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Van Woerkom A, Harney DJ, Nagarajan SR, Hakeem-Sanni MF, Lin J, Hooke M, Pilpitel T, Cooney GJ, Larance M, Saunders DN, Brandon AE, Hoy AJ. Hepatic lipid droplet-associated proteome changes distinguish dietary-induced fatty liver from glucose tolerance in male mice. Am J Physiol Endocrinol Metab 2024. [PMID: 38656127 DOI: 10.1152/ajpendo.00013.2024] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
Fatty liver is characterized by the expansion of lipid droplets (LDs) and is associated with the development of many metabolic diseases. We assessed the morphology of hepatic LDs and performed quantitative proteomics in lean, glucose-tolerant mice compared to high-fat diet (HFD) fed mice that displayed hepatic steatosis and glucose intolerance as well as high-starch diet (HStD) fed mice who exhibited similar levels of hepatic steatosis but remained glucose tolerant. Both HFD and HStD-fed mice had more and larger LDs than Chow-fed animals. We observed striking differences in liver LD proteomes of HFD and HStD-fed mice compared to Chow-fed mice, with fewer differences between HFD and HStD. Taking advantage of our diet strategy, we identified a fatty liver LD proteome consisting of proteins common in HFD- and HStD-fed mice, as well as a proteome associated with glucose tolerance that included proteins shared in Chow and HStD but not HFD-fed mice. Notably, glucose intolerance was associated with changes in the ratio of adipose triglyceride lipase to perilipin 5 in the LD proteome, suggesting dysregulation of neutral lipid homeostasis in glucose-intolerant fatty liver. We conclude that our novel dietary approach uncouples ectopic lipid burden from insulin resistance-associated changes in the hepatic lipid droplet proteome.
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Affiliation(s)
- Andries Van Woerkom
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Dylan J Harney
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Shilpa R Nagarajan
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Mariam F Hakeem-Sanni
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Jinfeng Lin
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Matthew Hooke
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Tamara Pilpitel
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Gregory J Cooney
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Mark Larance
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Darren N Saunders
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Amanda E Brandon
- Sydney Medical School, Charles Perking Centre D17, Univerity of Sydney, Sydney, New South Wales, Australia
| | - Andrew J Hoy
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
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2
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Pinello N, Song R, Lee Q, Calonne E, Larance M, Fuks F, Wong JJL. A multiomics dataset for the study of RNA modifications in human macrophage differentiation and polarisation. Sci Data 2024; 11:252. [PMID: 38418823 PMCID: PMC10902381 DOI: 10.1038/s41597-024-03076-8] [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: 09/26/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024] Open
Abstract
RNA modifications have emerged as central regulators of gene expression programs. Amongst RNA modifications are N6-methyladenosine (m6A) and RNA 5-hydroxymethylcytosine (5hmC). While m6A is established as a versatile regulator of RNA metabolism, the functions of RNA 5hmC are unclear. Despite some evidence linking RNA modifications to immunity, their implications in gene expression control in macrophage development and functions remain unclear. Here we present a multi-omics dataset capturing different layers of the gene expression programs driving macrophage differentiation and polarisation. We obtained mRNA-Seq, m6A-IP-Seq, 5hmC-IP-Seq, Polyribo-Seq and LC-MS/MS data from monocytes and resting-, pro- and anti-inflammatory-like macrophages. We present technical validation showing high quality and correlation between samples for all datasets, and evidence of biological consistency of modelled macrophages at the transcriptomic, epitranscriptomic, translational and proteomic levels. This multi-omics dataset provides a resource for the study of RNA m6A and 5hmC in the context of macrophage biology and spans the gene expression process from transcripts to proteins.
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Affiliation(s)
- Natalia Pinello
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
| | - Quintin Lee
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Mark Larance
- Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Camperdown, 2050, New South Wales, Australia
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.
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3
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Lee JY, Harney DJ, Teo JD, Kwok JB, Sutherland GT, Larance M, Don AS. Correction: The major TMEM106B dementia risk allele affects TMEM106B protein levels, fibril formation, and myelin lipid homeostasis in the ageing human hippocampus. Mol Neurodegener 2024; 19:21. [PMID: 38409051 PMCID: PMC10898024 DOI: 10.1186/s13024-024-00709-9] [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: 02/28/2024] Open
Affiliation(s)
- Jun Yup Lee
- Charles Perkins Centre, 2006, Camperdown, NSW, Australia
- School of Medical Sciences, 2006, Camperdown, NSW, Australia
| | - Dylan J Harney
- Charles Perkins Centre, 2006, Camperdown, NSW, Australia
- School of Medical Sciences, 2006, Camperdown, NSW, Australia
| | - Jonathan D Teo
- Charles Perkins Centre, 2006, Camperdown, NSW, Australia
- School of Medical Sciences, 2006, Camperdown, NSW, Australia
| | - John B Kwok
- Charles Perkins Centre, 2006, Camperdown, NSW, Australia
- Brain and Mind Centre, The University of Sydney, 2006, Camperdown, NSW, Australia
| | - Greg T Sutherland
- Charles Perkins Centre, 2006, Camperdown, NSW, Australia
- School of Medical Sciences, 2006, Camperdown, NSW, Australia
| | - Mark Larance
- Charles Perkins Centre, 2006, Camperdown, NSW, Australia
- School of Medical Sciences, 2006, Camperdown, NSW, Australia
| | - Anthony S Don
- Charles Perkins Centre, 2006, Camperdown, NSW, Australia.
