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Emery-Corbin SJ, Yousef JM, Adhikari S, Sumardy F, Nhu D, van Delft MF, Lessene G, Dziekan J, Webb AI, Dagley LF. Improved drug target deconvolution with PISA-DIA using an extended, overlapping temperature gradient. Proteomics 2024:e2300644. [PMID: 38766901 DOI: 10.1002/pmic.202300644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Thermal proteome profiling (TPP) is a powerful tool for drug target deconvolution. Recently, data-independent acquisition mass spectrometry (DIA-MS) approaches have demonstrated significant improvements to depth and missingness in proteome data, but traditional TPP (a.k.a. CEllular Thermal Shift Assay "CETSA") workflows typically employ multiplexing reagents reliant on data-dependent acquisition (DDA). Herein, we introduce a new experimental design for the Proteome Integral Solubility Alteration via label-free DIA approach (PISA-DIA). We highlight the proteome coverage and sensitivity achieved by using multiple overlapping thermal gradients alongside DIA-MS, which maximizes efficiencies in PISA sample concatenation and safeguards against missing protein targets that exist at high melting temperatures. We demonstrate our extended PISA-DIA design has superior proteome coverage as compared to using tandem-mass tags (TMT) necessitating DDA-MS analysis. Importantly, we demonstrate our PISA-DIA approach has the quantitative and statistical rigor using A-1331852, a specific inhibitor of BCL-xL. Due to the high melt temperature of this protein target, we utilized our extended multiple gradient PISA-DIA workflow to identify BCL-xL. We assert our novel overlapping gradient PISA-DIA-MS approach is ideal for unbiased drug target deconvolution, spanning a large temperature range whilst minimizing target dropout between gradients, increasing the likelihood of resolving the protein targets of novel compounds.
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Affiliation(s)
- Samantha J Emery-Corbin
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jumana M Yousef
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Subash Adhikari
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Fransisca Sumardy
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- ACRF Chemical Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Duong Nhu
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- ACRF Chemical Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Mark F van Delft
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Blood Cells and Blood Cancer Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Guillaume Lessene
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- ACRF Chemical Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Victoria, Australia
| | - Jerzy Dziekan
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Andrew I Webb
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Laura F Dagley
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
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Fietz D, Sgaier R, O’Donnell L, Stanton PG, Dagley LF, Webb AI, Schuppe HC, Diemer T, Pilatz A. Proteomic biomarkers in seminal plasma as predictors of reproductive potential in azoospermic men. Front Endocrinol (Lausanne) 2024; 15:1327800. [PMID: 38654926 PMCID: PMC11035875 DOI: 10.3389/fendo.2024.1327800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction Azoospermia, characterized by an absence of sperm in the ejaculate, represents the most severe form of male infertility. While surgical sperm retrieval in obstructive azoospermia (OA) is successful in the majority of cases, patients with non-obstructive azoospermia (NOA) show retrieval rates of only about 50% and thus frequently have unnecessary surgery. Surgical intervention could be avoided if patients without preserved spermatogenesis are identified preoperatively. This prospective study aimed to discover biomarkers in seminal plasma that could be employed for a non-invasive differential diagnosis of OA/NOA in order to rationalize surgery recommendations and improve success rates. Methods All patients signed written informed consent, underwent comprehensive andrological evaluation, received human genetics to exclude relevant pathologies, and patients with azoospermia underwent surgical sperm retrieval. Using label-free LC-MS/MS, we compared the proteomes of seminal plasma samples from fertile men (healthy controls (HC), n=8) and infertile men diagnosed with 1) OA (n=7), 2) NOA with successful sperm retrieval (mixed testicular atrophy (MTA), n=8), and 3) NOA without sperm retrieval (Sertoli cell-only phenotype (SCO), n=7). Relative abundance changes of two candidate markers of sperm retrieval, HSPA2 and LDHC, were confirmed by Western Blot. Results We found the protein expression levels of 42 proteins to be significantly down-regulated (p ≤ 0.05) in seminal plasma from SCO NOA patients relative to HC whereas only one protein was down-regulated in seminal plasma from MTA patients. Analysis of tissue and cell expression suggested that the testis-specific proteins LDHC, PGK2, DPEP3, and germ-cell enriched heat-shock proteins HSPA2 and HSPA4L are promising biomarkers of spermatogenic function. Western blotting revealed a significantly lower abundance of LDHC and HSPA2 in the seminal plasma of men with NOA (SCO and MTA) compared to controls. Discussion The results indicate that certain testis-specific proteins when measured in seminal plasma, could serve as indicators of the presence of sperm in the testis and predict the success of sperm retrieval. Used in conjunction with conventional clinical assessments, these proteomic biomarkers may assist in the non-invasive diagnosis of idiopathic male infertility.
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Affiliation(s)
- Daniela Fietz
- Department of Veterinary Anatomy, Histology and Embryology, Justus Liebig University Giessen, Giessen, Germany
| | - Raouda Sgaier
- Department of Veterinary Anatomy, Histology and Embryology, Justus Liebig University Giessen, Giessen, Germany
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University Giessen, Giessen, Germany
| | - Liza O’Donnell
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Peter G. Stanton
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Laura F. Dagley
- Advanced Technology and Biology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Molecular and Translational Sciences, School of Clinical Sciences, Monash University, Clayton, VIC, Australia
| | - Andrew I. Webb
- Advanced Technology and Biology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Molecular and Translational Sciences, School of Clinical Sciences, Monash University, Clayton, VIC, Australia
| | - Hans-Christian Schuppe
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University Giessen, Giessen, Germany
| | - Thorsten Diemer
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University Giessen, Giessen, Germany
| | - Adrian Pilatz
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University Giessen, Giessen, Germany
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Nicolson S, Manning JA, Lim Y, Jiang X, Kolze E, Dayan S, Umargamwala R, Xu T, Sandow JJ, Webb AI, Kumar S, Denton D. The Drosophila ZNRF1/2 homologue, detour, interacts with HOPS complex and regulates autophagy. Commun Biol 2024; 7:183. [PMID: 38360932 PMCID: PMC10869362 DOI: 10.1038/s42003-024-05834-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/18/2024] [Indexed: 02/17/2024] Open
Abstract
Autophagy, the process of elimination of cellular components by lysosomal degradation, is essential for animal development and homeostasis. Using the autophagy-dependent Drosophila larval midgut degradation model we identified an autophagy regulator, the RING domain ubiquitin ligase CG14435 (detour). Depletion of detour resulted in increased early-stage autophagic vesicles, premature tissue contraction, and overexpression of detour or mammalian homologues, ZNRF1 and ZNRF2, increased autophagic vesicle size. The ablation of ZNRF1 or ZNRF2 in mammalian cells increased basal autophagy. We identified detour interacting proteins including HOPS subunits, deep orange (dor/VPS18), Vacuolar protein sorting 16A (VPS16A), and light (lt/VPS41) and found that detour promotes their ubiquitination. The detour mutant accumulated autophagy-related proteins in young adults, displayed premature ageing, impaired motor function, and activation of innate immunity. Collectively, our findings suggest a role for detour in autophagy, likely through regulation of HOPS complex, with implications for healthy aging.
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Affiliation(s)
- Shannon Nicolson
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, 5001, Australia
| | - Jantina A Manning
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, 5001, Australia
| | - Yoon Lim
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, 5001, Australia
| | - Xin Jiang
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, 5001, Australia
| | - Erica Kolze
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, 5001, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5001, Australia
| | - Sonia Dayan
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, 5001, Australia
| | - Ruchi Umargamwala
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, 5001, Australia
| | - Tianqi Xu
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, 5001, Australia
| | - Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, 5001, Australia.
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5001, Australia.
| | - Donna Denton
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, 5001, Australia.
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Delconte RB, Kolesnik TB, Dagley LF, Rautela J, Shi W, Putz EM, Stannard K, Zhang JG, Teh C, Firth M, Ushiki T, Andoniou CE, Degli-Esposti MA, Sharp PP, Sanvitale CE, Infusini G, Liau NPD, Linossi EM, Burns CJ, Carotta S, Gray DHD, Seillet C, Hutchinson DS, Belz GT, Webb AI, Alexander WS, Li SS, Bullock AN, Babon JJ, Smyth MJ, Nicholson SE, Huntington ND. Author Correction: CIS is a potent checkpoint in NK cell-mediated tumor immunity. Nat Immunol 2024; 25:371-372. [PMID: 38087084 DOI: 10.1038/s41590-023-01714-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Affiliation(s)
- Rebecca B Delconte
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Tatiana B Kolesnik
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Jai Rautela
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Wei Shi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Eva M Putz
- Immunology in Cancer and Infection Laboratory QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Kimberley Stannard
- Immunology in Cancer and Infection Laboratory QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Jian-Guo Zhang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Charis Teh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Matt Firth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Takashi Ushiki
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Christopher E Andoniou
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia and Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Mariapia A Degli-Esposti
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia and Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Phillip P Sharp
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | | | - Giuseppe Infusini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Nicholas P D Liau
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Edmond M Linossi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Christopher J Burns
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Sebastian Carotta
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Daniel H D Gray
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Cyril Seillet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Dana S Hutchinson
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Gabrielle T Belz
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Warren S Alexander
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Shawn S Li
- Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Alex N Bullock
- Structural Genomics Consortium (SGC), University of Oxford, Oxford, UK
| | - Jeffrey J Babon
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Mark J Smyth
- Immunology in Cancer and Infection Laboratory QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- School of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Sandra E Nicholson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, The University of Melbourne, Victoria, Australia.
| | - Nicholas D Huntington
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, The University of Melbourne, Victoria, Australia.
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Pandey K, Wang SS, Mifsud NA, Faridi P, Davenport AJ, Webb AI, Sandow JJ, Ayala R, Monje M, Cross RS, Ramarathinam SH, Jenkins MR, Purcell AW. A combined immunopeptidomics, proteomics, and cell surface proteomics approach to identify immunotherapy targets for diffuse intrinsic pontine glioma. Front Oncol 2023; 13:1192448. [PMID: 37637064 PMCID: PMC10455951 DOI: 10.3389/fonc.2023.1192448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/19/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction Diffuse intrinsic pontine glioma (DIPG), recently reclassified as a subtype of diffuse midline glioma, is a highly aggressive brainstem tumor affecting children and young adults, with no cure and a median survival of only 9 months. Conventional treatments are ineffective, highlighting the need for alternative therapeutic strategies such as cellular immunotherapy. However, identifying unique and tumor-specific cell surface antigens to target with chimeric antigen receptor (CAR) or T-cell receptor (TCR) therapies is challenging. Methods In this study, a multi-omics approach was used to interrogate patient-derived DIPG cell lines and to identify potential targets for immunotherapy. Results Through immunopeptidomics, a range of targetable peptide antigens from cancer testis and tumor-associated antigens as well as peptides derived from human endogenous retroviral elements were identified. Proteomics analysis also revealed upregulation of potential drug targets and cell surface proteins such as Cluster of differentiation 27 (CD276) B7 homolog 3 protein (B7H3), Interleukin 13 alpha receptor 2 (IL-13Rα2), Human Epidermal Growth Factor Receptor 3 (HER2), Ephrin Type-A Receptor 2 (EphA2), and Ephrin Type-A Receptor 3 (EphA3). Discussion The results of this study provide a valuable resource for the scientific community to accelerate immunotherapeutic approaches for DIPG. Identifying potential targets for CAR and TCR therapies could open up new avenues for treating this devastating disease.
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Affiliation(s)
- Kirti Pandey
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Stacie S. Wang
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Children’s Cancer Centre, Royal Children’s Hospital, Parkville, VIC, Australia
| | - Nicole A. Mifsud
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Pouya Faridi
- Monash Proteomics and Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- School of Clinical Sciences, Department of Medicine, Monash University, Clayton, VIC, Australia
- Department of Medicine, Sub-Faculty of Clinical and Molecular Medicine, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Alexander J. Davenport
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Andrew I. Webb
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Jarrod J. Sandow
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Rochelle Ayala
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Michelle Monje
- Department of Neurology and Neurological Sciences and Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States
| | - Ryan S. Cross
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Sri H. Ramarathinam
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Misty R. Jenkins
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
- LaTrobe Institute for Molecular Science, LaTrobe University, Bundoora, VIC, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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Hediyeh-Zadeh S, Webb AI, Davis MJ. MsImpute: Estimation of Missing Peptide Intensity Data in Label-Free Quantitative Mass Spectrometry. Mol Cell Proteomics 2023; 22:100558. [PMID: 37105364 PMCID: PMC10368900 DOI: 10.1016/j.mcpro.2023.100558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 04/29/2023] Open
Abstract
Mass spectrometry (MS) enables high-throughput identification and quantification of proteins in complex biological samples and can provide insights into the global function of biological systems. Label-free quantification is cost-effective and suitable for the analysis of human samples. Despite rapid developments in label-free data acquisition workflows, the number of proteins quantified across samples can be limited by technical and biological variability. This variation can result in missing values which can in turn challenge downstream data analysis tasks. General purpose or gene expression-specific imputation algorithms are widely used to improve data completeness. Here, we propose an imputation algorithm designated for label-free MS data that is aware of the type of missingness affecting data. On published datasets acquired by data-dependent and data-independent acquisition workflows with variable degrees of biological complexity, we demonstrate that the proposed missing value estimation procedure by barycenter computation competes closely with the state-of-the-art imputation algorithms in differential abundance tasks while outperforming them in the accuracy of variance estimates of the peptide abundance measurements, and better controls the false discovery rate in label-free MS experiments. The barycenter estimation procedure is implemented in the msImpute software package and is available from the Bioconductor repository.
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Affiliation(s)
- Soroor Hediyeh-Zadeh
- Bioinformatics Division, WEHI, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Australia; Colonial Foundation Healthy Ageing Centre, WEHI, Melbourne, Australia
| | - Andrew I Webb
- Department of Medical Biology, University of Melbourne, Melbourne, Australia; Colonial Foundation Healthy Ageing Centre, WEHI, Melbourne, Australia; Advanced Technology and Biology Division, WEHI, Melbourne, Australia
| | - Melissa J Davis
- Bioinformatics Division, WEHI, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Australia; Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia; The Diamantina Institute, The University of Queensland, Brisbane, Australia; The South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, Australia.
