetic nanoparticles and magnetic hyperthermia. Finally, the effect of treatment on cancer cells was determined by Western blot analysis and flow cytometry.
Results
Our results showed that combined chemo-magnetic thermotherapy significantly increased the apoptosis in colon cancer cells compared to chemotherapy or hyperthermia alone (P < 0.05). Up-regulation of Bax, cleaved caspase 3&9, and cleaved PARP proteins was indicative of apoptosis induction in cancer cells, which are involved in the intrinsic pathway of apoptosis.
Conclusions
This study demonstrates that localized hyperthermia was able to significantly trigger the 5-Fu release and inhibit cell viability, which, due to the synchronization of hyperthermia and chemotherapy, exacerbated the damage of cancer cells.
Graphical Abstract
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Nucleolar Stress Functions Upstream to Stimulate Expression of Autophagy Regulators. Cancers (Basel) 2021; 13:cancers13246220. [PMID: 34944838 PMCID: PMC8699128 DOI: 10.3390/cancers13246220] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/04/2021] [Indexed: 01/18/2023] Open
Abstract
Simple Summary Ribosome biogenesis takes place in nucleoli and is essential for cellular survival and proliferation. In case this function is disturbed, either due to defects in regulatory factors or the structure of the nucleolus, nucleolar stress is provoked. Consequently, cells classically undergo cell cycle arrest and apoptosis. Induction of nucleolar stress is known to eliminate cells in the background of cancer therapy and paradoxically is also associated with increased cancer formation. Recent reports demonstrated that nucleolar stress triggers autophagy, a conserved pathway responsible for recycling endogenous material. Thus, it was suggested that autophagy might serve as compensatory pro-survival response. However, the mechanisms how nucleolar stress triggers autophagy are poorly understood. Here we show that induction of nucleolar stress by depleting ribosome biogenesis factors or by interfering with RNA polymerase I function, triggers expression of various key autophagy regulators. Moreover, we demonstrate that RNA pol I inhibition by CX-5461 correlates with increased ATG7 and ATGL16L1 levels, essential factors for generating autophagosomes, and stimulates autophagic flux. Abstract Ribosome biogenesis is essential for protein synthesis, cell growth and survival. The process takes places in nucleoli and is orchestrated by various proteins, among them RNA polymerases I–III as well as ribosome biogenesis factors. Perturbation of ribosome biogenesis activates the nucleolar stress response, which classically triggers cell cycle arrest and apoptosis. Nucleolar stress is utilized in modern anti-cancer therapies, however, also contributes to the development of various pathologies, including cancer. Growing evidence suggests that nucleolar stress stimulates compensatory cascades, for instance bulk autophagy. However, underlying mechanisms are poorly understood. Here we demonstrate that induction of nucleolar stress activates expression of key autophagic regulators such as ATG7 and ATG16L1, essential for generation of autophagosomes. We show that knockdown of the ribosomopathy factor SBDS, or of key ribosome biogenesis factors (PPAN, NPM, PES1) is associated with enhanced levels of ATG7 in cancer cells. The same holds true when interfering with RNA polymerase I function by either pharmacological inhibition (CX-5461) or depletion of the transcription factor UBF-1. Moreover, we demonstrate that RNA pol I inhibition by CX-5461 stimulates autophagic flux. Together, our data establish that nucleolar stress affects transcriptional regulation of autophagy. Given the contribution of both axes in propagation or cure of cancer, our data uncover a connection that might be targeted in future.