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4
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Tran A, Wang A, Mickaill J, Strbenac D, Larance M, Vernon ST, Grieve SM, Figtree GA, Patrick E, Yang JYH. Construction and optimization of multi-platform precision pathways for precision medicine. Sci Rep 2024; 14:4248. [PMID: 38378802 PMCID: PMC10879206 DOI: 10.1038/s41598-024-54517-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 02/13/2024] [Indexed: 02/22/2024] Open
Abstract
In the enduring challenge against disease, advancements in medical technology have empowered clinicians with novel diagnostic platforms. Whilst in some cases, a single test may provide a confident diagnosis, often additional tests are required. However, to strike a balance between diagnostic accuracy and cost-effectiveness, one must rigorously construct the clinical pathways. Here, we developed a framework to build multi-platform precision pathways in an automated, unbiased way, recommending the key steps a clinician would take to reach a diagnosis. We achieve this by developing a confidence score, used to simulate a clinical scenario, where at each stage, either a confident diagnosis is made, or another test is performed. Our framework provides a range of tools to interpret, visualize and compare the pathways, improving communication and enabling their evaluation on accuracy and cost, specific to different contexts. This framework will guide the development of novel diagnostic pathways for different diseases, accelerating the implementation of precision medicine into clinical practice.
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Affiliation(s)
- Andy Tran
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Andy Wang
- Westmead Medical Institute, Westmead, NSW, Australia
| | - Jamie Mickaill
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- School of Computer Science, The University of Sydney, Camperdown, NSW, Australia
| | - Dario Strbenac
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Mark Larance
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Stephen T Vernon
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Kolling Institute of Medical Research, St Leonards, NSW, Australia
| | - Stuart M Grieve
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Department of Radiology, Royal Prince Alfred Hospital, Camperdown, Australia
| | - Gemma A Figtree
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Kolling Institute of Medical Research, St Leonards, NSW, Australia
| | - Ellis Patrick
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
| | - Jean Yee Hwa Yang
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia.
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia.
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia.
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China.
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Houlahan CB, Kong Y, Johnston B, Cielesh M, Chau TH, Fenwick J, Coleman PR, Hao H, Haltiwanger RS, Thaysen-Andersen M, Passam FH, Larance M. Analysis of the Healthy Platelet Proteome Identifies a New Form of Domain-Specific O-Fucosylation. Mol Cell Proteomics 2024; 23:100717. [PMID: 38237698 PMCID: PMC10879016 DOI: 10.1016/j.mcpro.2024.100717] [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: 07/14/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 02/17/2024] Open
Abstract
Platelet activation induces the secretion of proteins that promote platelet aggregation and inflammation. However, detailed analysis of the released platelet proteome is hampered by platelets' tendency to preactivate during their isolation and a lack of sensitive protocols for low abundance releasate analysis. Here, we detail the most sensitive analysis to date of the platelet releasate proteome with the detection of >1300 proteins. Unbiased scanning for posttranslational modifications within releasate proteins highlighted O-glycosylation as being a major component. For the first time, we detected O-fucosylation on previously uncharacterized sites including multimerin-1 (MMRN1), a major alpha granule protein that supports platelet adhesion to collagen and is a carrier for platelet factor V. The N-terminal elastin microfibril interface (EMI) domain of MMRN1, a key site for protein-protein interaction, was O-fucosylated at a conserved threonine within a new domain context. Our data suggest that either protein O-fucosyltransferase 1, or a novel protein O-fucosyltransferase, may be responsible for this modification. Mutating this O-fucose site on the EMI domain led to a >50% reduction of MMRN1 secretion, supporting a key role of EMI O-fucosylation in MMRN1 secretion. By comparing releasates from resting and thrombin-treated platelets, 202 proteins were found to be significantly released after high-dose thrombin stimulation. Complementary quantification of the platelet lysates identified >3800 proteins, which confirmed the platelet origin of releasate proteins by anticorrelation analysis. Low-dose thrombin treatment yielded a smaller subset of significantly regulated proteins with fewer secretory pathway enzymes. The extensive platelet proteome resource provided here (larancelab.com/platelet-proteome) allows identification of novel regulatory mechanisms for drug targeting to address platelet dysfunction and thrombosis.
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Affiliation(s)
- Callum B Houlahan
- The Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Yvonne Kong
- Central Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Bede Johnston
- The Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Michelle Cielesh
- Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - The Huong Chau
- School of Natural Sciences, Macquarie University, Macquarie Park, New South Wales, Australia
| | - Jemma Fenwick
- The Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia; Central Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Paul R Coleman
- The Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Huilin Hao
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Robert S Haltiwanger
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Macquarie University, Macquarie Park, New South Wales, Australia; Institute for Glyco-Core Research, Nagoya University, Nagoya, Aichi, Japan
| | - Freda H Passam
- The Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia; Central Clinical School, The University of Sydney, Sydney, New South Wales, Australia.
| | - Mark Larance
- Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia.
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Yau B, Naghiloo S, Diaz-Vegas A, Carr AV, Van Gerwen J, Needham EJ, Jevon D, Chen SY, Hoehn KL, Brandon AE, Macia L, Cooney GJ, Shortreed MR, Smith LM, Keller MP, Thorn P, Larance M, James DE, Humphrey SJ, Kebede MA. Erratum: Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet. iScience 2024; 27:108707. [PMID: 38188515 PMCID: PMC10770518 DOI: 10.1016/j.isci.2023.108707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
[This corrects the article DOI: 10.1016/j.isci.2021.103099.].
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7
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Chen SY, Beretta M, Olzomer EM, Alexopoulos SJ, Shah DP, Byrne FL, Salamoun JM, Garcia CJ, Smith GC, Larance M, Philp A, Turner N, Santos WL, Cantley J, Hoehn KL. Head-to-head comparison of BAM15, semaglutide, rosiglitazone, NEN, and calorie restriction on metabolic physiology in female db/db mice. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166908. [PMID: 37793464 PMCID: PMC10908303 DOI: 10.1016/j.bbadis.2023.166908] [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: 07/31/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 10/06/2023]
Abstract
Metabolic disorders such as type 2 diabetes, fatty liver disease, hyperlipidemia, and obesity commonly co-occur but clinical treatment options do not effectively target all disorders. Calorie restriction, semaglutide, rosiglitazone, and mitochondrial uncouplers have all demonstrated efficacy against one or more obesity-related metabolic disorders, but it currently remains unclear which therapeutic strategy best targets the combination of hyperglycaemia, liver fat, hypertriglyceridemia, and adiposity. Herein we performed a head-to-head comparison of 5 treatment interventions in the female db/db mouse model of severe metabolic disease. Treatments included ∼60 % calorie restriction (CR), semaglutide, rosiglitazone, BAM15, and niclosamide ethanolamine (NEN). Results showed that BAM15 and CR improved body weight and liver steatosis to levels superior to semaglutide, NEN, and rosiglitazone, while BAM15, semaglutide, and rosiglitazone improved glucose tolerance better than CR and NEN. BAM15, CR, semaglutide, and rosiglitazone all had efficacy against hypertriglyceridaemia. These data provide a comprehensive head-to-head comparison of several key treatment strategies for metabolic disease and highlight the efficacy of mitochondrial uncoupling to correct multiple facets of the metabolic disease milieu in female db/db mice.