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7
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Wilding-McBride D, Webb AI. A de novo MS1 feature detector for the Bruker timsTOF Pro. PLoS One 2022; 17:e0277122. [PMID: 36449500 PMCID: PMC9710787 DOI: 10.1371/journal.pone.0277122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/21/2022] [Indexed: 12/05/2022] Open
Abstract
Identification of peptides by analysis of data acquired by the two established methods for bottom-up proteomics, DDA and DIA, relies heavily on the fragment spectra. In DDA, peptide features detected in mass spectrometry data are identified by matching their fragment spectra with a peptide database. In DIA, a peptide's fragment spectra are targeted for extraction and matched with observed spectra. Although fragment ion matching is a central aspect in most peptide identification strategies, the precursor ion in the MS1 data reveals important characteristics as well, including charge state, intensity, monoisotopic m/z, and apex in retention time. Most importantly, the precursor's mass is essential in determining the potential chemical modification state of the underlying peptide sequence. In the timsTOF, with its additional dimension of collisional cross-section, the data representing the precursor ion also reveals the peptide's peak in ion mobility. However, the availability of tools to survey precursor ions with a wide range of abundance in timsTOF data across the full mass range is very limited. Here we present a de novo feature detector called three-dimensional intensity descent (3DID). 3DID can detect and extract peptide features down to a configurable intensity level, and finds many more features than several existing tools. 3DID is written in Python and is freely available with an open-source MIT license to facilitate experimentation and further improvement (DOI 10.5281/zenodo.6513126). The dataset used for validation of the algorithm is publicly available (ProteomeXchange identifier PXD030706).
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Affiliation(s)
- Daryl Wilding-McBride
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Victoria, Australia
- * E-mail: (DWM); (AIW)
| | - Andrew I. Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Victoria, Australia
- * E-mail: (DWM); (AIW)
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Liu L, Sandow JJ, Leslie Pedrioli DM, Samson AL, Silke N, Kratina T, Ambrose RL, Doerflinger M, Hu Z, Morrish E, Chau D, Kueh AJ, Fitzibbon C, Pellegrini M, Pearson JS, Hottiger MO, Webb AI, Lalaoui N, Silke J. Tankyrase-mediated ADP-ribosylation is a regulator of TNF-induced death. Sci Adv 2022; 8:eabh2332. [PMID: 35544574 PMCID: PMC9094663 DOI: 10.1126/sciadv.abh2332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Tumor necrosis factor (TNF) is a key component of the innate immune response. Upon binding to its receptor, TNFR1, it promotes production of other cytokines via a membrane-bound complex 1 or induces cell death via a cytosolic complex 2. To understand how TNF-induced cell death is regulated, we performed mass spectrometry of complex 2 and identified tankyrase-1 as a native component that, upon a death stimulus, mediates complex 2 poly-ADP-ribosylation (PARylation). PARylation promotes recruitment of the E3 ligase RNF146, resulting in proteasomal degradation of complex 2, thereby limiting cell death. Expression of the ADP-ribose-binding/hydrolyzing severe acute respiratory syndrome coronavirus 2 macrodomain sensitizes cells to TNF-induced death via abolishing complex 2 PARylation. This suggests that disruption of ADP-ribosylation during an infection can prime a cell to retaliate with an inflammatory cell death.
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Affiliation(s)
- Lin Liu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jarrod J. Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Deena M. Leslie Pedrioli
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zürich, Switzerland
| | - Andre L. Samson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Natasha Silke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Tobias Kratina
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Rebecca L. Ambrose
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Clayton, VIC, Australia
| | - Marcel Doerflinger
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Zhaoqing Hu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Emma Morrish
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Diep Chau
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Andrew J. Kueh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Cheree Fitzibbon
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Marc Pellegrini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jaclyn S. Pearson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Michael O. Hottiger
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zürich, Switzerland
| | - Andrew I. Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Najoua Lalaoui
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
- Corresponding author. (N.L.); (J.S.)
| | - John Silke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
- Corresponding author. (N.L.); (J.S.)
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9
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Liu Z, Dagley LF, Shield-Artin K, Young SN, Bankovacki A, Wang X, Tang M, Howitt J, Stafford CA, Nachbur U, Fitzgibbon C, Garnish SE, Webb AI, Komander D, Murphy JM, Hildebrand JM, Silke J. Oligomerization-driven MLKL ubiquitylation antagonizes necroptosis. EMBO J 2021; 40:e103718. [PMID: 34698396 DOI: 10.15252/embj.2019103718] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 09/02/2021] [Accepted: 09/20/2021] [Indexed: 11/09/2022] Open
Abstract
Mixed lineage kinase domain-like (MLKL) is the executioner in the caspase-independent form of programmed cell death called necroptosis. Receptor-interacting serine/threonine protein kinase 3 (RIPK3) phosphorylates MLKL, triggering MLKL oligomerization, membrane translocation and membrane disruption. MLKL also undergoes ubiquitylation during necroptosis, yet neither the mechanism nor the significance of this event has been demonstrated. Here, we show that necroptosis-specific multi-mono-ubiquitylation of MLKL occurs following its activation and oligomerization. Ubiquitylated MLKL accumulates in a digitonin-insoluble cell fraction comprising organellar and plasma membranes and protein aggregates. Appearance of this ubiquitylated MLKL form can be reduced by expression of a plasma membrane-located deubiquitylating enzyme. Oligomerization-induced MLKL ubiquitylation occurs on at least four separate lysine residues and correlates with its proteasome- and lysosome-dependent turnover. Using a MLKL-DUB fusion strategy, we show that constitutive removal of ubiquitin from MLKL licences MLKL auto-activation independent of necroptosis signalling in mouse and human cells. Therefore, in addition to the role of ubiquitylation in the kinetic regulation of MLKL-induced death following an exogenous necroptotic stimulus, it also contributes to restraining basal levels of activated MLKL to avoid unwanted cell death.
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Affiliation(s)
- Zikou Liu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Kristy Shield-Artin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Samuel N Young
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Aleksandra Bankovacki
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Translational Research, CSL Limited, Melbourne, VIC, Australia
| | - Xiangyi Wang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Michelle Tang
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia.,Swinburne University of Technology, Hawthorn, VIC, Australia
| | - Jason Howitt
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia.,Swinburne University of Technology, Hawthorn, VIC, Australia
| | - Che A Stafford
- Gene Centre and Department of Biochemistry, Ludwig Maximilian University of Munich, Munich, Germany
| | - Ueli Nachbur
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Cheree Fitzgibbon
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Sarah E Garnish
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - David Komander
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Joanne M Hildebrand
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - John Silke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
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10
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Sandow JJ, Tan IK, Huang AS, Masaldan S, Bernardini JP, Wardak AZ, Birkinshaw RW, Ninnis RL, Liu Z, Dalseno D, Lio D, Infusini G, Czabotar PE, Webb AI, Dewson G. Dynamic reconfiguration of pro-apoptotic BAK on membranes. EMBO J 2021; 40:e107237. [PMID: 34523147 DOI: 10.15252/embj.2020107237] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022] Open
Abstract
BAK and BAX, the effectors of intrinsic apoptosis, each undergo major reconfiguration to an activated conformer that self-associates to damage mitochondria and cause cell death. However, the dynamic structural mechanisms of this reconfiguration in the presence of a membrane have yet to be fully elucidated. To explore the metamorphosis of membrane-bound BAK, we employed hydrogen-deuterium exchange mass spectrometry (HDX-MS). The HDX-MS profile of BAK on liposomes comprising mitochondrial lipids was consistent with known solution structures of inactive BAK. Following activation, HDX-MS resolved major reconfigurations in BAK. Mutagenesis guided by our HDX-MS profiling revealed that the BCL-2 homology (BH) 4 domain maintains the inactive conformation of BAK, and disrupting this domain is sufficient for constitutive BAK activation. Moreover, the entire N-terminal region preceding the BAK oligomerisation domains became disordered post-activation and remained disordered in the activated oligomer. Removal of the disordered N-terminus did not impair, but rather slightly potentiated, BAK-mediated membrane permeabilisation of liposomes and mitochondria. Together, our HDX-MS analyses reveal new insights into the dynamic nature of BAK activation on a membrane, which may provide new opportunities for therapeutic targeting.
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Affiliation(s)
- Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Iris Kl Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Alan S Huang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Shashank Masaldan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Jonathan P Bernardini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Ahmad Z Wardak
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
| | - Richard W Birkinshaw
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Robert L Ninnis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Ziyan Liu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Destiny Dalseno
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Daisy Lio
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
| | - Giuseppi Infusini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Grant Dewson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
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11
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O'Donnell L, Rebourcet D, Dagley LF, Sgaier R, Infusini G, O'Shaughnessy PJ, Chalmel F, Fietz D, Weidner W, Legrand JMD, Hobbs RM, McLachlan RI, Webb AI, Pilatz A, Diemer T, Smith LB, Stanton PG. Sperm proteins and cancer-testis antigens are released by the seminiferous tubules in mice and men. FASEB J 2021; 35:e21397. [PMID: 33565176 PMCID: PMC7898903 DOI: 10.1096/fj.202002484r] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/21/2020] [Accepted: 01/11/2021] [Indexed: 02/06/2023]
Abstract
Sperm develop from puberty in the seminiferous tubules, inside the blood-testis barrier to prevent their recognition as "non-self" by the immune system, and it is widely assumed that human sperm-specific proteins cannot access the circulatory or immune systems. Sperm-specific proteins aberrantly expressed in cancer, known as cancer-testis antigens (CTAs), are often pursued as cancer biomarkers and therapeutic targets based on the assumption they are neoantigens absent from the circulation in healthy men. Here, we identify a wide range of germ cell-derived and sperm-specific proteins, including multiple CTAs, that are selectively deposited by the Sertoli cells of the adult mouse and human seminiferous tubules into testicular interstitial fluid (TIF) that is "outside" the blood-testis barrier. From TIF, the proteins can access the circulatory- and immune systems. Disruption of spermatogenesis decreases the abundance of these proteins in mouse TIF, and a sperm-specific CTA is significantly decreased in TIF from infertile men, suggesting that exposure of certain CTAs to the immune system could depend on fertility status. The results provide a rationale for the development of blood-based tests useful in the management of male infertility and indicate CTA candidates for cancer immunotherapy and biomarker development that could show sex-specific and male-fertility-related responses.
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Affiliation(s)
- Liza O'Donnell
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia.,Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Diane Rebourcet
- Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Laura F Dagley
- Walter and Eliza Hall Institute, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Raouda Sgaier
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia.,Department of Urology, Pediatric Urology and Andrology, Medical Faculty, Justus-Liebig-University Giessen, UKGM GmbH, Giessen, Germany
| | - Giuseppe Infusini
- Walter and Eliza Hall Institute, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Peter J O'Shaughnessy
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Frederic Chalmel
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, University Rennes, Rennes, France
| | - Daniela Fietz
- Institute for Veterinary Anatomy, Histology and Embryology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Wolfgang Weidner
- Department of Urology, Pediatric Urology and Andrology, Medical Faculty, Justus-Liebig-University Giessen, UKGM GmbH, Giessen, Germany
| | - Julien M D Legrand
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Robin M Hobbs
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Robert I McLachlan
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Andrew I Webb
- Walter and Eliza Hall Institute, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Adrian Pilatz
- Department of Urology, Pediatric Urology and Andrology, Medical Faculty, Justus-Liebig-University Giessen, UKGM GmbH, Giessen, Germany
| | - Thorsten Diemer
- Department of Urology, Pediatric Urology and Andrology, Medical Faculty, Justus-Liebig-University Giessen, UKGM GmbH, Giessen, Germany
| | - Lee B Smith
- Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia.,MRC Centre for Reproductive Health, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Peter G Stanton
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
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12
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Foot NJ, Gonzalez MB, Gembus K, Fonseka P, Sandow JJ, Nguyen TT, Tran D, Webb AI, Mathivanan S, Robker RL, Kumar S. Arrdc4-dependent extracellular vesicle biogenesis is required for sperm maturation. J Extracell Vesicles 2021; 10:e12113. [PMID: 34188787 PMCID: PMC8217992 DOI: 10.1002/jev2.12113] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 01/04/2023] Open
Abstract
Extracellular vesicles (EVs) are important players in cell to cell communication in reproductive systems. Notably, EVs have been found and characterized in the male reproductive tract, however, direct functional evidence for their importance in mediating sperm function is lacking. We have previously demonstrated that Arrdc4, a member of the α-arrestin protein family, is involved in extracellular vesicle biogenesis and release. Here we show that Arrdc4-mediated extracellular vesicle biogenesis is required for proper sperm function. Sperm from Arrdc4-/- mice develop normally through the testis but fail to acquire adequate motility and fertilization capabilities through the epididymis, as observed by reduced motility, premature acrosome reaction, reduction in zona pellucida binding and two-cell embryo production. We found a significant reduction in extracellular vesicle production by Arrdc4-/- epididymal epithelial cells, and further, supplementation of Arrdc4-/- sperm with additional vesicles dampened the acrosome reaction defect and restored zona pellucida binding. These results indicate that Arrdc4 is important for proper sperm maturation through the control of extracellular vesicle biogenesis.