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Christ B, Collatz M, Dahmen U, Herrmann KH, Höpfl S, König M, Lambers L, Marz M, Meyer D, Radde N, Reichenbach JR, Ricken T, Tautenhahn HM. Hepatectomy-Induced Alterations in Hepatic Perfusion and Function - Toward Multi-Scale Computational Modeling for a Better Prediction of Post-hepatectomy Liver Function. Front Physiol 2021; 12:733868. [PMID: 34867441 PMCID: PMC8637208 DOI: 10.3389/fphys.2021.733868] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/26/2021] [Indexed: 01/17/2023] Open
Abstract
Liver resection causes marked perfusion alterations in the liver remnant both on the organ scale (vascular anatomy) and on the microscale (sinusoidal blood flow on tissue level). These changes in perfusion affect hepatic functions via direct alterations in blood supply and drainage, followed by indirect changes of biomechanical tissue properties and cellular function. Changes in blood flow impose compression, tension and shear forces on the liver tissue. These forces are perceived by mechanosensors on parenchymal and non-parenchymal cells of the liver and regulate cell-cell and cell-matrix interactions as well as cellular signaling and metabolism. These interactions are key players in tissue growth and remodeling, a prerequisite to restore tissue function after PHx. Their dysregulation is associated with metabolic impairment of the liver eventually leading to liver failure, a serious post-hepatectomy complication with high morbidity and mortality. Though certain links are known, the overall functional change after liver surgery is not understood due to complex feedback loops, non-linearities, spatial heterogeneities and different time-scales of events. Computational modeling is a unique approach to gain a better understanding of complex biomedical systems. This approach allows (i) integration of heterogeneous data and knowledge on multiple scales into a consistent view of how perfusion is related to hepatic function; (ii) testing and generating hypotheses based on predictive models, which must be validated experimentally and clinically. In the long term, computational modeling will (iii) support surgical planning by predicting surgery-induced perfusion perturbations and their functional (metabolic) consequences; and thereby (iv) allow minimizing surgical risks for the individual patient. Here, we review the alterations of hepatic perfusion, biomechanical properties and function associated with hepatectomy. Specifically, we provide an overview over the clinical problem, preoperative diagnostics, functional imaging approaches, experimental approaches in animal models, mechanoperception in the liver and impact on cellular metabolism, omics approaches with a focus on transcriptomics, data integration and uncertainty analysis, and computational modeling on multiple scales. Finally, we provide a perspective on how multi-scale computational models, which couple perfusion changes to hepatic function, could become part of clinical workflows to predict and optimize patient outcome after complex liver surgery.
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Affiliation(s)
- Bruno Christ
- Cell Transplantation/Molecular Hepatology Lab, Department of Visceral, Transplant, Thoracic and Vascular Surgery, University of Leipzig Medical Center, Leipzig, Germany
| | - Maximilian Collatz
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany
- Optisch-Molekulare Diagnostik und Systemtechnologié, Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus Jena, Jena, Germany
| | - Uta Dahmen
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, Jena University Hospital, Jena, Germany
| | - Karl-Heinz Herrmann
- Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital, Jena, Germany
| | - Sebastian Höpfl
- Faculty of Engineering Design, Production Engineering and Automotive Engineering, Institute for Systems Theory and Automatic Control, University of Stuttgart, Stuttgart, Germany
| | - Matthias König
- Systems Medicine of the Liver Lab, Institute for Theoretical Biology, Humboldt-University Berlin, Berlin, Germany
| | - Lena Lambers
- Faculty of Aerospace Engineering and Geodesy, Institute of Mechanics, Structural Analysis and Dynamics, University of Stuttgart, Stuttgart, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany
| | - Daria Meyer
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany
| | - Nicole Radde
- Faculty of Engineering Design, Production Engineering and Automotive Engineering, Institute for Systems Theory and Automatic Control, University of Stuttgart, Stuttgart, Germany
| | - Jürgen R. Reichenbach
- Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital, Jena, Germany
| | - Tim Ricken
- Faculty of Aerospace Engineering and Geodesy, Institute of Mechanics, Structural Analysis and Dynamics, University of Stuttgart, Stuttgart, Germany
| | - Hans-Michael Tautenhahn
- Department of General, Visceral and Vascular Surgery, Jena University Hospital, Jena, Germany
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Leroy K, Silva Costa CJ, Pieters A, dos Santos Rodrigues B, Van Campenhout R, Cooreman A, Tabernilla A, Cogliati B, Vinken M. Expression and Functionality of Connexin-Based Channels in Human Liver Cancer Cell Lines. Int J Mol Sci 2021; 22:12187. [PMID: 34830068 PMCID: PMC8623148 DOI: 10.3390/ijms222212187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 01/14/2023] Open
Abstract
Liver cancer cell lines are frequently used in vitro tools to test candidate anti-cancer agents as well as to elucidate mechanisms of liver carcinogenesis. Among such mechanisms is cellular communication mediated by connexin-based gap junctions. The present study investigated changes in connexin expression and gap junction functionality in liver cancer in vitro. For this purpose, seven human liver cancer cell lines, as well as primary human hepatocytes, were subjected to connexin and gap junction analysis at the transcriptional, translational and activity level. Real-time quantitative reverse transcription polymerase chain reaction analysis showed enhanced expression of connexin43 in the majority of liver cancer cell lines at the expense of connexin32 and connexin26. Some of these changes were paralleled at the protein level, as evidenced by immunoblot analysis and in situ immunocytochemistry. Gap junctional intercellular communication, assessed by the scrape loading/dye transfer assay, was generally low in all liver cancer cell lines. Collectively, these results provide a full scenario of modifications in hepatocyte connexin production and gap junction activity in cultured liver cancer cell lines. The findings may be valuable for the selection of neoplastic hepatocytes for future mechanistic investigation and testing of anti-cancer drugs that target connexins and their channels.