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Affiliation(s)
- Sing-Young Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Martina Beretta
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ellen M Olzomer
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Stephanie J Alexopoulos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Divya P Shah
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Frances L Byrne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Joseph M Salamoun
- Department of Chemistry and Virginia Tech Centre for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, USA
| | - Christopher J Garcia
- Department of Chemistry and Virginia Tech Centre for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, USA
| | - Greg C Smith
- School of Medical Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mark Larance
- Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Andrew Philp
- Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Centre for Healthy Ageing, Centenary Institute, Camperdown, NSW 2050, Australia; School of Sport, Exercise and Rehabilitation Sciences, Faculty of Health, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Nigel Turner
- Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Centre for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, USA
| | - James Cantley
- School of Medicine, University of Dundee, Dundee DD1 4HN, UK
| | - Kyle L Hoehn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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Lee JY, Harney DJ, Teo JD, Kwok JB, Sutherland GT, Larance M, Don AS. The major TMEM106B dementia risk allele affects TMEM106B protein levels, fibril formation, and myelin lipid homeostasis in the ageing human hippocampus. Mol Neurodegener 2023; 18:63. [PMID: 37726834 PMCID: PMC10510131 DOI: 10.1186/s13024-023-00650-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 12/19/2022] [Accepted: 08/17/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND The risk for dementia increases exponentially from the seventh decade of life. Identifying and understanding the biochemical changes that sensitize the ageing brain to neurodegeneration will provide new opportunities for dementia prevention and treatment. This study aimed to determine how ageing and major genetic risk factors for dementia affect the hippocampal proteome and lipidome of neurologically-normal humans over the age of 65. The hippocampus was chosen as it is highly susceptible to atrophy with ageing and in several neurodegenerative diseases. METHODS Mass spectrometry-based proteomic and lipidomic analysis of CA1 hippocampus samples from 74 neurologically normal human donors, aged 66-104, was used in combination with multiple regression models and gene set enrichment analysis to identify age-dependent changes in the proteome and lipidome. ANOVA was used to test the effect of major dementia risk alleles in the TMEM106B and APOE genes on the hippocampal proteome and lipidome, adjusting for age, gender, and post-mortem interval. Fibrillar C-terminal TMEM106B fragments were isolated using sarkosyl fractionation and quantified by immunoblotting. RESULTS Forty proteins were associated with age at false discovery rate-corrected P < 0.05, including proteins that regulate cell adhesion, the cytoskeleton, amino acid and lipid metabolism, and ribosomal subunits. TMEM106B, a regulator of lysosomal and oligodendrocyte function, was regulated with greatest effect size. The increase in TMEM106B levels with ageing was specific to carriers of the rs1990622-A allele in the TMEM106B gene that increases risk for frontotemporal dementia, Alzheimer's disease, Parkinson's disease, and hippocampal sclerosis with ageing. Rs1990622-A was also associated with higher TMEM106B fibril content. Hippocampal lipids were not significantly affected by APOE genotype, however levels of myelin-enriched sulfatides and hexosylceramides were significantly lower, and polyunsaturated phospholipids were higher, in rs1990622-A carriers after controlling for APOE genotype. CONCLUSIONS Our study demonstrates that TMEM106B protein abundance is increased with brain ageing in humans, establishes that dementia risk allele rs1990622-A predisposes to TMEM106B fibril formation in the hippocampus, and provides the first evidence that rs1990622-A affects brain lipid homeostasis, particularly myelin lipids. Our data suggests that TMEM106B is one of a growing list of major dementia risk genes that affect glial lipid metabolism.
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Affiliation(s)
- Jun Yup Lee
- Charles Perkins Centre, Camperdown, NSW, 2006, Australia
- School of Medical Sciences, Camperdown, NSW, 2006, Australia
| | - Dylan J Harney
- Charles Perkins Centre, Camperdown, NSW, 2006, Australia
- School of Medical Sciences, Camperdown, NSW, 2006, Australia
| | - Jonathan D Teo
- Charles Perkins Centre, Camperdown, NSW, 2006, Australia
- School of Medical Sciences, Camperdown, NSW, 2006, Australia
| | - John B Kwok
- School of Medical Sciences, Camperdown, NSW, 2006, Australia
- Brain and Mind Centre, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Greg T Sutherland
- Charles Perkins Centre, Camperdown, NSW, 2006, Australia
- School of Medical Sciences, Camperdown, NSW, 2006, Australia
| | - Mark Larance
- Charles Perkins Centre, Camperdown, NSW, 2006, Australia
- School of Medical Sciences, Camperdown, NSW, 2006, Australia
| | - Anthony S Don
- Charles Perkins Centre, Camperdown, NSW, 2006, Australia.
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Sjøberg KA, Sigvardsen CM, Alvarado-Diaz A, Andersen NR, Larance M, Seeley RJ, Schjerling P, Knudsen JG, Katzilieris-Petras G, Clemmensen C, Jørgensen SB, De Bock K, Richter EA. GDF15 increases insulin action in the liver and adipose tissue via a β-adrenergic receptor-mediated mechanism. Cell Metab 2023; 35:1327-1340.e5. [PMID: 37473755 DOI: 10.1016/j.cmet.2023.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/10/2023] [Accepted: 06/27/2023] [Indexed: 07/22/2023]
Abstract
Growth differentiation factor 15 (GDF15) induces weight loss and increases insulin action in obese rodents. Whether and how GDF15 improves insulin action without weight loss is unknown. Obese rats were treated with GDF15 and displayed increased insulin tolerance 5 h later. Lean and obese female and male mice were treated with GDF15 on days 1, 3, and 5 without weight loss and displayed increased insulin sensitivity during a euglycemic hyperinsulinemic clamp on day 6 due to enhanced suppression of endogenous glucose production and increased glucose uptake in WAT and BAT. GDF15 also reduced glucagon levels during clamp independently of the GFRAL receptor. The insulin-sensitizing effect of GDF15 was completely abrogated in GFRAL KO mice and also by treatment with the β-adrenergic antagonist propranolol and in β1,β2-adrenergic receptor KO mice. GDF15 activation of the GFRAL receptor increases β-adrenergic signaling, in turn, improving insulin action in the liver and white and brown adipose tissue.