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Affiliation(s)
- Natalie J. Foot
- Centre for Cancer BiologyUniversity of South Australia and SA PathologyAdelaideSouth AustraliaAustralia
- School of MedicineRobinson Research InstituteUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Macarena B. Gonzalez
- School of MedicineRobinson Research InstituteUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Kelly Gembus
- Centre for Cancer BiologyUniversity of South Australia and SA PathologyAdelaideSouth AustraliaAustralia
| | - Pamali Fonseka
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular SciencesLa Trobe UniversityMelbourneVictoriaAustralia
| | - Jarrod J. Sandow
- Advanced Technology and Biology DivisionWalter and Eliza Hall InstituteParkvilleVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneParkvilleVICAustralia
| | - Thuy Tien Nguyen
- Centre for Cancer BiologyUniversity of South Australia and SA PathologyAdelaideSouth AustraliaAustralia
- School of Biological SciencesUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Diana Tran
- School of Chemical Engineering & Advanced MaterialsUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Andrew I. Webb
- Advanced Technology and Biology DivisionWalter and Eliza Hall InstituteParkvilleVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneParkvilleVICAustralia
| | - Suresh Mathivanan
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular SciencesLa Trobe UniversityMelbourneVictoriaAustralia
| | - Rebecca L. Robker
- School of MedicineRobinson Research InstituteUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Department of Anatomy and Developmental BiologyBiomedicine Discovery InstituteMonash UniversityMelbourneVictoriaAustralia
| | - Sharad Kumar
- Centre for Cancer BiologyUniversity of South Australia and SA PathologyAdelaideSouth AustraliaAustralia
- Faculty of Health and Medical SciencesUniversity of AdelaideAdelaideSouth AustraliaAustralia
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13
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Paule SG, Heng S, Samarajeewa N, Li Y, Mansilla M, Webb AI, Nebl T, Young SL, Lessey BA, Hull ML, Scelwyn M, Lim R, Vollenhoven B, Rombauts LJ, Nie G. Podocalyxin is a key negative regulator of human endometrial epithelial receptivity for embryo implantation. Hum Reprod 2021; 36:1353-1366. [PMID: 33822049 DOI: 10.1093/humrep/deab032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 12/09/2020] [Indexed: 02/02/2023] Open
Abstract
STUDY QUESTION How is endometrial epithelial receptivity, particularly adhesiveness, regulated at the luminal epithelial surface for embryo implantation in the human? SUMMARY ANSWER Podocalyxin (PCX), a transmembrane protein, was identified as a key negative regulator of endometrial epithelial receptivity; specific downregulation of PCX in the luminal epithelium in the mid-secretory phase, likely mediated by progesterone, may act as a critical step in converting endometrial surface from a non-receptive to an implantation-permitting state. WHAT IS KNOWN ALREADY The human endometrium must undergo major molecular and cellular changes to transform from a non-receptive to a receptive state to accommodate embryo implantation. However, the fundamental mechanisms governing receptivity, particularly at the luminal surface where the embryo first interacts with, are not well understood. A widely held view is that upregulation of adhesion-promoting molecules is important, but the details are not well characterized. STUDY DESIGN, SIZE, DURATION This study first aimed to identify novel adhesion-related membrane proteins with potential roles in receptivity in primary human endometrial epithelial cells (HEECs). Further experiments were then conducted to determine candidates' in vivo expression pattern in the human endometrium across the menstrual cycle, regulation by progesterone using cell culture, and functional importance in receptivity using in vitro human embryo attachment and invasion models. PARTICIPANTS/MATERIALS, SETTING, METHODS Primary HEECs (n = 9) were isolated from the proliferative phase endometrial tissue, combined into three pools, subjected to plasma membrane protein enrichment by ultracentrifugation followed by proteomics analysis, which led to the discovery of PCX as a novel candidate of interest. Immunohistochemical analysis determined the in vivo expression pattern and cellular localization of PCX in the human endometrium across the menstrual cycle (n = 23). To investigate whether PCX is regulated by progesterone, the master driver of endometrial differentiation, primary HEECs were treated in culture with estradiol and progesterone and analyzed by RT-PCR (n = 5) and western blot (n = 4). To demonstrate that PCX acts as a negative regulator of receptivity, PCX was overexpressed in Ishikawa cells (a receptive line) and the impact on receptivity was determined using in vitro attachment (n = 3-5) and invasion models (n = 4-6), in which an Ishikawa monolayer mimicked the endometrial surface and primary human trophoblast spheroids mimicked embryos. Mann-Whitney U-test and ANOVA analyses established statistical significance at *P ≤ 0.05 and **P ≤ 0.01. MAIN RESULTS AND THE ROLE OF CHANCE PCX was expressed on the apical surface of all epithelial and endothelial cells in the non-receptive endometrium, but selectively downregulated in the luminal epithelium from the mid-secretory phase coinciding with the establishment of receptivity. Progesterone was confirmed to be able to suppress PCX in primary HEECs, suggesting this hormone likely mediates the downregulation of luminal PCX in vivo for receptivity. Overexpression of PCX in Ishikawa monolayer inhibited not only the attachment but also the penetration of human embryo surrogates, demonstrating that PCX acts as an important negative regulator of epithelial receptivity for implantation. LIMITATIONS, REASONS FOR CAUTION Primary HEECs isolated from the human endometrial tissue contained a mixture of luminal and glandular epithelial cells, as further purification into subtypes was not possible due to the lack of specific markers. Future study would need to investigate how progesterone differentially regulates PCX in endometrial epithelial subtypes. In addition, this study used primary human trophoblast spheroids as human embryo mimics and Ishikawa as endometrial epithelial cells in functional models, future studies with human blastocysts and primary epithelial cells would further validate the findings. WIDER IMPLICATIONS OF THE FINDINGS The findings of this study add important new knowledge to the understanding of human endometrial remodeling for receptivity. The identification of PCX as a negative regulator of epithelial receptivity and the knowledge that its specific downregulation in the luminal epithelium coincides with receptivity development may provide new avenues to assess endometrial receptivity and individualize endometrial preparation protocols in assisted reproductive technology (ART). The study also discovered PCX as progesterone target in HEECs, identifying a potentially useful functional biomarker to monitor progesterone action, such as in the optimization of progesterone type/dose/route of administration for luteal support. STUDY FUNDING/COMPETING INTEREST(S) Study funding was obtained from ESHRE, Monash IVF and NHMRC. LR reports potential conflict of interests (received grants from Ferring Australia; personal fees from Monash IVF Group and Ferring Australia; and non-financial support from Merck Serono, MSD, and Guerbet outside the submitted work. LR is also a minority shareholder and the Group Medical Director for Monash IVF Group, a provider of fertility preservation services). The remaining authors have no potential conflict of interest to declare. TRIAL REGISTRATION NUMBER NA.
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Affiliation(s)
- Sarah G Paule
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Sophea Heng
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Implantation and Pregnancy Research Laboratory, School of Health and Biomedical Sciences, RMIT University, VIC, Australia
| | - Nirukshi Samarajeewa
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Implantation and Pregnancy Research Laboratory, School of Health and Biomedical Sciences, RMIT University, VIC, Australia
| | - Ying Li
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Implantation and Pregnancy Research Laboratory, School of Health and Biomedical Sciences, RMIT University, VIC, Australia
| | - Mary Mansilla
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Implantation and Pregnancy Research Laboratory, School of Health and Biomedical Sciences, RMIT University, VIC, Australia
| | - Andrew I Webb
- Advance Technology and Biology Division, The Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Thomas Nebl
- Advance Technology and Biology Division, The Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Steven L Young
- Department of Obstetrics and Gynecology, University of North Carolina, Chapel Hill, NC, USA
| | - Bruce A Lessey
- Department of Obstetrics and Gynecology, Greenville Health System, Greenville, SC, USA
| | - M Louise Hull
- The Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | | | - Rebecca Lim
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, VIC, Australia
| | - Beverley Vollenhoven
- Department of Obstetrics and Gynaecology, Monash University, Clayton, VIC, Australia.,Womens and Newborn Programme, Monash Health, Clayton, VIC, Australia
| | - Luk J Rombauts
- Department of Obstetrics and Gynaecology, Monash University, Clayton, VIC, Australia.,Womens and Newborn Programme, Monash Health, Clayton, VIC, Australia
| | - Guiying Nie
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Implantation and Pregnancy Research Laboratory, School of Health and Biomedical Sciences, RMIT University, VIC, Australia
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14
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Hogg SJ, Motorna O, Cluse LA, Johanson TM, Coughlan HD, Raviram R, Myers RM, Costacurta M, Todorovski I, Pijpers L, Bjelosevic S, Williams T, Huskins SN, Kearney CJ, Devlin JR, Fan Z, Jabbari JS, Martin BP, Fareh M, Kelly MJ, Dupéré-Richer D, Sandow JJ, Feran B, Knight D, Khong T, Spencer A, Harrison SJ, Gregory G, Wickramasinghe VO, Webb AI, Taberlay PC, Bromberg KD, Lai A, Papenfuss AT, Smyth GK, Allan RS, Licht JD, Landau DA, Abdel-Wahab O, Shortt J, Vervoort SJ, Johnstone RW. Targeting histone acetylation dynamics and oncogenic transcription by catalytic P300/CBP inhibition. Mol Cell 2021; 81:2183-2200.e13. [PMID: 34019788 PMCID: PMC8183601 DOI: 10.1016/j.molcel.2021.04.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 01/19/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023]
Abstract
To separate causal effects of histone acetylation on chromatin accessibility and transcriptional output, we used integrated epigenomic and transcriptomic analyses following acute inhibition of major cellular lysine acetyltransferases P300 and CBP in hematological malignancies. We found that catalytic P300/CBP inhibition dynamically perturbs steady-state acetylation kinetics and suppresses oncogenic transcriptional networks in the absence of changes to chromatin accessibility. CRISPR-Cas9 screening identified NCOR1 and HDAC3 transcriptional co-repressors as the principal antagonists of P300/CBP by counteracting acetylation turnover kinetics. Finally, deacetylation of H3K27 provides nucleation sites for reciprocal methylation switching, a feature that can be exploited therapeutically by concomitant KDM6A and P300/CBP inhibition. Overall, this study indicates that the steady-state histone acetylation-methylation equilibrium functions as a molecular rheostat governing cellular transcription that is amenable to therapeutic exploitation as an anti-cancer regimen.
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Affiliation(s)
- Simon J Hogg
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Olga Motorna
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Monash Haematology, Monash Health, Clayton, 3168, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton, 3800, Australia
| | - Leonie A Cluse
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Hannah D Coughlan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | | | - Robert M Myers
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Matteo Costacurta
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Izabela Todorovski
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Lizzy Pijpers
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Stefan Bjelosevic
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Tobias Williams
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
| | - Shannon N Huskins
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, 7000, Australia
| | - Conor J Kearney
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Jennifer R Devlin
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Zheng Fan
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Jafar S Jabbari
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, 3000, Australia
| | - Ben P Martin
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia
| | - Mohamed Fareh
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Madison J Kelly
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Daphné Dupéré-Richer
- Division of Hematology/Oncology, The University of Florida Health Cancer Center, Gainesville, FL 32608, USA
| | - Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Breon Feran
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Deborah Knight
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia
| | - Tiffany Khong
- Australian Center for Blood Diseases, Monash University, Melbourne, 3004, Australia
| | - Andrew Spencer
- Australian Center for Blood Diseases, Monash University, Melbourne, 3004, Australia
| | - Simon J Harrison
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Clinical Hematology, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Royal Melbourne Hospital, Melbourne, 3000, Australia
| | - Gareth Gregory
- Monash Haematology, Monash Health, Clayton, 3168, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton, 3800, Australia
| | - Vihandha O Wickramasinghe
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Phillippa C Taberlay
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, 7000, Australia
| | - Kenneth D Bromberg
- Discovery, Global Pharmaceutical Research and Development, AbbVie, North Chicago, IL 60064, USA
| | - Albert Lai
- Discovery, Global Pharmaceutical Research and Development, AbbVie, North Chicago, IL 60064, USA
| | - Anthony T Papenfuss
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; School of Mathematics and Statistics, The University of Melbourne, Parkville, 3010, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Jonathan D Licht
- Division of Hematology/Oncology, The University of Florida Health Cancer Center, Gainesville, FL 32608, USA
| | - Dan A Landau
- New York Genome Center, New York, NY 10013, USA; Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jake Shortt
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Monash Haematology, Monash Health, Clayton, 3168, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton, 3800, Australia
| | - Stephin J Vervoort
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia.
| | - Ricky W Johnstone
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia.
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15
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Sandow JJ, Webb AI, Stockwell D, Kershaw NJ, Tan C, Ishido S, Alexander WS, Hilton DJ, Babon JJ, Nicola NA. Proteomic analyses reveal that immune integrins are major targets for regulation by Membrane-Associated Ring-CH (MARCH) proteins MARCH2, 3, 4 and 9. Proteomics 2021; 21:e2000244. [PMID: 33945654 DOI: 10.1002/pmic.202000244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 03/30/2021] [Accepted: 04/23/2021] [Indexed: 11/06/2022]
Abstract
MARCH proteins are membrane-associated Ring-CH E3 ubiquitin ligases that dampen immune responses by downregulating cell surface expression of major histocompatibility complexes I and II as well as immune co-stimulatory receptors. We recently showed that MARCH2,3,4 and 9 also downregulate cell surface expression of the inflammatory cytokine receptor for interleukin-6 (IL6Rα). Here we use over-expression of these MARCH proteins in the M1 myeloid leukaemia cell line and cell surface proteomic analyses to globally analyse other potential targets of these proteins. A large range of cell surface proteins regulated by more than one MARCH protein in addition to several MARCH protein-specific cell surface targets were identified most of which were downregulated by MARCH expression. Prominent among these were several integrin complexes associated with immune cell homing, adhesion and migration. Integrin α4β1 (VLA4 or VCAM-1 receptor) was downregulated only by MARCH2 and we showed that in MARCH2 knockout mice, Integrin α4 was upregulated specifically in mature B-lymphocytes and this was accompanied by decreased numbers of B-cells in the spleen.
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Affiliation(s)
- Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,The University of Melbourne, Parkville, Victoria, Australia
| | - Dina Stockwell
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Nadia J Kershaw
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,The University of Melbourne, Parkville, Victoria, Australia
| | - Cyrus Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,The University of Melbourne, Parkville, Victoria, Australia
| | - Satoshi Ishido
- Department of Microbiology, Hyogo College of Medicine, Nishinomiya, Japan
| | - Warren S Alexander
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,The University of Melbourne, Parkville, Victoria, Australia
| | - Douglas J Hilton
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,The University of Melbourne, Parkville, Victoria, Australia
| | - Jeffrey J Babon
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,The University of Melbourne, Parkville, Victoria, Australia
| | - Nicos A Nicola
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,The University of Melbourne, Parkville, Victoria, Australia
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16
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Vijayaraj SL, Feltham R, Rashidi M, Frank D, Liu Z, Simpson DS, Ebert G, Vince A, Herold MJ, Kueh A, Pearson JS, Dagley LF, Murphy JM, Webb AI, Lawlor KE, Vince JE. The ubiquitylation of IL-1β limits its cleavage by caspase-1 and targets it for proteasomal degradation. Nat Commun 2021; 12:2713. [PMID: 33976225 PMCID: PMC8113568 DOI: 10.1038/s41467-021-22979-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 04/09/2021] [Indexed: 02/06/2023] Open
Abstract
Interleukin-1β (IL-1β) is activated by inflammasome-associated caspase-1 in rare autoinflammatory conditions and in a variety of other inflammatory diseases. Therefore, IL-1β activity must be fine-tuned to enable anti-microbial responses whilst limiting collateral damage. Here, we show that precursor IL-1β is rapidly turned over by the proteasome and this correlates with its decoration by K11-linked, K63-linked and K48-linked ubiquitin chains. The ubiquitylation of IL-1β is not just a degradation signal triggered by inflammasome priming and activating stimuli, but also limits IL-1β cleavage by caspase-1. IL-1β K133 is modified by ubiquitin and forms a salt bridge with IL-1β D129. Loss of IL-1β K133 ubiquitylation, or disruption of the K133:D129 electrostatic interaction, stabilizes IL-1β. Accordingly, Il1bK133R/K133R mice have increased levels of precursor IL-1β upon inflammasome priming and increased production of bioactive IL-1β, both in vitro and in response to LPS injection. These findings identify mechanisms that can limit IL-1β activity and safeguard against damaging inflammation.
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Affiliation(s)
- Swarna L Vijayaraj
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Rebecca Feltham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Maryam Rashidi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Daniel Frank
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Zhengyang Liu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Daniel S Simpson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Gregor Ebert
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Angelina Vince
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Andrew Kueh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Jaclyn S Pearson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Microbiology, Monash University, Clayton, VIC, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Kate E Lawlor
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia. .,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia. .,Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia.
| | - James E Vince
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
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17
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Garnish SE, Meng Y, Koide A, Sandow JJ, Denbaum E, Jacobsen AV, Yeung W, Samson AL, Horne CR, Fitzgibbon C, Young SN, Smith PPC, Webb AI, Petrie EJ, Hildebrand JM, Kannan N, Czabotar PE, Koide S, Murphy JM. Conformational interconversion of MLKL and disengagement from RIPK3 precede cell death by necroptosis. Nat Commun 2021; 12:2211. [PMID: 33850121 PMCID: PMC8044208 DOI: 10.1038/s41467-021-22400-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Phosphorylation of the MLKL pseudokinase by the RIPK3 kinase leads to MLKL oligomerization, translocation to, and permeabilization of, the plasma membrane to induce necroptotic cell death. The precise choreography of MLKL activation remains incompletely understood. Here, we report Monobodies, synthetic binding proteins, that bind the pseudokinase domain of MLKL within human cells and their crystal structures in complex with the human MLKL pseudokinase domain. While Monobody-32 constitutively binds the MLKL hinge region, Monobody-27 binds MLKL via an epitope that overlaps the RIPK3 binding site and is only exposed after phosphorylated MLKL disengages from RIPK3 following necroptotic stimulation. The crystal structures identified two distinct conformations of the MLKL pseudokinase domain, supporting the idea that a conformational transition accompanies MLKL disengagement from RIPK3. These studies provide further evidence that MLKL undergoes a large conformational change upon activation, and identify MLKL disengagement from RIPK3 as a key regulatory step in the necroptosis pathway.