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Affiliation(s)
- Kaat Leroy
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (K.L.); (A.P.); (B.d.S.R.); (R.V.C.); (A.C.); (A.T.)
| | - Cícero Júlio Silva Costa
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva 87, Cidade Universitária, São Paulo 05508-270, Brazil; (C.J.S.C.); (B.C.)
| | - Alanah Pieters
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (K.L.); (A.P.); (B.d.S.R.); (R.V.C.); (A.C.); (A.T.)
| | - Bruna dos Santos Rodrigues
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (K.L.); (A.P.); (B.d.S.R.); (R.V.C.); (A.C.); (A.T.)
| | - Raf Van Campenhout
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (K.L.); (A.P.); (B.d.S.R.); (R.V.C.); (A.C.); (A.T.)
| | - Axelle Cooreman
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (K.L.); (A.P.); (B.d.S.R.); (R.V.C.); (A.C.); (A.T.)
| | - Andrés Tabernilla
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (K.L.); (A.P.); (B.d.S.R.); (R.V.C.); (A.C.); (A.T.)
| | - Bruno Cogliati
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva 87, Cidade Universitária, São Paulo 05508-270, Brazil; (C.J.S.C.); (B.C.)
| | - Mathieu Vinken
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (K.L.); (A.P.); (B.d.S.R.); (R.V.C.); (A.C.); (A.T.)
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Möller S, Laskay T. Purinergic Enhancement of Anti-Leishmanial Effector Functions of Neutrophil Granulocytes. Front Immunol 2021; 12:747049. [PMID: 34733282 PMCID: PMC8558537 DOI: 10.3389/fimmu.2021.747049] [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: 07/25/2021] [Accepted: 09/06/2021] [Indexed: 11/22/2022] Open
Abstract
Although macrophages are considered for host cells for the multiplication of Leishmania, recent studies indicate the important role of neutrophil granulocytes as host cells for these intracellular parasites. Neutrophils have been shown to be massively and rapidly recruited to the site of Leishmania infection where they represent the first cells to encounter the parasites. Exposure to ATP and UTP have been shown to enhance anti-Leishmania activity of macrophages and intralesional injection of UTP led to strongly reduced parasite load in vivo. Since the in vivo anti-leishmanial effect of extracellular UTP correlated with enhanced neutrophil recruitment and enhanced ROS production at the site of Leishmania infection we hypothesized that exposure to extracellular nucleotides can directly enhance the killing of Leishmania by neutrophils. Since purinergic signaling is an essential mechanism of neutrophil activation the aim of the present study was to assess whether purinergic exposure results in the activation of anti-leishmanial neutrophil functions and, therefore, represent an essential component of enhanced anti-leishmanial defense in leishmaniasis. We could show that exposure to ATP and UTP led to activation and enhanced CD11b expression of primary human neutrophils in vitro. Leishmania-induced ROS production was strongly enhanced by extracellular ATP and UTP. Importantly, exposure to ATP and UTP resulted in enhanced killing of Leishmania donovani by neutrophils. In addition, ATP strongly enhanced the secretion of IL-8 and IL-1β by Leishmania-exposed neutrophils. Our results suggest that signaling via the P2 receptor and phosphorylation of Erk1/2, Akt and p38 are involved in the purinergic enhancement of anti-leishmanial functions of neutrophils.
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Affiliation(s)
- Sonja Möller
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Tamás Laskay
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
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Burckhardt CJ, Minna JD, Danuser G. Co-immunoprecipitation and semi-quantitative immunoblotting for the analysis of protein-protein interactions. STAR Protoc 2021; 2:100644. [PMID: 34278331 PMCID: PMC8264609 DOI: 10.1016/j.xpro.2021.100644] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Co-immunoprecipitation (co-IP) of protein complexes from cell lysates is widely used to study protein-protein interactions. However, establishing robust co-IP assays often involves considerable optimization. Moreover, co-IP results are frequently presented in non-quantitative ways. This protocol presents an optimized co-IP workflow with an analysis based on semi-quantitative immunoblot densitometry to increase reliability and reproducibility. For complete details on the use and execution of this protocol, please refer to Burckhardt et al. (2021).