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Affiliation(s)
- Kim A Sjøberg
- Department of Nutrition, Exercise, and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Casper M Sigvardsen
- Department of Nutrition, Exercise, and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Abdiel Alvarado-Diaz
- Laboratory of Exercise and Health, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH Zürich), Zurich, Switzerland
| | - Nicoline Resen Andersen
- Department of Nutrition, Exercise, and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Mark Larance
- Faculty of Medicine and Health, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Sydney, Australia
| | - Randy J Seeley
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Peter Schjerling
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark; Center for Healthy Aging, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jakob G Knudsen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Georgios Katzilieris-Petras
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Christoffer Clemmensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sebastian Beck Jørgensen
- Global Drug Discovery, Obesity Research, Novo Nordisk, Maaloev, Denmark; Bio Innovation Hub Transformational Research Unit, Novo Nordisk, Boston, MA, USA
| | - Katrien De Bock
- Laboratory of Exercise and Health, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH Zürich), Zurich, Switzerland.
| | - Erik A Richter
- Department of Nutrition, Exercise, and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.
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10
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Lee Q, Song R, Phan DAV, Pinello N, Tieng J, Su A, Halstead JM, Wong ACH, van Geldermalsen M, Lee BSL, Rong B, Cook KM, Larance M, Liu R, Lan F, Tiffen JC, Wong JJL. Correction: Overexpression of VIRMA confers vulnerability to breast cancers via the m 6A-dependent regulation of unfolded protein response. Cell Mol Life Sci 2023; 80:204. [PMID: 37450040 PMCID: PMC10348946 DOI: 10.1007/s00018-023-04825-5] [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: 07/18/2023]
Affiliation(s)
- Quintin Lee
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Dang Anh Vu Phan
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Natalia Pinello
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Jessica Tieng
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Anni Su
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - James M Halstead
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Alex C H Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Michelle van Geldermalsen
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Bob S-L Lee
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - Bowen Rong
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Kristina M Cook
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Mark Larance
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Renjing Liu
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Fei Lan
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jessamy C Tiffen
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Melanoma Epigenetics Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia.
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia.
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, 2006, Australia.
- , Locked Bag 6, Newtown, NSW, 2042, Australia.
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11
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Harney DJ, Cielesh M, Roberts GE, Vila IK, Viengkhou B, Hofer MJ, Laguette N, Larance M. Dietary restriction induces a sexually dimorphic type I interferon response in mice with gene-environment interactions. Cell Rep 2023; 42:112559. [PMID: 37243595 DOI: 10.1016/j.celrep.2023.112559] [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: 07/12/2022] [Revised: 03/20/2023] [Accepted: 05/08/2023] [Indexed: 05/29/2023] Open
Abstract
Intermittent fasting (IF) is an established intervention to treat the growing obesity epidemic. However, the interaction between dietary interventions and sex remains a significant knowledge gap. In this study, we use unbiased proteome analysis to identify diet-sex interactions. We report sexual dimorphism in response to intermittent fasting within lipid and cholesterol metabolism and, unexpectedly, in type I interferon signaling, which was strongly induced in females. We verify that secretion of type I interferon is required for the IF response in females. Gonadectomy differentially alters the every-other-day fasting (EODF) response and demonstrates that sex hormone signaling can either suppress or enhance the interferon response to IF. IF fails to potentiate a stronger innate immune response when IF-treated animals were challenged with a viral mimetic. Lastly, the IF response changes with genotype and environment. These data reveal an interesting interaction between diet, sex, and the innate immune system.
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Affiliation(s)
- Dylan J Harney
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, 2006 NSW, Australia
| | - Michelle Cielesh
- Charles Perkins Centre and School of Medical Sciences, The University of Sydney, Sydney, 2006 NSW, Australia
| | - Georgia E Roberts
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, 2006 NSW, Australia
| | | | - Barney Viengkhou
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, 2006 NSW, Australia
| | - Markus J Hofer
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, 2006 NSW, Australia
| | | | - Mark Larance
- Charles Perkins Centre and School of Medical Sciences, The University of Sydney, Sydney, 2006 NSW, Australia.
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12
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Lee Q, Song R, Phan DAV, Pinello N, Tieng J, Su A, Halstead JM, Wong ACH, van Geldermalsen M, Lee BSL, Rong B, Cook KM, Larance M, Liu R, Lan F, Tiffen JC, Wong JJL. Overexpression of VIRMA confers vulnerability to breast cancers via the m 6A-dependent regulation of unfolded protein response. Cell Mol Life Sci 2023; 80:157. [PMID: 37208522 DOI: 10.1007/s00018-023-04799-4] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/21/2023]
Abstract
Virilizer-like m6A methyltransferase-associated protein (VIRMA) maintains the stability of the m6A writer complex. Although VIRMA is critical for RNA m6A deposition, the impact of aberrant VIRMA expression in human diseases remains unclear. We show that VIRMA is amplified and overexpressed in 15-20% of breast cancers. Of the two known VIRMA isoforms, the nuclear-enriched full-length but not the cytoplasmic-localised N-terminal VIRMA promotes m6A-dependent breast tumourigenesis in vitro and in vivo. Mechanistically, we reveal that VIRMA overexpression upregulates the m6A-modified long non-coding RNA, NEAT1, which contributes to breast cancer cell growth. We also show that VIRMA overexpression enriches m6A on transcripts that regulate the unfolded protein response (UPR) pathway but does not promote their translation to activate the UPR under optimal growth conditions. Under stressful conditions that are often present in tumour microenvironments, VIRMA-overexpressing cells display enhanced UPR and increased susceptibility to death. Our study identifies oncogenic VIRMA overexpression as a vulnerability that may be exploited for cancer therapy.