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Affiliation(s)
- Sarah E Garnish
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Yanxiang Meng
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Akiko Koide
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Eric Denbaum
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Annette V Jacobsen
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Andre L Samson
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Cheree Fitzgibbon
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Phoebe P C Smith
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Andrew I Webb
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Emma J Petrie
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Joanne M Hildebrand
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA.
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
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18
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Oliver MR, Horne CR, Shrestha S, Keown JR, Liang LY, Young SN, Sandow JJ, Webb AI, Goldstone DC, Lucet IS, Kannan N, Metcalf P, Murphy JM. Granulovirus PK-1 kinase activity relies on a side-to-side dimerization mode centered on the regulatory αC helix. Nat Commun 2021; 12:1002. [PMID: 33579933 PMCID: PMC7881018 DOI: 10.1038/s41467-021-21191-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/19/2021] [Indexed: 12/19/2022] Open
Abstract
The life cycle of Baculoviridae family insect viruses depends on the viral protein kinase, PK-1, to phosphorylate the regulatory protein, p6.9, to induce baculoviral genome release. Here, we report the crystal structure of Cydia pomenella granulovirus PK-1, which, owing to its likely ancestral origin among host cell AGC kinases, exhibits a eukaryotic protein kinase fold. PK-1 occurs as a rigid dimer, where an antiparallel arrangement of the αC helices at the dimer core stabilizes PK-1 in a closed, active conformation. Dimerization is facilitated by C-lobe:C-lobe and N-lobe:N-lobe interactions between protomers, including the domain-swapping of an N-terminal helix that crowns a contiguous β-sheet formed by the two N-lobes. PK-1 retains a dimeric conformation in solution, which is crucial for catalytic activity. Our studies raise the prospect that parallel, side-to-side dimeric arrangements that lock kinase domains in a catalytically-active conformation could function more broadly as a regulatory mechanism among eukaryotic protein kinases. The viral Protein Kinase-1 (PK-1) phosphorylates the regulatory protein p6.9, which facilitates baculoviral genome release. Here, the authors combine X-ray crystallography with biophysical and biochemical analyses as well as molecular dynamics simulations to characterize Cydia pomenella granulovirus PK-1, which forms a dimer with a parallel side-to-side arrangement of the kinase domains and furthermore, they provide insights into its catalytic mechanism and evolutionary relationships with other kinases.
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Affiliation(s)
- Michael R Oliver
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Safal Shrestha
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Jeremy R Keown
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lung-Yu Liang
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Andrew I Webb
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - David C Goldstone
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Isabelle S Lucet
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Peter Metcalf
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
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19
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Ju Y, Kelly HG, Dagley LF, Reynaldi A, Schlub TE, Spall SK, Bell CA, Cui J, Mitchell AJ, Lin Z, Wheatley AK, Thurecht KJ, Davenport MP, Webb AI, Caruso F, Kent SJ. Person-Specific Biomolecular Coronas Modulate Nanoparticle Interactions with Immune Cells in Human Blood. ACS Nano 2020; 14:15723-15737. [PMID: 33112593 DOI: 10.1021/acsnano.0c06679] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
When nanoparticles interact with human blood, a multitude of plasma components adsorb onto the surface of the nanoparticles, forming a biomolecular corona. Corona composition is known to be influenced by the chemical composition of nanoparticles. In contrast, the possible effects of variations in the human blood proteome between healthy individuals on the formation of the corona and its subsequent interactions with immune cells in blood are unknown. Herein, we prepared and examined a matrix of 11 particles (including organic and inorganic particles of three sizes and five surface chemistries) and plasma samples from 23 healthy donors to form donor-specific biomolecular coronas (personalized coronas) and investigated the impact of the personalized coronas on particle interactions with immune cells in human blood. Among the particles examined, poly(ethylene glycol) (PEG)-coated mesoporous silica (MS) particles, irrespective of particle size (800, 450, or 100 nm in diameter), displayed the widest range (up to 60-fold difference) of donor-dependent variance in immune cell association. In contrast, PEG particles (after MS core removal) of 860, 518, or 133 nm in diameter displayed consistent stealth behavior (negligible cell association), irrespective of plasma donor. For comparison, clinically relevant PEGylated doxorubicin-encapsulated liposomes (Doxil) (74 nm in diameter) showed significant variance in association with monocytes and B cells across all plasma donors studied. An in-depth proteomic analysis of each biomolecular corona studied was performed, and the results were compared against the nanoparticle-blood cell association results, with individual variance in the proteome driving differential association with specific immune cell types. We identified key immunoglobulin and complement proteins that explicitly enriched or depleted within the corona and which strongly correlated with the cell association pattern observed across the 23 donors. This study demonstrates how plasma variance in healthy individuals significantly influences the blood immune cell interactions of nanoparticles.
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Affiliation(s)
- Yi Ju
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hannah G Kelly
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Arnold Reynaldi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales Australia, Sydney, New South Wales 2052, Australia
| | - Timothy E Schlub
- Sydney School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Sukhdeep K Spall
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Craig A Bell
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jiwei Cui
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Andrew J Mitchell
- Department of Chemical Engineering, Materials Characterisation and Fabrication Platform, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Zhixing Lin
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Adam K Wheatley
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kristofer J Thurecht
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Miles P Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales Australia, Sydney, New South Wales 2052, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Frank Caruso
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Stephen J Kent
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia
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20
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Foers AD, Dagley LF, Chatfield S, Webb AI, Cheng L, Hill AF, Wicks IP, Pang KC. Proteomic analysis of extracellular vesicles reveals an immunogenic cargo in rheumatoid arthritis synovial fluid. Clin Transl Immunology 2020; 9:e1185. [PMID: 33204424 PMCID: PMC7648259 DOI: 10.1002/cti2.1185] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 08/12/2020] [Accepted: 09/09/2020] [Indexed: 02/06/2023] Open
Abstract
Objectives Extracellular vesicles (EVs) from rheumatoid arthritis (RA) synovial fluid (SF) have been reported to stimulate the release of pro-inflammatory mediators from recipient cells. We recently developed a size exclusion chromatography (SEC)-based method for EV isolation capable of high-quality enrichments from human SF. Here, we employed this method to accurately characterise the SF EV proteome and investigate potential contributions to inflammatory pathways in RA. Methods Using our SEC-based approach, SF EVs were purified from the joints of RA patients classified as having high-level (n = 7) or low-level inflammation (n = 5), and from osteoarthritis (OA) patients (n = 5). Protein profiles were characterised by mass spectrometry. Potential contributions of EV proteins to pathological pathways and differences in protein expression between disease groups were investigated. Results Synovial fluid EVs were present at higher concentrations in RA joints with high-level inflammation (P-value = 0.004) but were smaller in diameter (P-value = 0.03) than in low-level inflammation. In total, 1058 SF EV proteins were identified by mass spectrometry analysis. Neutrophil and fibroblast markers were overrepresented in all disease groups. Numerous proteins with potential to modulate inflammatory and immunological processes were detected, including nine citrullinated peptides. Forty-five and 135 EV-associated proteins were significantly elevated in RA joints with high-level inflammation than in RA joints with low-level inflammation and OA joints, respectively. Gene ontology analysis revealed significant enrichment for proteins associated with 'neutrophil degranulation' within SF EVs from RA joints with high-level inflammation. Conclusion Our results provide new information about SF EVs and insight into how EVs might contribute to the perpetuation of RA.
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Affiliation(s)
- Andrew D Foers
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,Department of Medical Biology University of Melbourne Parkville VIC Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,Department of Medical Biology University of Melbourne Parkville VIC Australia
| | - Simon Chatfield
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,Department of Medical Biology University of Melbourne Parkville VIC Australia.,Department of Rheumatology Royal Melbourne Hospital Parkville VIC Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,Department of Medical Biology University of Melbourne Parkville VIC Australia
| | - Lesley Cheng
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Bundoora VIC Australia
| | - Andrew F Hill
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Bundoora VIC Australia
| | - Ian P Wicks
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,Department of Medical Biology University of Melbourne Parkville VIC Australia.,Department of Rheumatology Royal Melbourne Hospital Parkville VIC Australia
| | - Ken C Pang
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,Murdoch Children's Research Institute Parkville VIC Australia.,Department of Paediatrics University of Melbourne Parkville VIC Australia.,Department of Adolescent Medicine Royal Children's Hospital. Parkville VIC Australia
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21
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Heim VJ, Dagley LF, Stafford CA, Hansen FM, Clayer E, Bankovacki A, Webb AI, Lucet IS, Silke J, Nachbur U. A regulatory region on RIPK2 is required for XIAP binding and NOD signaling activity. EMBO Rep 2020; 21:e50400. [PMID: 32954645 DOI: 10.15252/embr.202050400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/30/2020] [Accepted: 08/13/2020] [Indexed: 01/01/2023] Open
Abstract
Signaling via the intracellular pathogen receptors nucleotide-binding oligomerization domain-containing proteins NOD1 and NOD2 requires receptor interacting kinase 2 (RIPK2), an adaptor kinase that can be targeted for the treatment of various inflammatory diseases. However, the molecular mechanisms of how RIPK2 contributes to NOD signaling are not completely understood. We generated FLAG-tagged RIPK2 knock-in mice using CRISPR/Cas9 technology to study NOD signaling mechanisms at the endogenous level. Using cells from these mice, we were able to generate a detailed map of post-translational modifications on RIPK2. Similar to other reports, we did not detect ubiquitination of RIPK2 lysine 209 during NOD2 signaling. However, using site-directed mutagenesis we identified a new regulatory region on RIPK2, which dictates the crucial interaction with the E3 ligase XIAP and downstream signaling outcomes.
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Affiliation(s)
- Valentin J Heim
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
| | - Che A Stafford
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fynn M Hansen
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elise Clayer
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
| | - Aleksandra Bankovacki
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
| | - Isabelle S Lucet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
| | - John Silke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
| | - Ueli Nachbur
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Vic., Australia
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22
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Xu T, Nicolson S, Sandow JJ, Dayan S, Jiang X, Manning JA, Webb AI, Kumar S, Denton D. Cp1/cathepsin L is required for autolysosomal clearance in Drosophila. Autophagy 2020; 17:2734-2749. [PMID: 33112206 DOI: 10.1080/15548627.2020.1838105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Macroautophagy/autophagy is a highly conserved lysosomal degradative pathway important for maintaining cellular homeostasis. Much of our current knowledge of autophagy is focused on the initiation steps in this process. Recently, an understanding of later steps, particularly lysosomal fusion leading to autolysosome formation and the subsequent role of lysosomal enzymes in degradation and recycling, is becoming evident. Autophagy can function in both cell survival and cell death, however, the mechanisms that distinguish adaptive/survival autophagy from autophagy-dependent cell death remain to be established. Here, using proteomic analysis of Drosophila larval midguts during degradation, we identify a group of proteins with peptidase activity, suggesting a role in autophagy-dependent cell death. We show that Cp1/cathepsin L-deficient larval midgut cells accumulate aberrant autophagic vesicles due to a block in autophagic flux, yet later stages of midgut degradation are not compromised. The accumulation of large aberrant autolysosomes in the absence of Cp1 appears to be the consequence of decreased degradative capacity as they contain undigested cytoplasmic material, rather than a defect in autophagosome-lysosome fusion. Finally, we find that other cathepsins may also contribute to proper autolysosomal degradation in Drosophila larval midgut cells. Our findings provide evidence that cathepsins play an essential role in the autolysosome to maintain basal autophagy flux by balancing autophagosome production and turnover.
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Affiliation(s)
- Tianqi Xu
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
| | - Shannon Nicolson
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
| | - Jarrod J Sandow
- Advanced Technology and Biology, The Walter & Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Sonia Dayan
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
| | - Xin Jiang
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
| | - Jantina A Manning
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
| | - Andrew I Webb
- Advanced Technology and Biology, The Walter & Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
| | - Donna Denton
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
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23
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Petrie EJ, Sandow JJ, Lehmann WIL, Liang LY, Coursier D, Young SN, Kersten WJA, Fitzgibbon C, Samson AL, Jacobsen AV, Lowes KN, Au AE, Jousset Sabroux H, Lalaoui N, Webb AI, Lessene G, Manning G, Lucet IS, Murphy JM. Viral MLKL Homologs Subvert Necroptotic Cell Death by Sequestering Cellular RIPK3. Cell Rep 2020; 28:3309-3319.e5. [PMID: 31553902 DOI: 10.1016/j.celrep.2019.08.055] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 07/04/2019] [Accepted: 08/16/2019] [Indexed: 11/30/2022] Open
Abstract
Necroptotic cell death has been implicated in many human pathologies and is thought to have evolved as an innate immunity mechanism. The pathway relies on two key effectors: the kinase receptor-interacting protein kinase 3 (RIPK3) and the terminal effector, the pseudokinase mixed-lineage kinase-domain-like (MLKL). We identify proteins with high sequence similarity to the pseudokinase domain of MLKL in poxvirus genomes. Expression of these proteins from the BeAn 58058 and Cotia poxviruses, but not swinepox, in human and mouse cells blocks cellular MLKL activation and necroptotic cell death. We show that viral MLKL-like proteins function as dominant-negative mimics of host MLKL, which inhibit necroptosis by sequestering RIPK3 via its kinase domain to thwart MLKL engagement and phosphorylation. These data support an ancestral role for necroptosis in defense against pathogens. Furthermore, mimicry of a cellular pseudokinase by a pathogen adds to the growing repertoire of functions performed by pseudokinases in signal transduction.
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Affiliation(s)
- Emma J Petrie
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia.
| | - Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Wil I L Lehmann
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Lung-Yu Liang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Diane Coursier
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Samuel N Young
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Wilhelmus J A Kersten
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Cheree Fitzgibbon
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - André L Samson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Annette V Jacobsen
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Kym N Lowes
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Amanda E Au
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Hélène Jousset Sabroux
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Najoua Lalaoui
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Guillaume Lessene
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Gerard Manning
- Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Isabelle S Lucet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia.