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Affiliation(s)
- Christoph J. Burckhardt
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - John D. Minna
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Departments of Internal Medicine and Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
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Zhang M, Spencer HF, Berman RY, Radford KD, Choi KH. Effects of subanesthetic intravenous ketamine infusion on neuroplasticity-related proteins in male and female Sprague-Dawley rats. IBRO Neurosci Rep 2021; 11:42-51. [PMID: 34286313 PMCID: PMC8273220 DOI: 10.1016/j.ibneur.2021.06.005] [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: 03/04/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 10/30/2022] Open
Abstract
Although ketamine, a multimodal dissociative anesthetic, is frequently used for analgesia and treatment-resistant major depression, molecular mechanisms of ketamine remain unclear. Specifically, differences in the effects of ketamine on neuroplasticity-related proteins in the brains of males and females need further investigation. In the current study, adult male and female Sprague-Dawley rats with an indwelling jugular venous catheter received an intravenous ketamine infusion (0, 10, or 40 mg/kg, 2-h), starting with a 2 mg/kg bolus for ketamine groups. Spontaneous locomotor activity was monitored by infrared photobeams during the infusion. Two hours after the infusion, brain tissue was dissected to obtain the medial prefrontal cortex (mPFC), hippocampus including the CA1, CA3, and dentate gyrus, and amygdala followed by Western blot analyses of a transcription factor (c-Fos), brain-derived neurotrophic factor (BDNF), and phosphorylated extracellular signal-regulated kinase (pERK). The 10 mg/kg ketamine infusion suppressed locomotor activity in male and female rats while the 40 mg/kg infusion stimulated activity only in female rats. In the mPFC, 10 mg/kg ketamine reduced pERK levels in male rats while 40 mg/kg ketamine increased c-Fos levels in male and female rats. Female rats in proestrus/estrus phases showed greater ketamine-induced c-Fos elevation as compared to those in diestrus phase. In the amygdala, 10 and 40 mg/kg ketamine increased c-Fos levels in female, but not male, rats. In the hippocampus, 10 mg/kg ketamine reduced BDNF levels in male, but not female, rats. Taken together, the current data suggest that subanesthetic doses of intravenous ketamine infusions produce differences in neuroplasticity-related proteins in the brains of male and female rats.
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Affiliation(s)
- Michael Zhang
- Department of Psychiatry, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA.,Center for the Study of Traumatic Stress, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Haley F Spencer
- Program in Neuroscience, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Rina Y Berman
- Department of Psychiatry, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA.,Center for the Study of Traumatic Stress, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Kennett D Radford
- Daniel K. Inouye Graduate School of Nursing, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Kwang H Choi
- Department of Psychiatry, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA.,Center for the Study of Traumatic Stress, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA.,Program in Neuroscience, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA.,Daniel K. Inouye Graduate School of Nursing, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
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Nguyen BV, O’Donnell B, Villamagna AM. The environmental context of inducible HSP70 expression in Eastern Brook Trout. CONSERVATION PHYSIOLOGY 2021; 9:coab022. [PMID: 33996100 PMCID: PMC8111384 DOI: 10.1093/conphys/coab022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/22/2020] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Much research has focused on the population-level effects of climate change on Eastern Brook Trout (Salvelinus fontinalis). While some studies have considered here sub-lethal stress caused by warming waters, the role of multiple, interacting stressors remains largely unexplored. We used inducible heat shock protein 70 (HSP70) as a molecular biomarker to assess in situ response of Eastern Brook Trout in headwater streams to multiple potential stressors, including temperature. Over 7 sampling events during 2018 and 2019, we sampled 141 fish and found that HSP70 expression and 3-day mean water temperature exhibited a quadratic relationship (R 2-adj = 0.68). Further analyses showed that HSP70 expression was explained by temperature, relative water level and their interaction (R 2-adj = 0.75), while fish size and capture location were not factors. We observed a significant increase in HSP70 expression during periods of low relative water level with warm temperatures (~18°C) and also during high relative water level with cold temperatures (~8°C). Our results suggest that temperatures at the edges of the preferred range coupled with relative water level might act together to trigger the cellular stress response in Eastern Brook Trout and that there is greater variation in response at colder temperatures. These findings reinforce the need to consider complex, interactive stressors in influencing the health and persistence of Eastern Brook Trout populations into the future.
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Affiliation(s)
- Bao V Nguyen
- Molecular and Cellular Biology, University of Massachusetts - Amherst, MA, USA
| | | | - Amy M Villamagna
- Environmental Science & Policy, Plymouth State University, NH, USA
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