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Affiliation(s)
- Quintin Lee
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Dang Anh Vu Phan
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Natalia Pinello
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Jessica Tieng
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Anni Su
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - James M Halstead
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Alex C H Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Michelle van Geldermalsen
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Bob S-L Lee
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - Bowen Rong
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Kristina M Cook
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Mark Larance
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Renjing Liu
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Fei Lan
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jessamy C Tiffen
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Melanoma Epigenetics Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2006, Australia.
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia.
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- , Locked Bag 6, Newtown, NSW, 2042, Australia.
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13
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Samant RS, Batista S, Larance M, Ozer B, Milton CI, Bludau I, Wu E, Biggins L, Andrews S, Hervieu A, Johnston HE, Al-Lazikhani B, Lamond AI, Clarke PA, Workman P. Native Size-Exclusion Chromatography-Based Mass Spectrometry Reveals New Components of the Early Heat Shock Protein 90 Inhibition Response Among Limited Global Changes. Mol Cell Proteomics 2023; 22:100485. [PMID: 36549590 PMCID: PMC9898794 DOI: 10.1016/j.mcpro.2022.100485] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/16/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
The molecular chaperone heat shock protein 90 (HSP90) works in concert with co-chaperones to stabilize its client proteins, which include multiple drivers of oncogenesis and malignant progression. Pharmacologic inhibitors of HSP90 have been observed to exert a wide range of effects on the proteome, including depletion of client proteins, induction of heat shock proteins, dissociation of co-chaperones from HSP90, disruption of client protein signaling networks, and recruitment of the protein ubiquitylation and degradation machinery-suggesting widespread remodeling of cellular protein complexes. However, proteomics studies to date have focused on inhibitor-induced changes in total protein levels, often overlooking protein complex alterations. Here, we use size-exclusion chromatography in combination with mass spectrometry (SEC-MS) to characterize the early changes in native protein complexes following treatment with the HSP90 inhibitor tanespimycin (17-AAG) for 8 h in the HT29 colon adenocarcinoma cell line. After confirming the signature cellular response to HSP90 inhibition (e.g., induction of heat shock proteins, decreased total levels of client proteins), we were surprised to find only modest perturbations to the global distribution of protein elution profiles in inhibitor-treated HT29 cells at this relatively early time-point. Similarly, co-chaperones that co-eluted with HSP90 displayed no clear difference between control and treated conditions. However, two distinct analysis strategies identified multiple inhibitor-induced changes, including known and unknown components of the HSP90-dependent proteome. We validate two of these-the actin-binding protein Anillin and the mitochondrial isocitrate dehydrogenase 3 complex-as novel HSP90 inhibitor-modulated proteins. We present this dataset as a resource for the HSP90, proteostasis, and cancer communities (https://www.bioinformatics.babraham.ac.uk/shiny/HSP90/SEC-MS/), laying the groundwork for future mechanistic and therapeutic studies related to HSP90 pharmacology. Data are available via ProteomeXchange with identifier PXD033459.
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Affiliation(s)
- Rahul S Samant
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom; Signalling Programme, The Babraham Institute, Cambridge, United Kingdom.
| | - Silvia Batista
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom
| | - Mark Larance
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, United Kingdom
| | - Bugra Ozer
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom
| | - Christopher I Milton
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom
| | - Isabell Bludau
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Estelle Wu
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Laura Biggins
- Bioinformatics Group, The Babraham Institute, Cambridge, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, United Kingdom
| | - Alexia Hervieu
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom
| | - Harvey E Johnston
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Bissan Al-Lazikhani
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Angus I Lamond
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, United Kingdom
| | - Paul A Clarke
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom
| | - Paul Workman
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom.
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14
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Lee JY, Harney D, Kwok J, Larance M, Don AS. The major TMEM106B dementia risk allele affects TMEM106B protein levels and myelin lipid homeostasis in the ageing human hippocampus. Res Sq 2023:rs.3.rs-2392941. [PMID: 36711721 PMCID: PMC9882607 DOI: 10.21203/rs.3.rs-2392941/v1] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Background The risk for dementia increases exponentially from the seventh decade of life. Identifying and understanding the biochemical changes that sensitize the ageing brain to neurodegeneration will provide new opportunities for dementia prevention and treatment. This study aimed to determine how ageing and major genetic risk factors for dementia affect the hippocampal proteome and lipidome of neurologically-normal humans over the age of 65. The hippocampus was chosen as it is highly susceptible to atrophy with ageing and in several neurodegenerative diseases. Methods Mass spectrometry-based proteomic and lipidomic analysis of CA1 hippocampus samples from 74 neurologically normal human donors, aged 66-104, was used in combination with multiple regression models and gene set enrichment analysis to identify age-dependent changes in the proteome and lipidome. ANOVA was used to test the effect of major dementia risk alleles in the TMEM106B and APOE genes on the hippocampal proteome and lipidome, adjusting for age, gender, and post-mortem interval. Results Forty proteins were associated with age at false discovery rate-corrected P < 0.05, including proteins that regulate cell adhesion, the cytoskeleton, amino acid and lipid metabolism, and ribosomal subunits. Transmembrane protein 106B (TMEM106B), a regulator of lysosomal and oligodendrocyte function, was regulated with greatest effect size. The increase in TMEM106B levels with age was specific to carriers of the rs1990622-A allele in the TMEM106B gene that is associated with increased risk for frontotemporal dementia, Alzheimer's disease, Parkinson's disease, and hippocampal sclerosis with ageing. Hippocampal lipids were not significantly affected by APOE genotype, however levels of myelin-enriched sulfatides and hexosylceramides were significantly lower, and polyunsaturated phospholipids were higher, in rs1990622-A carriers after controlling for APOE genotype. Conclusions Our study provides the first evidence that TMEM106B protein abundance is increased with brain ageing in humans, and the first evidence that the major TMEM106B dementia risk allele affects brain lipid homeostasis, with a clear effect on myelin lipid content. Our data implies that TMEM106B is one of a growing list of major dementia risk genes that affect glial lipid metabolism.