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24
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Galeano Niño JL, Pageon SV, Tay SS, Colakoglu F, Kempe D, Hywood J, Mazalo JK, Cremasco J, Govendir MA, Dagley LF, Hsu K, Rizzetto S, Zieba J, Rice G, Prior V, O'Neill GM, Williams RJ, Nisbet DR, Kramer B, Webb AI, Luciani F, Read MN, Biro M. Cytotoxic T cells swarm by homotypic chemokine signalling. eLife 2020; 9:56554. [PMID: 33046212 PMCID: PMC7669268 DOI: 10.7554/elife.56554] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/27/2020] [Indexed: 12/30/2022] Open
Abstract
Cytotoxic T lymphocytes (CTLs) are thought to arrive at target sites either via random search or following signals by other leukocytes. Here, we reveal independent emergent behaviour in CTL populations attacking tumour masses. Primary murine CTLs coordinate their migration in a process reminiscent of the swarming observed in neutrophils. CTLs engaging cognate targets accelerate the recruitment of distant T cells through long-range homotypic signalling, in part mediated via the diffusion of chemokines CCL3 and CCL4. Newly arriving CTLs augment the chemotactic signal, further accelerating mass recruitment in a positive feedback loop. Activated effector human T cells and chimeric antigen receptor (CAR) T cells similarly employ intra-population signalling to drive rapid convergence. Thus, CTLs recognising a cognate target can induce a localised mass response by amplifying the direct recruitment of additional T cells independently of other leukocytes.
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Affiliation(s)
- Jorge Luis Galeano Niño
- EMBL Australia, Single Molecule Science node, University of New South Wales, Sydney, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Sophie V Pageon
- EMBL Australia, Single Molecule Science node, University of New South Wales, Sydney, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Szun S Tay
- EMBL Australia, Single Molecule Science node, University of New South Wales, Sydney, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Feyza Colakoglu
- EMBL Australia, Single Molecule Science node, University of New South Wales, Sydney, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Daryan Kempe
- EMBL Australia, Single Molecule Science node, University of New South Wales, Sydney, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Jack Hywood
- Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Jessica K Mazalo
- EMBL Australia, Single Molecule Science node, University of New South Wales, Sydney, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - James Cremasco
- EMBL Australia, Single Molecule Science node, University of New South Wales, Sydney, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Matt A Govendir
- EMBL Australia, Single Molecule Science node, University of New South Wales, Sydney, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Kenneth Hsu
- Children's Cancer Research Unit, The Children's Hospital at Westmead, Sydney, Australia
| | - Simone Rizzetto
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia.,The Kirby Institute for Infection and Immunity in Society, UNSW, Sydney, Australia
| | - Jerzy Zieba
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia.,Neuroscience Research Australia (NeuRA), Randwick, Australia
| | - Gregory Rice
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, Canada
| | - Victoria Prior
- Children's Cancer Research Unit, The Children's Hospital at Westmead, Sydney, Australia.,Discipline of Child and Adolescent Health, University of Sydney, Sydney, Australia
| | - Geraldine M O'Neill
- Children's Cancer Research Unit, The Children's Hospital at Westmead, Sydney, Australia.,Discipline of Child and Adolescent Health, University of Sydney, Sydney, Australia
| | - Richard J Williams
- Biofab3D, St. Vincent's Hospital, Melbourne, Australia.,Institute for Innovation in Mental and Physical Health and Clinical Translation (iMPACT), School of Medicine, Deakin University, Victoria, Australia
| | - David R Nisbet
- Biofab3D, St. Vincent's Hospital, Melbourne, Australia.,Advanced Biomaterials Lab, Research School of Engineering, ANU, Canberra, Australia
| | - Belinda Kramer
- Children's Cancer Research Unit, The Children's Hospital at Westmead, Sydney, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Fabio Luciani
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia.,The Kirby Institute for Infection and Immunity in Society, UNSW, Sydney, Australia
| | - Mark N Read
- School of Computer Science, Westmead Initiative, and Charles Perkins Centre, University of Sydney, Sydney, Australia
| | - Maté Biro
- EMBL Australia, Single Molecule Science node, University of New South Wales, Sydney, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
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25
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Cowan AD, Smith NA, Sandow JJ, Kapp EA, Rustam YH, Murphy JM, Brouwer JM, Bernardini JP, Roy MJ, Wardak AZ, Tan IK, Webb AI, Gulbis JM, Smith BJ, Reid GE, Dewson G, Colman PM, Czabotar PE. BAK core dimers bind lipids and can be bridged by them. Nat Struct Mol Biol 2020; 27:1024-1031. [DOI: 10.1038/s41594-020-0494-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/31/2020] [Indexed: 12/27/2022]
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26
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Xu Y, Kirk NS, Venugopal H, Margetts MB, Croll TI, Sandow JJ, Webb AI, Delaine CA, Forbes BE, Lawrence MC. How IGF-II Binds to the Human Type 1 Insulin-like Growth Factor Receptor. Structure 2020; 28:786-798.e6. [PMID: 32459985 PMCID: PMC7343240 DOI: 10.1016/j.str.2020.05.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/23/2020] [Accepted: 05/05/2020] [Indexed: 02/06/2023]
Abstract
Human type 1 insulin-like growth factor receptor (IGF-1R) signals chiefly in response to the binding of insulin-like growth factor I. Relatively little is known about the role of insulin-like growth factor II signaling via IGF-1R, despite the affinity of insulin-like growth factor II for IGF-1R being within an order of magnitude of that of insulin-like growth factor I. Here, we describe the cryoelectron microscopy structure of insulin-like growth factor II bound to a leucine-zipper-stabilized IGF-1R ectodomain, determined in two conformations to a maximum average resolution of 3.2 Å. The two conformations differ in the relative separation of their respective points of membrane entry, and comparison with the structure of insulin-like growth factor I bound to IGF-1R reveals long-suspected differences in the way in which the critical C domain of the respective growth factors interact with IGF-1R.
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Affiliation(s)
- Yibin Xu
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3050, Australia
| | - Nicholas S Kirk
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3050, Australia
| | - Hariprasad Venugopal
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC 3800, Australia
| | - Mai B Margetts
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Tristan I Croll
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge CB2 0XY, UK
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3050, Australia
| | - Andrew I Webb
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3050, Australia
| | - Carlie A Delaine
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, SA 5042, Australia
| | - Briony E Forbes
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, SA 5042, Australia
| | - Michael C Lawrence
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3050, Australia.
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27
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Chen K, Birkinshaw RW, Gurzau AD, Wanigasuriya I, Wang R, Iminitoff M, Sandow JJ, Young SN, Hennessy PJ, Willson TA, Heckmann DA, Webb AI, Blewitt ME, Czabotar PE, Murphy JM. Crystal structure of the hinge domain of Smchd1 reveals its dimerization mode and nucleic acid-binding residues. Sci Signal 2020; 13:13/636/eaaz5599. [PMID: 32546545 DOI: 10.1126/scisignal.aaz5599] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1) is an epigenetic regulator in which polymorphisms cause the human developmental disorder, Bosma arhinia micropthalmia syndrome, and the degenerative disease, facioscapulohumeral muscular dystrophy. SMCHD1 is considered a noncanonical SMC family member because its hinge domain is C-terminal, because it homodimerizes rather than heterodimerizes, and because SMCHD1 contains a GHKL-type, rather than an ABC-type ATPase domain at its N terminus. The hinge domain has been previously implicated in chromatin association; however, the underlying mechanism involved and the basis for SMCHD1 homodimerization are unclear. Here, we used x-ray crystallography to solve the three-dimensional structure of the Smchd1 hinge domain. Together with structure-guided mutagenesis, we defined structural features of the hinge domain that participated in homodimerization and nucleic acid binding, and we identified a functional hotspot required for chromatin localization in cells. This structure provides a template for interpreting the mechanism by which patient polymorphisms within the SMCHD1 hinge domain could compromise function and lead to facioscapulohumeral muscular dystrophy.
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Affiliation(s)
- Kelan Chen
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Richard W Birkinshaw
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Alexandra D Gurzau
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Iromi Wanigasuriya
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Ruoyun Wang
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Megan Iminitoff
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia
| | - Patrick J Hennessy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia
| | - Tracy A Willson
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Denise A Heckmann
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Andrew I Webb
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Marnie E Blewitt
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia.,School of Biosciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
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28
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Le Nours J, Gherardin NA, Ramarathinam SH, Awad W, Wiede F, Gully BS, Khandokar Y, Praveena T, Wubben JM, Sandow JJ, Webb AI, von Borstel A, Rice MT, Redmond SJ, Seneviratna R, Sandoval-Romero ML, Li S, Souter MNT, Eckle SBG, Corbett AJ, Reid HH, Liu L, Fairlie DP, Giles EM, Westall GP, Tothill RW, Davey MS, Berry R, Tiganis T, McCluskey J, Pellicci DG, Purcell AW, Uldrich AP, Godfrey DI, Rossjohn J. A class of γδ T cell receptors recognize the underside of the antigen-presenting molecule MR1. Science 2020; 366:1522-1527. [PMID: 31857486 DOI: 10.1126/science.aav3900] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 09/20/2019] [Accepted: 11/21/2019] [Indexed: 12/12/2022]
Abstract
T cell receptors (TCRs) recognize antigens presented by major histocompatibility complex (MHC) and MHC class I-like molecules. We describe a diverse population of human γδ T cells isolated from peripheral blood and tissues that exhibit autoreactivity to the monomorphic MHC-related protein 1 (MR1). The crystal structure of a γδTCR-MR1-antigen complex starkly contrasts with all other TCR-MHC and TCR-MHC-I-like complex structures. Namely, the γδTCR binds underneath the MR1 antigen-binding cleft, where contacts are dominated by the MR1 α3 domain. A similar pattern of reactivity was observed for diverse MR1-restricted γδTCRs from multiple individuals. Accordingly, we simultaneously report MR1 as a ligand for human γδ T cells and redefine the parameters for TCR recognition.
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Affiliation(s)
- Jérôme Le Nours
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Nicholas A Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Sri H Ramarathinam
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Wael Awad
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Florian Wiede
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Benjamin S Gully
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Yogesh Khandokar
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - T Praveena
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jacinta M Wubben
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Anouk von Borstel
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Michael T Rice
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Samuel J Redmond
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Rebecca Seneviratna
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Maria L Sandoval-Romero
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Michael N T Souter
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Hugh H Reid
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Ligong Liu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P Fairlie
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Edward M Giles
- Department of Paediatrics, Monash University, and Centre for Innate Immunity and Infectious Disease, Hudson Institute of Medicine, Clayton, Victoria 3168, Australia
| | - Glen P Westall
- Lung Transplant Service, Alfred Hospital, Melbourne, Victoria 3004, Australia.,Department of Medicine, Monash University, Clayton, Victoria 3800, Australia
| | - Richard W Tothill
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Parkville, Victoria 3052, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3000, Australia
| | - Martin S Davey
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Richard Berry
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Tony Tiganis
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Daniel G Pellicci
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Adam P Uldrich
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia. .,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia. .,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
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Rautela J, Dagley LF, Kratina T, Anthony A, Goh W, Surgenor E, Delconte RB, Webb AI, Elwood N, Groom JR, Souza-Fonseca-Guimaraes F, Corcoran L, Huntington ND. Generation of novel Id2 and E2-2, E2A and HEB antibodies reveals novel Id2 binding partners and species-specific expression of E-proteins in NK cells. Mol Immunol 2019; 115:56-63. [DOI: 10.1016/j.molimm.2018.08.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/13/2018] [Accepted: 08/17/2018] [Indexed: 12/11/2022]
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30
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Hayman TJ, Hsu AC, Kolesnik TB, Dagley LF, Willemsen J, Tate MD, Baker PJ, Kershaw NJ, Kedzierski L, Webb AI, Wark PA, Kedzierska K, Masters SL, Belz GT, Binder M, Hansbro PM, Nicola NA, Nicholson SE. RIPLET, and not TRIM25, is required for endogenous RIG-I-dependent antiviral responses. Immunol Cell Biol 2019; 97:840-852. [PMID: 31335993 DOI: 10.1111/imcb.12284] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/24/2022]
Abstract
The innate immune system is our first line of defense against viral pathogens. Host cell pattern recognition receptors sense viral components and initiate immune signaling cascades that result in the production of an array of cytokines to combat infection. Retinoic acid-inducible gene-I (RIG-I) is a pattern recognition receptor that recognizes viral RNA and, when activated, results in the production of type I and III interferons (IFNs) and the upregulation of IFN-stimulated genes. Ubiquitination of RIG-I by the E3 ligases tripartite motif-containing 25 (TRIM25) and Riplet is thought to be requisite for RIG-I activation; however, recent studies have questioned the relative importance of these two enzymes for RIG-I signaling. In this study, we show that deletion of Trim25 does not affect the IFN response to either influenza A virus (IAV), influenza B virus, Sendai virus or several RIG-I agonists. This is in contrast to deletion of either Rig-i or Riplet, which completely abrogated RIG-I-dependent IFN responses. This was consistent in both mouse and human cell lines, as well as in normal human bronchial cells. With most of the current TRIM25 literature based on exogenous expression, these findings provide critical evidence that Riplet, and not TRIM25, is required endogenously for the ubiquitination of RIG-I. Despite this, loss of TRIM25 results in greater susceptibility to IAV infection in vivo, suggesting that it may have an alternative role in host antiviral defense. This study refines our understanding of RIG-I signaling in viral infections and will inform future studies in the field.
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Affiliation(s)
- Thomas J Hayman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Alan C Hsu
- Priority Research Centre for Asthma and Respiratory Diseases, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
| | - Tatiana B Kolesnik
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Joschka Willemsen
- Research Group Dynamics of Early Viral Infection and the Innate Antiviral Response, Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michelle D Tate
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular Translational Science, School of Clinical Sciences, Monash University, Clayton, VIC, Australia
| | - Paul J Baker
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Nadia J Kershaw
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Lukasz Kedzierski
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Peter A Wark
- Priority Research Centre for Asthma and Respiratory Diseases, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
- Centre for Inflammation, Centenary Institute, The University of Technology Sydney, Sydney, NSW, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Seth L Masters
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Gabrielle T Belz
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Marco Binder
- Research Group Dynamics of Early Viral Infection and the Innate Antiviral Response, Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philip M Hansbro
- Priority Research Centre for Asthma and Respiratory Diseases, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
- Centre for Inflammation, Centenary Institute, The University of Technology Sydney, Sydney, NSW, Australia
| | - Nicos A Nicola
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Sandra E Nicholson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
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31
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Rautela J, Dagley LF, de Oliveira CC, Schuster IS, Hediyeh-Zadeh S, Delconte RB, Cursons J, Hennessy R, Hutchinson DS, Harrison C, Kita B, Vivier E, Webb AI, Degli-Esposti MA, Davis MJ, Huntington ND, Souza-Fonseca-Guimaraes F. Therapeutic blockade of activin-A improves NK cell function and antitumor immunity. Sci Signal 2019; 12:12/596/eaat7527. [PMID: 31455725 DOI: 10.1126/scisignal.aat7527] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Natural killer (NK) cells are innate lymphocytes that play a major role in immunosurveillance against tumor initiation and metastatic spread. The signals and checkpoints that regulate NK cell fitness and function in the tumor microenvironment are not well defined. Transforming growth factor-β (TGF-β) is a suppressor of NK cells that inhibits interleukin-15 (IL-15)-dependent signaling events and increases the abundance of receptors that promote tissue residency. Here, we showed that NK cells express the type I activin receptor ALK4, which, upon binding to its ligand activin-A, phosphorylated SMAD2/3 to suppress IL-15-mediated NK cell metabolism. Activin-A impaired human and mouse NK cell proliferation and reduced the production of granzyme B to impair tumor killing. Similar to TGF-β, activin-A also induced SMAD2/3 phosphorylation and stimulated NK cells to increase their cell surface expression of several markers of ILC1 cells. Activin-A also induced these changes in TGF-β receptor-deficient NK cells, suggesting that activin-A and TGF-β stimulate independent pathways that drive SMAD2/3-mediated NK cell suppression. Last, inhibition of activin-A by follistatin substantially slowed orthotopic melanoma growth in mice. These data highlight the relevance of examining TGF-β-independent SMAD2/3 signaling mechanisms as a therapeutic axis to relieve NK cell suppression and promote antitumor immunity.
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Affiliation(s)
- Jai Rautela
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Laura F Dagley
- Systems Biology and Personalized Medicine Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Carolina C de Oliveira
- Laboratório de Células Inflamatórias e Neoplásicas, Departamento de Biologia Celular, SCB, Centro Politecnico, Universidade Federal do Paraná, Curitiba, CEP 81531-980, PR, Brazil
| | - Iona S Schuster
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, University of Western Australia, Crawley, Western Australia, Australia.,Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia.,Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Soroor Hediyeh-Zadeh
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology and Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Rebecca B Delconte
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Joseph Cursons
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology and Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Robert Hennessy
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Dana S Hutchinson
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Craig Harrison
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Badia Kita
- Paranta Biosciences Limited, Melbourne, Victoria 3004, Australia
| | - Eric Vivier
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Inserm, CNRS, 13288 Marseille, France
| | - Andrew I Webb
- Systems Biology and Personalized Medicine Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Mariapia A Degli-Esposti
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, University of Western Australia, Crawley, Western Australia, Australia.,Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia.,Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Melissa J Davis
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology and Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Nicholas D Huntington
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Fernando Souza-Fonseca-Guimaraes
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia. .,University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
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32
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Dagley LF, Infusini G, Larsen RH, Sandow JJ, Webb AI. Universal Solid-Phase Protein Preparation (USP3) for Bottom-up and Top-down Proteomics. J Proteome Res 2019; 18:2915-2924. [DOI: 10.1021/acs.jproteome.9b00217] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Laura F. Dagley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Giuseppe Infusini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Rune H. Larsen
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jarrod J. Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Andrew I. Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
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33
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Dengler MA, Robin AY, Gibson L, Li MX, Sandow JJ, Iyer S, Webb AI, Westphal D, Dewson G, Adams JM. BAX Activation: Mutations Near Its Proposed Non-canonical BH3 Binding Site Reveal Allosteric Changes Controlling Mitochondrial Association. Cell Rep 2019; 27:359-373.e6. [DOI: 10.1016/j.celrep.2019.03.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/13/2019] [Accepted: 03/12/2019] [Indexed: 12/26/2022] Open
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34
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Wong W, Huang R, Menant S, Hong C, Sandow JJ, Birkinshaw RW, Healer J, Hodder AN, Kanjee U, Tonkin CJ, Heckmann D, Soroka V, Søgaard TMM, Jørgensen T, Duraisingh MT, Czabotar PE, de Jongh WA, Tham WH, Webb AI, Yu Z, Cowman AF. Structure of Plasmodium falciparum Rh5-CyRPA-Ripr invasion complex. Nature 2018; 565:118-121. [PMID: 30542156 DOI: 10.1038/s41586-018-0779-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/25/2018] [Indexed: 01/24/2023]
Abstract
Plasmodium falciparum causes the severe form of malaria that has high levels of mortality in humans. Blood-stage merozoites of P. falciparum invade erythrocytes, and this requires interactions between multiple ligands from the parasite and receptors in hosts. These interactions include the binding of the Rh5-CyRPA-Ripr complex with the erythrocyte receptor basigin1,2, which is an essential step for entry into human erythrocytes. Here we show that the Rh5-CyRPA-Ripr complex binds the erythrocyte cell line JK-1 significantly better than does Rh5 alone, and that this binding occurs through the insertion of Rh5 and Ripr into host membranes as a complex with high molecular weight. We report a cryo-electron microscopy structure of the Rh5-CyRPA-Ripr complex at subnanometre resolution, which reveals the organization of this essential invasion complex and the mode of interactions between members of the complex, and shows that CyRPA is a critical mediator of complex assembly. Our structure identifies blades 4-6 of the β-propeller of CyRPA as contact sites for Rh5 and Ripr. The limited contacts between Rh5-CyRPA and CyRPA-Ripr are consistent with the dissociation of Rh5 and Ripr from CyRPA for membrane insertion. A comparision of the crystal structure of Rh5-basigin with the cryo-electron microscopy structure of Rh5-CyRPA-Ripr suggests that Rh5 and Ripr are positioned parallel to the erythrocyte membrane before membrane insertion. This provides information on the function of this complex, and thereby provides insights into invasion by P. falciparum.
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Affiliation(s)
- Wilson Wong
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Rick Huang
- CryoEM Shared Resources, Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Sebastien Menant
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Chuan Hong
- CryoEM Shared Resources, Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Richard W Birkinshaw
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Julie Healer
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Anthony N Hodder
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Usheer Kanjee
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Christopher J Tonkin
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Denise Heckmann
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | | | | | | | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | | | - Wai-Hong Tham
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew I Webb
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Zhiheng Yu
- CryoEM Shared Resources, Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Alan F Cowman
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
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35
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Uboldi AD, Wilde ML, McRae EA, Stewart RJ, Dagley LF, Yang L, Katris NJ, Hapuarachchi SV, Coffey MJ, Lehane AM, Botte CY, Waller RF, Webb AI, McConville MJ, Tonkin CJ. Protein kinase A negatively regulates Ca2+ signalling in Toxoplasma gondii. PLoS Biol 2018; 16:e2005642. [PMID: 30208022 PMCID: PMC6152992 DOI: 10.1371/journal.pbio.2005642] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 09/24/2018] [Accepted: 08/20/2018] [Indexed: 11/18/2022] Open
Abstract
The phylum Apicomplexa comprises a group of obligate intracellular parasites that alternate between intracellular replicating stages and actively motile extracellular forms that move through tissue. Parasite cytosolic Ca2+ signalling activates motility, but how this is switched off after invasion is complete to allow for replication to begin is not understood. Here, we show that the cyclic adenosine monophosphate (cAMP)-dependent protein kinase A catalytic subunit 1 (PKAc1) of Toxoplasma is responsible for suppression of Ca2+ signalling upon host cell invasion. We demonstrate that PKAc1 is sequestered to the parasite periphery by dual acylation of PKA regulatory subunit 1 (PKAr1). Upon genetic depletion of PKAc1 we show that newly invaded parasites exit host cells shortly thereafter, in a perforin-like protein 1 (PLP-1)-dependent fashion. Furthermore, we demonstrate that loss of PKAc1 prevents rapid down-regulation of cytosolic [Ca2+] levels shortly after invasion. We also provide evidence that loss of PKAc1 sensitises parasites to cyclic GMP (cGMP)-induced Ca2+ signalling, thus demonstrating a functional link between cAMP and these other signalling modalities. Together, this work provides a new paradigm in understanding how Toxoplasma and related apicomplexan parasites regulate infectivity. Central to pathogenesis and infectivity of Toxoplasma and related parasites is their ability to move through tissue, invade host cells, and establish a replicative niche. Ca2+-dependent signalling pathways are important for activating motility, host cell invasion, and egress, yet how this signalling is turned off after invasion is unclear. Here, we show that a cAMP-dependent protein kinase A (PKA) is essential for rapid suppression of Ca2+ signalling upon completion of host cell invasion. Parasites lacking this kinase rapidly invoke an egress program to re-exit host cells, thus preventing the establishment of a stable infection. This finding therefore highlights the first factor required for Toxoplasma (and any related apicomplexan parasite) to switch from invasive to the replicative forms.
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Affiliation(s)
- Alessandro D. Uboldi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Mary-Louise Wilde
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Emi A. McRae
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Rebecca J. Stewart
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Laura F. Dagley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Luning Yang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- School of Medicine, Tsinghua University, Beijing, China
| | - Nicholas J. Katris
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Institute of Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | | | - Michael J. Coffey
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Adele M. Lehane
- Research School of Biology, The Australian National University, A.C.T., Australia
| | - Cyrille Y. Botte
- Institute of Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Ross F. Waller
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Andrew I. Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Malcolm J. McConville
- Department of Biochemistry and Molecular Biology, Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Christopher J. Tonkin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- * E-mail:
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36
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Seidi A, Muellner-Wong LS, Rajendran E, Tjhin ET, Dagley LF, Aw VY, Faou P, Webb AI, Tonkin CJ, van Dooren GG. Elucidating the mitochondrial proteome of Toxoplasma gondii reveals the presence of a divergent cytochrome c oxidase. eLife 2018; 7:38131. [PMID: 30204084 PMCID: PMC6156079 DOI: 10.7554/elife.38131] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 09/09/2018] [Indexed: 12/17/2022] Open
Abstract
The mitochondrion of apicomplexan parasites is critical for parasite survival, although the full complement of proteins that localize to this organelle has not been defined. Here we undertake two independent approaches to elucidate the mitochondrial proteome of the apicomplexan Toxoplasma gondii. We identify approximately 400 mitochondrial proteins, many of which lack homologs in the animals that these parasites infect, and most of which are important for parasite growth. We demonstrate that one such protein, termed TgApiCox25, is an important component of the parasite cytochrome c oxidase (COX) complex. We identify numerous other apicomplexan-specific components of COX, and conclude that apicomplexan COX, and apicomplexan mitochondria more generally, differ substantially in their protein composition from the hosts they infect. Our study highlights the diversity that exists in mitochondrial proteomes across the eukaryotic domain of life, and provides a foundation for defining unique aspects of mitochondrial biology in an important phylum of parasites.
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Affiliation(s)
- Azadeh Seidi
- Research School of Biology, Australian National University, Canberra, Australia
| | | | - Esther Rajendran
- Research School of Biology, Australian National University, Canberra, Australia
| | - Edwin T Tjhin
- Research School of Biology, Australian National University, Canberra, Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Victoria, Australia
| | - Vincent Yt Aw
- Research School of Biology, Australian National University, Canberra, Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Victoria, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Victoria, Australia
| | - Christopher J Tonkin
- The Walter and Eliza Hall Institute of Medical Research, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Victoria, Australia
| | - Giel G van Dooren
- Research School of Biology, Australian National University, Canberra, Australia
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37
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Furniss RCD, Low WW, Mavridou DAI, Dagley LF, Webb AI, Tate EW, Clements A. Plasma membrane profiling during enterohemorrhagic E. coli infection reveals that the metalloprotease StcE cleaves CD55 from host epithelial surfaces. J Biol Chem 2018; 293:17188-17199. [PMID: 30190327 PMCID: PMC6222108 DOI: 10.1074/jbc.ra118.005114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 08/29/2018] [Indexed: 01/01/2023] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is one of several E. coli pathotypes that infect the intestinal tract and cause disease. Formation of the characteristic attaching and effacing lesion on the surface of infected cells causes significant remodeling of the host cell surface; however, limited information is available about changes at the protein level. Here we employed plasma membrane profiling, a quantitative cell-surface proteomics technique, to identify host proteins whose cell-surface levels are altered during infection. Using this method, we quantified more than 1100 proteins, 280 of which showed altered cell-surface levels after exposure to EHEC. 22 host proteins were significantly reduced on the surface of infected epithelial cells. These included both known and unknown targets of EHEC infection. The complement decay–accelerating factor cluster of differentiation 55 (CD55) exhibited the greatest reduction in cell-surface levels during infection. We showed by flow cytometry and Western blot analysis that CD55 is cleaved from the cell surface by the EHEC-specific protease StcE and found that StcE-mediated CD55 cleavage results in increased neutrophil adhesion to the apical surface of intestinal epithelial cells. This suggests that StcE alters host epithelial surfaces to depress neutrophil transepithelial migration during infection. This work is the first report of the global manipulation of the epithelial cell surface by a bacterial pathogen and illustrates the power of quantitative cell-surface proteomics in uncovering critical aspects of bacterial infection biology.
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Affiliation(s)
- R Christopher D Furniss
- From the MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ United Kingdom
| | - Wen Wen Low
- From the MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ United Kingdom
| | - Despoina A I Mavridou
- From the MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ United Kingdom
| | - Laura F Dagley
- Walter and Eliza Hall Institute of Medical Research, Melbourne 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne 3050, Australia, and
| | - Andrew I Webb
- Walter and Eliza Hall Institute of Medical Research, Melbourne 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne 3050, Australia, and
| | - Edward W Tate
- Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| | - Abigail Clements
- From the MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ United Kingdom,
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38
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Marapana DS, Dagley LF, Sandow JJ, Nebl T, Triglia T, Pasternak M, Dickerman BK, Crabb BS, Gilson PR, Webb AI, Boddey JA, Cowman AF. Plasmepsin V cleaves malaria effector proteins in a distinct endoplasmic reticulum translocation interactome for export to the erythrocyte. Nat Microbiol 2018; 3:1010-1022. [DOI: 10.1038/s41564-018-0219-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 07/13/2018] [Indexed: 01/10/2023]
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39
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Foers AD, Chatfield S, Dagley LF, Scicluna BJ, Webb AI, Cheng L, Hill AF, Wicks IP, Pang KC. Enrichment of extracellular vesicles from human synovial fluid using size exclusion chromatography. J Extracell Vesicles 2018; 7:1490145. [PMID: 29963299 PMCID: PMC6022248 DOI: 10.1080/20013078.2018.1490145] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/12/2018] [Indexed: 12/22/2022] Open
Abstract
As a complex biological fluid, human synovial fluid (SF) presents challenges for extracellular vesicle (EV) enrichment using standard methods. In this study of human SF, a size exclusion chromatography (SEC)-based method of EV enrichment is shown to deplete contaminants that remain after standard ultracentrifugation-based enrichment methods. Specifically, considerable levels of serum albumin, the high-density lipoprotein marker, apolipoprotein A-I, fibronectin and other extracellular proteins and debris are present in EVs prepared by differential ultracentrifugation. While the addition of a sucrose density gradient purification step improved purification quality, some contamination remained. In contrast, using a SEC-based approach, SF EVs were efficiently separated from serum albumin, apolipoprotein A-I and additional contaminating proteins that co-purified with high-speed centrifugation. Finally, using high-resolution mass spectrometry analysis, we found that residual contaminants which remain after SEC, such as fibronectin and other extracellular proteins, can be successfully depleted by proteinase K. Taken together, our results highlight the limitations of ultracentrifugation-based methods of EV isolation from complex biological fluids and suggest that SEC can be used to obtain higher purity EV samples. In this way, SEC-based methods are likely to be useful for identifying EV-enriched components and improving understanding of EV function in disease.