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Affiliation(s)
- Jun Yup Lee
- The University of Sydney SMS: The University of Sydney School of Medical Sciences
| | | | - John Kwok
- The University of Sydney SMS: The University of Sydney School of Medical Sciences
| | - Mark Larance
- The University of Sydney SMS: The University of Sydney School of Medical Sciences
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15
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Koay YC, Larance M, O'Sullivan J. Uncovering metabolic drivers of heart failure with preserved ejection fraction (HFpEF). J Mol Cell Cardiol 2022. [DOI: 10.1016/j.yjmcc.2022.08.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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16
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Dowman LJ, Kulkarni SS, Alegre-Requena JV, Giltrap AM, Norman AR, Sharma A, Gallegos LC, Mackay AS, Welegedara AP, Watson EE, van Raad D, Niederacher G, Huhmann S, Proschogo N, Patel K, Larance M, Becker CFW, Mackay JP, Lakhwani G, Huber T, Paton RS, Payne RJ. Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine. Nat Commun 2022; 13:6885. [PMID: 36371402 PMCID: PMC9653470 DOI: 10.1038/s41467-022-34530-z] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/27/2022] [Indexed: 11/15/2022] Open
Abstract
The importance of modified peptides and proteins for applications in drug discovery, and for illuminating biological processes at the molecular level, is fueling a demand for efficient methods that facilitate the precise modification of these biomolecules. Herein, we describe the development of a photocatalytic method for the rapid and efficient dimerization and site-specific functionalization of peptide and protein diselenides. This methodology, dubbed the photocatalytic diselenide contraction, involves irradiation at 450 nm in the presence of an iridium photocatalyst and a phosphine and results in rapid and clean conversion of diselenides to reductively stable selenoethers. A mechanism for this photocatalytic transformation is proposed, which is supported by photoluminescence spectroscopy and density functional theory calculations. The utility of the photocatalytic diselenide contraction transformation is highlighted through the dimerization of selenopeptides, and by the generation of two families of protein conjugates via the site-selective modification of calmodulin containing the 21st amino acid selenocysteine, and the C-terminal modification of a ubiquitin diselenide.
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Affiliation(s)
- Luke J. Dowman
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Sameer S. Kulkarni
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Juan V. Alegre-Requena
- grid.47894.360000 0004 1936 8083Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872 USA
| | - Andrew M. Giltrap
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Alexander R. Norman
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Ashish Sharma
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence in Exciton Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Liliana C. Gallegos
- grid.47894.360000 0004 1936 8083Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872 USA
| | - Angus S. Mackay
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Adarshi P. Welegedara
- grid.1001.00000 0001 2180 7477Research School of Chemistry, Australian National University, Canberra, ACT 2601 Australia
| | - Emma E. Watson
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Damian van Raad
- grid.1001.00000 0001 2180 7477Research School of Chemistry, Australian National University, Canberra, ACT 2601 Australia
| | - Gerhard Niederacher
- grid.10420.370000 0001 2286 1424Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Susanne Huhmann
- grid.10420.370000 0001 2286 1424Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Nicholas Proschogo
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia
| | - Karishma Patel
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006 Australia
| | - Mark Larance
- grid.1013.30000 0004 1936 834XCharles Perkins Centre and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006 Australia
| | - Christian F. W. Becker
- grid.10420.370000 0001 2286 1424Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Joel P. Mackay
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006 Australia
| | - Girish Lakhwani
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence in Exciton Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Thomas Huber
- grid.1001.00000 0001 2180 7477Research School of Chemistry, Australian National University, Canberra, ACT 2601 Australia
| | - Robert S. Paton
- grid.47894.360000 0004 1936 8083Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872 USA
| | - Richard J. Payne
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
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17
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Ruan T, Harney D, Koay YC, Loo L, Larance M, Caron L. Anabolic Factors and Myokines Improve Differentiation of Human Embryonic Stem Cell Derived Skeletal Muscle Cells. Cells 2022; 11:cells11060963. [PMID: 35326414 PMCID: PMC8946006 DOI: 10.3390/cells11060963] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 02/04/2023] Open
Abstract
Skeletal muscle weakness is linked to many adverse health outcomes. Current research to identify new drugs has often been inconclusive due to lack of adequate cellular models. We previously developed a scalable monolayer system to differentiate human embryonic stem cells (hESCs) into mature skeletal muscle cells (SkMCs) within 26 days without cell sorting or genetic manipulation. Here, building on our previous work, we show that differentiation and fusion of myotubes can be further enhanced using the anabolic factors testosterone (T) and follistatin (F) in combination with a cocktail of myokines (C). Importantly, combined TFC treatment significantly enhanced both the hESC-SkMC fusion index and the expression levels of various skeletal muscle markers, including the motor protein myosin heavy chain (MyHC). Transcriptomic and proteomic analysis revealed oxidative phosphorylation as the most up-regulated pathway, and a significantly higher level of ATP and increased mitochondrial mass were also observed in TFC-treated hESC-SkMCs, suggesting enhanced energy metabolism is coupled with improved muscle differentiation. This cellular model will be a powerful tool for studying in vitro myogenesis and for drug discovery pertaining to further enhancing muscle development or treating muscle diseases.
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Affiliation(s)
- Travis Ruan
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (T.R.); (L.L.)
| | - Dylan Harney
- Larance Laboratory, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (D.H.); (M.L.)
| | - Yen Chin Koay
- Cardiometabolic Disease Group, Heart Research Institute, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Lipin Loo
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (T.R.); (L.L.)
| | - Mark Larance
- Larance Laboratory, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (D.H.); (M.L.)
| | - Leslie Caron
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (T.R.); (L.L.)