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Affiliation(s)
- Andrew D Foers
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Simon Chatfield
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.,Department of Rheumatology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Laura F Dagley
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Benjamin J Scicluna
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Andrew I Webb
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Lesley Cheng
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Andrew F Hill
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Ian P Wicks
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.,Department of Rheumatology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ken C Pang
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Department of Psychiatry, University of Melbourne, Parkville, Victoria, Australia.,Genetics Theme, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Adolescent Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
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40
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Schuelein R, Spencer H, Dagley LF, Li PF, Luo L, Stow JL, Abraham G, Naderer T, Gomez-Valero L, Buchrieser C, Sugimoto C, Yamagishi J, Webb AI, Pasricha S, Hartland EL. Targeting of RNA Polymerase II by a nuclear Legionella pneumophila Dot/Icm effector SnpL. Cell Microbiol 2018; 20:e12852. [PMID: 29691989 DOI: 10.1111/cmi.12852] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 03/24/2018] [Accepted: 04/11/2018] [Indexed: 12/28/2022]
Abstract
The intracellular pathogen Legionella pneumophila influences numerous eukaryotic cellular processes through the Dot/Icm-dependent translocation of more than 300 effector proteins into the host cell. Although many translocated effectors localise to the Legionella replicative vacuole, other effectors can affect remote intracellular sites. Following infection, a subset of effector proteins localises to the nucleus where they subvert host cell transcriptional responses to infection. Here, we identified Lpw27461 (Lpp2587), Lpg2519 as a new nuclear-localised effector that we have termed SnpL. Upon ectopic expression or during L. pneumophila infection, SnpL showed strong nuclear localisation by immunofluorescence microscopy but was excluded from nucleoli. Using immunoprecipitation and mass spectrometry, we determined the host-binding partner of SnpL as the eukaryotic transcription elongation factor, Suppressor of Ty5 (SUPT5H)/Spt5. SUPT5H is an evolutionarily conserved component of the DRB sensitivity-inducing factor complex that regulates RNA Polymerase II dependent mRNA processing and transcription elongation. Protein interaction studies showed that SnpL bound to the central Kyprides, Ouzounis, Woese motif region of SUPT5H. Ectopic expression of SnpL led to massive upregulation of host gene expression and macrophage cell death. The activity of SnpL further highlights the ability of L. pneumophila to control fundamental eukaryotic processes such as transcription that, in the case of SnpL, leads to global upregulation of host gene expression.
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Affiliation(s)
- Ralf Schuelein
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Hugh Spencer
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Peng Fei Li
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
| | - Lin Luo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Jennifer L Stow
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Gilu Abraham
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Clayton, Australia
| | - Thomas Naderer
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Clayton, Australia
| | - Laura Gomez-Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France.,CNRS UMR 3525, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France.,CNRS UMR 3525, Paris, France
| | - Chihiro Sugimoto
- Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, Sapporo, Hokkaido, Japan.,Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Junya Yamagishi
- Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, Sapporo, Hokkaido, Japan.,Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Shivani Pasricha
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
| | - Elizabeth L Hartland
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia.,Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France.,Department of Molecular and Translational Science, Monash University, Clayton, Australia
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41
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Sandow JJ, Rainczuk A, Infusini G, Makanji M, Bilandzic M, Wilson AL, Fairweather N, Stanton PG, Garama D, Gough D, Jobling TW, Webb AI, Stephens AN. Discovery and Validation of Novel Protein Biomarkers in Ovarian Cancer Patient Urine. Proteomics Clin Appl 2018; 12:e1700135. [DOI: 10.1002/prca.201700135] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/16/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Jarrod J. Sandow
- Walter and Eliza Hall Institute, Department of Medical Biology; University of Melbourne; Parkville VIC Australia
| | - Adam Rainczuk
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
- Centre for Cancer Research; Hudson Institute of Medical Research; VIC Australia
| | - Giuseppe Infusini
- Walter and Eliza Hall Institute, Department of Medical Biology; University of Melbourne; Parkville VIC Australia
| | - Ming Makanji
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
- Centre for Cancer Research; Hudson Institute of Medical Research; VIC Australia
| | - Maree Bilandzic
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
- Centre for Cancer Research; Hudson Institute of Medical Research; VIC Australia
| | - Amy L. Wilson
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
- Centre for Cancer Research; Hudson Institute of Medical Research; VIC Australia
| | | | - Peter G. Stanton
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
| | - Daniel Garama
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
- Centre for Cancer Research; Hudson Institute of Medical Research; VIC Australia
| | - Daniel Gough
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
- Centre for Cancer Research; Hudson Institute of Medical Research; VIC Australia
| | - Thomas W. Jobling
- Obstetrics and Gynaecology; Monash Medical Centre; Clayton VIC Australia
| | - Andrew I. Webb
- Walter and Eliza Hall Institute, Department of Medical Biology; University of Melbourne; Parkville VIC Australia
| | - Andrew N. Stephens
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
- Centre for Cancer Research; Hudson Institute of Medical Research; VIC Australia
- Epworth Research Institute; Epworth HealthCare; Richmond VIC Australia
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42
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Woodcock JM, Goodwin KL, Sandow JJ, Coolen C, Perugini MA, Webb AI, Pitson SM, Lopez AF, Carver JA. Role of salt bridges in the dimer interface of 14-3-3ζ in dimer dynamics, N-terminal α-helical order, and molecular chaperone activity. J Biol Chem 2017; 293:89-99. [PMID: 29109150 DOI: 10.1074/jbc.m117.801019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/24/2017] [Indexed: 11/06/2022] Open
Abstract
The 14-3-3 family of intracellular proteins are dimeric, multifunctional adaptor proteins that bind to and regulate the activities of many important signaling proteins. The subunits within 14-3-3 dimers are predicted to be stabilized by salt bridges that are largely conserved across the 14-3-3 protein family and allow the different isoforms to form heterodimers. Here, we have examined the contributions of conserved salt-bridging residues in stabilizing the dimeric state of 14-3-3ζ. Using analytical ultracentrifugation, our results revealed that Asp21 and Glu89 both play key roles in dimer dynamics and contribute to dimer stability. Furthermore, hydrogen-deuterium exchange coupled with mass spectrometry showed that mutation of Asp21 promoted disorder in the N-terminal helices of 14-3-3ζ, suggesting that this residue plays an important role in maintaining structure across the dimer interface. Intriguingly, a D21N 14-3-3ζ mutant exhibited enhanced molecular chaperone ability that prevented amorphous protein aggregation, suggesting a potential role for N-terminal disorder in 14-3-3ζ's poorly understood chaperone action. Taken together, these results imply that disorder in the N-terminal helices of 14-3-3ζ is a consequence of the dimer-monomer dynamics and may play a role in conferring chaperone function to 14-3-3ζ protein.
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Affiliation(s)
- Joanna M Woodcock
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000.
| | - Katy L Goodwin
- School of Physical Sciences, University of Adelaide, Adelaide, South Australia 5005
| | - Jarrod J Sandow
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052
| | - Carl Coolen
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086
| | - Andrew I Webb
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052
| | - Stuart M Pitson
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000
| | - Angel F Lopez
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000
| | - John A Carver
- Research School of Chemistry, Australian National University, Acton, Australian Capital Territory 2601, Australia
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43
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Scott NE, Giogha C, Pollock GL, Kennedy CL, Webb AI, Williamson NA, Pearson JS, Hartland EL. The bacterial arginine glycosyltransferase effector NleB preferentially modifies Fas-associated death domain protein (FADD). J Biol Chem 2017; 292:17337-17350. [PMID: 28860194 DOI: 10.1074/jbc.m117.805036] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 08/28/2017] [Indexed: 01/01/2023] Open
Abstract
The inhibition of host innate immunity pathways is essential for the persistence of attaching and effacing pathogens such as enteropathogenic Escherichia coli (EPEC) and Citrobacter rodentium during mammalian infections. To subvert these pathways and suppress the antimicrobial response, attaching and effacing pathogens use type III secretion systems to introduce effectors targeting key signaling pathways in host cells. One such effector is the arginine glycosyltransferase NleB1 (NleBCR in C. rodentium) that modifies conserved arginine residues in death domain-containing host proteins with N-acetylglucosamine (GlcNAc), thereby blocking extrinsic apoptosis signaling. Ectopically expressed NleB1 modifies the host proteins Fas-associated via death domain (FADD), TNFRSF1A-associated via death domain (TRADD), and receptor-interacting serine/threonine protein kinase 1 (RIPK1). However, the full repertoire of arginine GlcNAcylation induced by pathogen-delivered NleB1 is unknown. Using an affinity proteomic approach for measuring arginine-GlcNAcylated glycopeptides, we assessed the global profile of arginine GlcNAcylation during ectopic expression of NleB1, EPEC infection in vitro, or C. rodentium infection in vivo NleB overexpression resulted in arginine GlcNAcylation of multiple host proteins. However, NleB delivery during EPEC and C. rodentium infection caused rapid and preferential modification of Arg117 in FADD. This FADD modification was extremely stable and insensitive to physiological temperatures, glycosidases, or host cell degradation. Despite its stability and effect on the inhibition of apoptosis, arginine GlcNAcylation did not elicit any proteomic changes, even in response to prolonged NleB1 expression. We conclude that, at normal levels of expression during bacterial infection, NleB1/NleBCR antagonizes death receptor-induced apoptosis of infected cells by modifying FADD in an irreversible manner.
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Affiliation(s)
- Nichollas E Scott
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia,
| | - Cristina Giogha
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Georgina L Pollock
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Catherine L Kennedy
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Melbourne, Australia.,the Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia, and
| | - Nicholas A Williamson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Jaclyn S Pearson
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Elizabeth L Hartland
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
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44
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Sandow JJ, Infusini G, Holik AZ, Brumatti G, Averink TV, Ekert PG, Webb AI. Quantitative proteomic analysis of EZH2 inhibition in acute myeloid leukemia reveals the targets and pathways that precede the induction of cell death. Proteomics Clin Appl 2017; 11. [DOI: 10.1002/prca.201700013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 04/13/2017] [Accepted: 04/24/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Jarrod J. Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology; The University of Melbourne; Parkville Australia
| | - Giuseppe Infusini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology; The University of Melbourne; Parkville Australia
| | - Aliaksei Z. Holik
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology; The University of Melbourne; Parkville Australia
| | - Gabriela Brumatti
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology; The University of Melbourne; Parkville Australia
| | - Tessa V. Averink
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology; The University of Melbourne; Parkville Australia
- Murdoch Children's Research Institute; Royal Children's Hospital; Parkville Australia
- Vrije Universiteit; Amsterdam
| | - Paul G. Ekert
- Murdoch Children's Research Institute; Royal Children's Hospital; Parkville Australia
| | - Andrew I. Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology; The University of Melbourne; Parkville Australia
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45
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Harding CM, Pulido MR, Di Venanzio G, Kinsella RL, Webb AI, Scott NE, Pachón J, Feldman MF. Pathogenic Acinetobacter species have a functional type I secretion system and contact-dependent inhibition systems. J Biol Chem 2017; 292:9075-9087. [PMID: 28373284 DOI: 10.1074/jbc.m117.781575] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/31/2017] [Indexed: 01/09/2023] Open
Abstract
Pathogenic Acinetobacter species, including Acinetobacter baumannii and Acinetobacter nosocomialis, are opportunistic human pathogens of increasing relevance worldwide. Although their mechanisms of drug resistance are well studied, the virulence factors that govern Acinetobacter pathogenesis are incompletely characterized. Here we define the complete secretome of A. nosocomialis strain M2 in minimal medium and demonstrate that pathogenic Acinetobacter species produce both a functional type I secretion system (T1SS) and a contact-dependent inhibition (CDI) system. Using bioinformatics, quantitative proteomics, and mutational analyses, we show that Acinetobacter uses its T1SS for exporting two putative T1SS effectors, an Repeats-in-Toxin (RTX)-serralysin-like toxin, and the biofilm-associated protein (Bap). Moreover, we found that mutation of any component of the T1SS system abrogated type VI secretion activity under nutrient-limited conditions, indicating a previously unrecognized cross-talk between these two systems. We also demonstrate that the Acinetobacter T1SS is required for biofilm formation. Last, we show that both A. nosocomialis and A. baumannii produce functioning CDI systems that mediate growth inhibition of sister cells lacking the cognate immunity protein. The Acinetobacter CDI systems are widely distributed across pathogenic Acinetobacter species, with many A. baumannii isolates harboring two distinct CDI systems. Collectively, these data demonstrate the power of differential, quantitative proteomics approaches to study secreted proteins, define the role of previously uncharacterized protein export systems, and observe cross-talk between secretion systems in the pathobiology of medically relevant Acinetobacter species.
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Affiliation(s)
- Christian M Harding
- From the Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Marina R Pulido
- From the Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110.,the Unit of Infectious Diseases, Microbiology, and Preventive Medicine and Biomedical Institute of Seville, University Hospital Virgen del Rocío/Consejo Superior de Investigaciones Científicas, University of Sevilla, 41004 Seville, Spain
| | - Gisela Di Venanzio
- From the Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Rachel L Kinsella
- From the Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110.,the Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Andrew I Webb
- the Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia.,the Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia, and
| | - Nichollas E Scott
- the Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Jerónimo Pachón
- the Unit of Infectious Diseases, Microbiology, and Preventive Medicine and Biomedical Institute of Seville, University Hospital Virgen del Rocío/Consejo Superior de Investigaciones Científicas, University of Sevilla, 41004 Seville, Spain
| | - Mario F Feldman
- From the Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110,
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46
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Pearson JS, Giogha C, Mühlen S, Nachbur U, Pham CLL, Zhang Y, Hildebrand JM, Oates CV, Lung TWF, Ingle D, Dagley LF, Bankovacki A, Petrie EJ, Schroeder GN, Crepin VF, Frankel G, Masters SL, Vince J, Murphy JM, Sunde M, Webb AI, Silke J, Hartland EL. EspL is a bacterial cysteine protease effector that cleaves RHIM proteins to block necroptosis and inflammation. Nat Microbiol 2017; 2:16258. [PMID: 28085133 DOI: 10.1038/nmicrobiol.2016.258] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 11/28/2016] [Indexed: 11/09/2022]
Abstract
Cell death signalling pathways contribute to tissue homeostasis and provide innate protection from infection. Adaptor proteins such as receptor-interacting serine/threonine-protein kinase 1 (RIPK1), receptor-interacting serine/threonine-protein kinase 3 (RIPK3), TIR-domain-containing adapter-inducing interferon-β (TRIF) and Z-DNA-binding protein 1 (ZBP1)/DNA-dependent activator of IFN-regulatory factors (DAI) that contain receptor-interacting protein (RIP) homotypic interaction motifs (RHIM) play a key role in cell death and inflammatory signalling1-3. RHIM-dependent interactions help drive a caspase-independent form of cell death termed necroptosis4,5. Here, we report that the bacterial pathogen enteropathogenic Escherichia coli (EPEC) uses the type III secretion system (T3SS) effector EspL to degrade the RHIM-containing proteins RIPK1, RIPK3, TRIF and ZBP1/DAI during infection. This requires a previously unrecognized tripartite cysteine protease motif in EspL (Cys47, His131, Asp153) that cleaves within the RHIM of these proteins. Bacterial infection and/or ectopic expression of EspL leads to rapid inactivation of RIPK1, RIPK3, TRIF and ZBP1/DAI and inhibition of tumour necrosis factor (TNF), lipopolysaccharide or polyinosinic:polycytidylic acid (poly(I:C))-induced necroptosis and inflammatory signalling. Furthermore, EPEC infection inhibits TNF-induced phosphorylation and plasma membrane localization of mixed lineage kinase domain-like pseudokinase (MLKL). In vivo, EspL cysteine protease activity contributes to persistent colonization of mice by the EPEC-like mouse pathogen Citrobacter rodentium. The activity of EspL defines a family of T3SS cysteine protease effectors found in a range of bacteria and reveals a mechanism by which gastrointestinal pathogens directly target RHIM-dependent inflammatory and necroptotic signalling pathways.