- MMG, Marseille Medical Genetics, Aix Marseille Univ, INSERM U1251, 13005 Marseille, France
- Correspondence:
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18
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Ashhurst A, Tang AH, Fajtová P, Yoon MC, Aggarwal A, Bedding MJ, Stoye A, Beretta L, Pwee D, Drelich A, Skinner D, Li L, Meek TD, McKerrow JH, Hook V, Tseng CT, Larance M, Turville S, Gerwick WH, O’Donoghue AJ, Payne RJ. Potent Anti-SARS-CoV-2 Activity by the Natural Product Gallinamide A and Analogues via Inhibition of Cathepsin L. J Med Chem 2022; 65:2956-2970. [PMID: 34730959 PMCID: PMC8577376 DOI: 10.1021/acs.jmedchem.1c01494] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Indexed: 12/15/2022]
Abstract
Cathepsin L is a key host cysteine protease utilized by coronaviruses for cell entry and is a promising drug target for novel antivirals against SARS-CoV-2. The marine natural product gallinamide A and several synthetic analogues were identified as potent inhibitors of cathepsin L with IC50 values in the picomolar range. Lead molecules possessed selectivity over other cathepsins and alternative host proteases involved in viral entry. Gallinamide A directly interacted with cathepsin L in cells and, together with two lead analogues, potently inhibited SARS-CoV-2 infection in vitro, with EC50 values in the nanomolar range. Reduced antiviral activity was observed in cells overexpressing transmembrane protease, serine 2 (TMPRSS2); however, a synergistic improvement in antiviral activity was achieved when combined with a TMPRSS2 inhibitor. These data highlight the potential of cathepsin L as a COVID-19 drug target as well as the likely need to inhibit multiple routes of viral entry to achieve efficacy.
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Affiliation(s)
- Anneliese
S. Ashhurst
- School
of Chemistry, The University of Sydney, Sydney, NSW2006, Australia
- School
of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW2006, Australia
| | - Arthur H. Tang
- School
of Chemistry, The University of Sydney, Sydney, NSW2006, Australia
| | - Pavla Fajtová
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
- Institute
of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, 16610Prague, Czech Republic
| | - Michael C. Yoon
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Anupriya Aggarwal
- Kirby
Institute, University of New South Wales, Sydney, NSW2052, Australia
| | - Max J. Bedding
- School
of Chemistry, The University of Sydney, Sydney, NSW2006, Australia
| | - Alexander Stoye
- School
of Chemistry, The University of Sydney, Sydney, NSW2006, Australia
| | - Laura Beretta
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Dustin Pwee
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Aleksandra Drelich
- Department
of Microbiology and Immunology, University
of Texas, Medical Branch, 3000 University Boulevard, Galveston, Texas77755-1001, United States
| | - Danielle Skinner
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Linfeng Li
- Department
of Biochemistry and Biophysics, Texas A&M
University, 301 Old Main
Drive, College Station, Texas77843, United States
| | - Thomas D. Meek
- Department
of Biochemistry and Biophysics, Texas A&M
University, 301 Old Main
Drive, College Station, Texas77843, United States
| | - James H. McKerrow
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Vivian Hook
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Chien-Te Tseng
- Department
of Microbiology and Immunology, University
of Texas, Medical Branch, 3000 University Boulevard, Galveston, Texas77755-1001, United States
| | - Mark Larance
- Charles
Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Stuart Turville
- Kirby
Institute, University of New South Wales, Sydney, NSW2052, Australia
| | - William H. Gerwick
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California92093, United States
| | - Anthony J. O’Donoghue
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Richard J. Payne
- School
of Chemistry, The University of Sydney, Sydney, NSW2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, NSW2006, Australia
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19
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Harney DJ, Larance M. Annotated Protein Database Using Known Cleavage Sites for Rapid Detection of Secreted Proteins. J Proteome Res 2022; 21:965-974. [DOI: 10.1021/acs.jproteome.1c00806] [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: 11/30/2022]
Affiliation(s)
- Dylan J. Harney
- Charles Perkins Centre and School of Life and Environmental Sciences, University of Sydney, 2006 Sydney, Australia
| | - Mark Larance
- Charles Perkins Centre and School of Life and Environmental Sciences, University of Sydney, 2006 Sydney, Australia
- Charles Perkins Centre and School of Medical Sciences, University of Sydney, 2006 Sydney, Australia
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20
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Johansen-Leete J, Ullrich S, Fry SE, Frkic R, Bedding MJ, Aggarwal A, Ashhurst AS, Ekanayake KB, Mahawaththa MC, Sasi VM, Luedtke S, Ford DJ, O'Donoghue AJ, Passioura T, Larance M, Otting G, Turville S, Jackson CJ, Nitsche C, Payne RJ. Antiviral cyclic peptides targeting the main protease of SARS-CoV-2. Chem Sci 2022; 13:3826-3836. [PMID: 35432913 PMCID: PMC8966731 DOI: 10.1039/d1sc06750h] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 12/02/2021] [Accepted: 02/28/2022] [Indexed: 12/17/2022] Open
Abstract
Antivirals that specifically target SARS-CoV-2 are needed to control the COVID-19 pandemic. The main protease (Mpro) is essential for SARS-CoV-2 replication and is an attractive target for antiviral development. Here we report the use of the Random nonstandard Peptide Integrated Discovery (RaPID) mRNA display on a chemically cross-linked SARS-CoV-2 Mpro dimer, which yielded several high-affinity thioether-linked cyclic peptide inhibitors of the protease. Structural analysis of Mpro complexed with a selenoether analogue of the highest-affinity peptide revealed key binding interactions, including glutamine and leucine residues in sites S1 and S2, respectively, and a binding epitope straddling both protein chains in the physiological dimer. Several of these Mpro peptide inhibitors possessed antiviral activity against SARS-CoV-2 in vitro with EC50 values in the low micromolar range. These cyclic peptides serve as a foundation for the development of much needed antivirals that specifically target SARS-CoV-2. RaPID mRNA display was used for the discovery of antiviral cyclic peptides that potently and selectively inhibit SARS-CoV-2 Mpro. The most potent inhibitor exhibited a novel binding mode, interacting with residues across the homodimer interface.![]()
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Affiliation(s)
- Jason Johansen-Leete
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Sarah E. Fry
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Rebecca Frkic
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
| | - Max J. Bedding
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Anneliese S. Ashhurst
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Kasuni B. Ekanayake
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
| | - Mithun C. Mahawaththa
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
| | - Vishnu M. Sasi
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
| | - Stephanie Luedtke
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Daniel J. Ford
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Toby Passioura
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Analytical, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mark Larance
- Sydney Analytical, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
| | | | - Colin J. Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
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21
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Byrne SA, Bedding MJ, Corcilius L, Ford DJ, Zhong Y, Franck C, Larance M, Mackay JP, Payne RJ. Late-stage modification of peptides and proteins at cysteine with diaryliodonium salts. Chem Sci 2021; 12:14159-14166. [PMID: 34760200 PMCID: PMC8565360 DOI: 10.1039/d1sc03127a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/21/2021] [Indexed: 01/03/2023] Open
Abstract
The modification of peptides and proteins has emerged as a powerful means to efficiently prepare high value bioconjugates for a range of applications in chemical biology and for the development of next-generation therapeutics. Herein, we report a novel method for the chemoselective late-stage modification of peptides and proteins at cysteine in aqueous buffer with suitably functionalised diaryliodonium salts, furnishing stable thioether-linked synthetic conjugates. The power of this new platform is showcased through the late-stage modification of the affibody zEGFR and the histone protein H2A.