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Affiliation(s)
- Jaclyn S Pearson
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Cristina Giogha
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Sabrina Mühlen
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia.,Department of Molecular Infection Biology, Helmholtz-Centre for Infection Research, 38124 Braunschweig, Germany
| | - Ueli Nachbur
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Victoria 3010, Australia
| | - Chi L L Pham
- Discipline of Pharmacology, School of Medical Sciences, University of Sydney, New South Wales 2006, Australia
| | - Ying Zhang
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Joanne M Hildebrand
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Victoria 3010, Australia
| | - Clare V Oates
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Tania Wong Fok Lung
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Danielle Ingle
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute and Centre for Systems Genomics, University of Melbourne, Victoria 3010, Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Victoria 3010, Australia
| | - Aleksandra Bankovacki
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Victoria 3010, Australia
| | - Emma J Petrie
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Victoria 3010, Australia
| | - Gunnar N Schroeder
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ, UK.,Centre for Experimental Medicine, Queen's University Belfast, BT9 7BL, UK
| | - Valerie F Crepin
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ, UK
| | - Gad Frankel
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ, UK
| | - Seth L Masters
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Victoria 3010, Australia
| | - James Vince
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Victoria 3010, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Victoria 3010, Australia
| | - Margaret Sunde
- Discipline of Pharmacology, School of Medical Sciences, University of Sydney, New South Wales 2006, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Victoria 3010, Australia
| | - John Silke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Victoria 3010, Australia
| | - Elizabeth L Hartland
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
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47
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Masters SL, Lagou V, Jéru I, Baker PJ, Van Eyck L, Parry DA, Lawless D, De Nardo D, Garcia-Perez JE, Dagley LF, Holley CL, Dooley J, Moghaddas F, Pasciuto E, Jeandel PY, Sciot R, Lyras D, Webb AI, Nicholson SE, De Somer L, van Nieuwenhove E, Ruuth-Praz J, Copin B, Cochet E, Medlej-Hashim M, Megarbane A, Schroder K, Savic S, Goris A, Amselem S, Wouters C, Liston A. Familial autoinflammation with neutrophilic dermatosis reveals a regulatory mechanism of pyrin activation. Sci Transl Med 2016; 8:332ra45. [PMID: 27030597 DOI: 10.1126/scitranslmed.aaf1471] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/03/2016] [Indexed: 12/16/2022]
Abstract
Pyrin responds to pathogen signals and loss of cellular homeostasis by forming an inflammasome complex that drives the cleavage and secretion of interleukin-1β (IL-1β). Mutations in the B30.2/SPRY domain cause pathogen-independent activation of pyrin and are responsible for the autoinflammatory disease familial Mediterranean fever (FMF). We studied a family with a dominantly inherited autoinflammatory disease, distinct from FMF, characterized by childhood-onset recurrent episodes of neutrophilic dermatosis, fever, elevated acute-phase reactants, arthralgia, and myalgia/myositis. The disease was caused by a mutation in MEFV, the gene encoding pyrin (S242R). The mutation results in the loss of a 14-3-3 binding motif at phosphorylated S242, which was not perturbed by FMF mutations in the B30.2/SPRY domain. However, loss of both S242 phosphorylation and 14-3-3 binding was observed for bacterial effectors that activate the pyrin inflammasome, such as Clostridium difficile toxin B (TcdB). The S242R mutation thus recapitulated the effect of pathogen sensing, triggering inflammasome activation and IL-1β production. Successful therapy targeting IL-1β has been initiated in one patient, resolving pyrin-associated autoinflammation with neutrophilic dermatosis. This disease provides evidence that a guard-like mechanism of pyrin regulation, originally identified for Nod-like receptors in plant innate immunity, also exists in humans.
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Affiliation(s)
- Seth L Masters
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia. Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Vasiliki Lagou
- Department of Neurosciences, KU Leuven, Leuven 3000, Belgium. Department of Microbiology and Immunology, KU Leuven, Leuven 3000, Belgium. Translational Immunology Laboratory, VIB, Leuven 3000, Belgium
| | - Isabelle Jéru
- INSERM, UMR S933, Paris F-75012, France. Université Pierre et Marie Curie-Paris, UMR S933, Paris F-75012, France. Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Service de Génétique et d'Embryologie médicales, Paris F-75012, France
| | - Paul J Baker
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia. Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lien Van Eyck
- Department of Microbiology and Immunology, KU Leuven, Leuven 3000, Belgium. Translational Immunology Laboratory, VIB, Leuven 3000, Belgium
| | - David A Parry
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh LS7 4SA, UK
| | - Dylan Lawless
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Wellcome Trust Brenner Building, Saint James's University Hospital, Leeds LS7 4SA, UK
| | - Dominic De Nardo
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia. Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Josselyn E Garcia-Perez
- Department of Microbiology and Immunology, KU Leuven, Leuven 3000, Belgium. Translational Immunology Laboratory, VIB, Leuven 3000, Belgium
| | - Laura F Dagley
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia. Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia. Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Caroline L Holley
- Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - James Dooley
- Department of Microbiology and Immunology, KU Leuven, Leuven 3000, Belgium. Translational Immunology Laboratory, VIB, Leuven 3000, Belgium
| | - Fiona Moghaddas
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia. Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Emanuela Pasciuto
- Department of Microbiology and Immunology, KU Leuven, Leuven 3000, Belgium. Translational Immunology Laboratory, VIB, Leuven 3000, Belgium
| | - Pierre-Yves Jeandel
- Département de Médecine Interne, Hôpital Archet 1, Université Nice Sophia-Antipolis, 06202 Nice, France
| | - Raf Sciot
- Department of Pathology, KU Leuven, Leuven 3000, Belgium. University Hospitals Leuven, Leuven 3000, Belgium
| | - Dena Lyras
- Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia
| | - Andrew I Webb
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia. Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Sandra E Nicholson
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia. Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - Erika van Nieuwenhove
- Department of Microbiology and Immunology, KU Leuven, Leuven 3000, Belgium. Translational Immunology Laboratory, VIB, Leuven 3000, Belgium. University Hospitals Leuven, Leuven 3000, Belgium
| | - Julia Ruuth-Praz
- Université Pierre et Marie Curie-Paris, UMR S933, Paris F-75012, France. Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Service de Génétique et d'Embryologie médicales, Paris F-75012, France
| | - Bruno Copin
- Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Service de Génétique et d'Embryologie médicales, Paris F-75012, France
| | - Emmanuelle Cochet
- Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Service de Génétique et d'Embryologie médicales, Paris F-75012, France
| | - Myrna Medlej-Hashim
- Department of Life and Earth Sciences, Faculty of Sciences II, Lebanese University, Beirut 1102 2801, Lebanon
| | - Andre Megarbane
- Al-Jawhara Center, Arabian Gulf University, Manama 26671, Bahrain
| | - Kate Schroder
- Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sinisa Savic
- Department of Allergy and Clinical Immunology, Saint James's University Hospital, Leeds LS9 7TF, UK. National Institute for Health Research-Leeds Musculoskeletal Biomedical Research Unit and Leeds Institute of Rheumatic and Musculoskeletal Medicine, Wellcome Trust Brenner Building, Saint James's University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - An Goris
- Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
| | - Serge Amselem
- INSERM, UMR S933, Paris F-75012, France. Université Pierre et Marie Curie-Paris, UMR S933, Paris F-75012, France. Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Service de Génétique et d'Embryologie médicales, Paris F-75012, France
| | - Carine Wouters
- Department of Microbiology and Immunology, KU Leuven, Leuven 3000, Belgium. University Hospitals Leuven, Leuven 3000, Belgium.
| | - Adrian Liston
- Department of Microbiology and Immunology, KU Leuven, Leuven 3000, Belgium. Translational Immunology Laboratory, VIB, Leuven 3000, Belgium.
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48
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Affiliation(s)
- Rebecca Feltham
- The Walter and Eliza Hall Institute, Melbourne, Vic., Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute, Melbourne, Vic., Australia
| | - John Silke
- The Walter and Eliza Hall Institute, Melbourne, Vic., Australia
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49
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Delconte RB, Kolesnik TB, Dagley LF, Rautela J, Shi W, Putz EM, Stannard K, Zhang JG, Teh C, Firth M, Ushiki T, Andoniou CE, Degli-Esposti MA, Sharp PP, Sanvitale CE, Infusini G, Liau NPD, Linossi EM, Burns CJ, Carotta S, Gray DHD, Seillet C, Hutchinson DS, Belz GT, Webb AI, Alexander WS, Li SS, Bullock AN, Babon JJ, Smyth MJ, Nicholson SE, Huntington ND. CIS is a potent checkpoint in NK cell-mediated tumor immunity. Nat Immunol 2016; 17:816-24. [PMID: 27213690 DOI: 10.1038/ni.3470] [Citation(s) in RCA: 245] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 04/27/2016] [Indexed: 12/14/2022]
Abstract
The detection of aberrant cells by natural killer (NK) cells is controlled by the integration of signals from activating and inhibitory ligands and from cytokines such as IL-15. We identified cytokine-inducible SH2-containing protein (CIS, encoded by Cish) as a critical negative regulator of IL-15 signaling in NK cells. Cish was rapidly induced in response to IL-15, and deletion of Cish rendered NK cells hypersensitive to IL-15, as evidenced by enhanced proliferation, survival, IFN-γ production and cytotoxicity toward tumors. This was associated with increased JAK-STAT signaling in NK cells in which Cish was deleted. Correspondingly, CIS interacted with the tyrosine kinase JAK1, inhibiting its enzymatic activity and targeting JAK for proteasomal degradation. Cish(-/-) mice were resistant to melanoma, prostate and breast cancer metastasis in vivo, and this was intrinsic to NK cell activity. Our data uncover a potent intracellular checkpoint in NK cell-mediated tumor immunity and suggest possibilities for new cancer immunotherapies directed at blocking CIS function.
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Affiliation(s)
- Rebecca B Delconte
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Tatiana B Kolesnik
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Jai Rautela
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Wei Shi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Eva M Putz
- Immunology in Cancer and Infection Laboratory QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Kimberley Stannard
- Immunology in Cancer and Infection Laboratory QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Jian-Guo Zhang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Charis Teh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Matt Firth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Takashi Ushiki
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Christopher E Andoniou
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia and Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Mariapia A Degli-Esposti
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia and Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Phillip P Sharp
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | | | - Giuseppe Infusini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Nicholas P D Liau
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Edmond M Linossi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Christopher J Burns
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Sebastian Carotta
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Daniel H D Gray
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Cyril Seillet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Dana S Hutchinson
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Gabrielle T Belz
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Warren S Alexander
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Shawn S Li
- Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Alex N Bullock
- Structural Genomics Consortium (SGC), University of Oxford, Oxford, UK
| | - Jeffery J Babon
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Mark J Smyth
- Immunology in Cancer and Infection Laboratory QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- School of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Sandra E Nicholson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Nicholas D Huntington
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
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50
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Nachbur U, Stafford CA, Bankovacki A, Zhan Y, Lindqvist LM, Fiil BK, Khakham Y, Ko HJ, Sandow JJ, Falk H, Holien JK, Chau D, Hildebrand J, Vince JE, Sharp PP, Webb AI, Jackman KA, Mühlen S, Kennedy CL, Lowes KN, Murphy JM, Gyrd-Hansen M, Parker MW, Hartland EL, Lew AM, Huang DCS, Lessene G, Silke J. A RIPK2 inhibitor delays NOD signalling events yet prevents inflammatory cytokine production. Nat Commun 2015; 6:6442. [PMID: 25778803 DOI: 10.1038/ncomms7442] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/29/2015] [Indexed: 12/22/2022] Open
Abstract
Intracellular nucleotide binding and oligomerization domain (NOD) receptors recognize antigens including bacterial peptidoglycans and initiate immune responses by triggering the production of pro-inflammatory cytokines through activating NF-κB and MAP kinases. Receptor interacting protein kinase 2 (RIPK2) is critical for NOD-mediated NF-κB activation and cytokine production. Here we develop and characterize a selective RIPK2 kinase inhibitor, WEHI-345, which delays RIPK2 ubiquitylation and NF-κB activation downstream of NOD engagement. Despite only delaying NF-κB activation on NOD stimulation, WEHI-345 prevents cytokine production in vitro and in vivo and ameliorates experimental autoimmune encephalomyelitis in mice. Our study highlights the importance of the kinase activity of RIPK2 for proper immune responses and demonstrates the therapeutic potential of inhibiting RIPK2 in NOD-driven inflammatory diseases.
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Affiliation(s)
- Ueli Nachbur
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Che A Stafford
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Aleksandra Bankovacki
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Yifan Zhan
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Lisa M Lindqvist
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Berthe K Fiil
- 1] Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark [2] Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Yelena Khakham
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Hyun-Ja Ko
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jarrod J Sandow
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Hendrik Falk
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia [3] Cancer Therapeutics CRC, Bundoora, Victoria 3083, Australia
| | - Jessica K Holien
- ACRF Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Diep Chau
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Joanne Hildebrand
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - James E Vince
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Phillip P Sharp
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Andrew I Webb
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Katherine A Jackman
- The Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, Austin Campus, 245 Burgundy Street, Heidelberg, Victoria 3084, Australia
| | - Sabrina Mühlen
- Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia
| | - Catherine L Kennedy
- Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia
| | - Kym N Lowes
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - James M Murphy
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Mads Gyrd-Hansen
- 1] Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark [2] Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Michael W Parker
- 1] ACRF Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia [2] Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Elizabeth L Hartland
- Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia
| | - Andrew M Lew
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - David C S Huang
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Guillaume Lessene
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - John Silke
- 1] The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
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