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Affiliation(s)
- Stephen A Byrne
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
| | - Max J Bedding
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
| | - Leo Corcilius
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
| | - Daniel J Ford
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
| | - Yichen Zhong
- School of Life and Environmental Sciences, The University of Sydney Sydney NSW 2006 Australia
| | - Charlotte Franck
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
- School of Life and Environmental Sciences, The University of Sydney Sydney NSW 2006 Australia
| | - Mark Larance
- School of Life and Environmental Sciences, The University of Sydney Sydney NSW 2006 Australia
- Charles Perkins Centre, The University of Sydney NSW 2006 Australia
| | - Joel P Mackay
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
- School of Life and Environmental Sciences, The University of Sydney Sydney NSW 2006 Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
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22
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Yau B, Naghiloo S, Diaz-Vegas A, Carr AV, Van Gerwen J, Needham EJ, Jevon D, Chen SY, Hoehn KL, Brandon AE, Macia L, Cooney GJ, Shortreed MR, Smith LM, Keller MP, Thorn P, Larance M, James DE, Humphrey SJ, Kebede MA. Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet. iScience 2021; 24:103099. [PMID: 34622154 PMCID: PMC8479695 DOI: 10.1016/j.isci.2021.103099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/09/2021] [Accepted: 09/06/2021] [Indexed: 12/13/2022] Open
Abstract
Pancreatic islets are essential for maintaining physiological blood glucose levels, and declining islet function is a hallmark of type 2 diabetes. We employ mass spectrometry-based proteomics to systematically analyze islets from 9 genetic or diet-induced mouse models representing a broad cross-section of metabolic health. Quantifying the islet proteome to a depth of >11,500 proteins, this study represents the most detailed analysis of mouse islet proteins to date. Our data highlight that the majority of islet proteins are expressed in all strains and diets, but more than half of the proteins vary in expression levels, principally due to genetics. Associating these varied protein expression levels on an individual animal basis with individual phenotypic measures reveals islet mitochondrial function as a major positive indicator of metabolic health regardless of strain. This compendium of strain-specific and dietary changes to mouse islet proteomes represents a comprehensive resource for basic and translational islet cell biology.
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Affiliation(s)
- Belinda Yau
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
| | - Sheyda Naghiloo
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
| | - Alexis Diaz-Vegas
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Austin V. Carr
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Julian Van Gerwen
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Elise J. Needham
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Dillon Jevon
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
| | - Sing-Young Chen
- Department of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia
| | - Kyle L. Hoehn
- Department of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA
| | - Amanda E. Brandon
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
| | - Laurance Macia
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
| | - Gregory J. Cooney
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
| | | | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark P. Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Peter Thorn
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
| | - Mark Larance
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - David E. James
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Sean J. Humphrey
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Melkam A. Kebede
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
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23
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Yang G, Francis D, Krycer JR, Larance M, Zhang Z, Novotny CJ, Diaz-Vegas A, Shokat KM, James DE. Dissecting the biology of mTORC1 beyond rapamycin. Sci Signal 2021; 14:eabe0161. [PMID: 34546793 DOI: 10.1126/scisignal.abe0161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Guang Yang
- University of Sydney, School of life and Environmental Sciences, Charles Perkins Centre, Sydney, New South Wales 2006, Australia
| | - Deanne Francis
- University of Sydney, School of life and Environmental Sciences, Charles Perkins Centre, Sydney, New South Wales 2006, Australia
| | - James R Krycer
- University of Sydney, School of life and Environmental Sciences, Charles Perkins Centre, Sydney, New South Wales 2006, Australia
| | - Mark Larance
- University of Sydney, School of life and Environmental Sciences, Charles Perkins Centre, Sydney, New South Wales 2006, Australia
| | - Ziyang Zhang
- Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, 600 16th Street, San Francisco, CA 94143, USA
| | - Chris J Novotny
- Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, 600 16th Street, San Francisco, CA 94143, USA
| | - Alexis Diaz-Vegas
- University of Sydney, School of life and Environmental Sciences, Charles Perkins Centre, Sydney, New South Wales 2006, Australia
| | - Kevan M Shokat
- Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, 600 16th Street, San Francisco, CA 94143, USA
| | - David E James
- University of Sydney, School of life and Environmental Sciences, Charles Perkins Centre, Sydney, New South Wales 2006, Australia.,University of Sydney, Sydney Medical School, Sydney, New South Wales 2006, Australia
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24
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Richman TR, Ermer JA, Siira SJ, Kuznetsova I, Brosnan CA, Rossetti G, Baker J, Perks KL, Cserne Szappanos H, Viola HM, Gray N, Larance M, Hool LC, Zuryn S, Rackham O, Filipovska A. Mitochondrial mistranslation modulated by metabolic stress causes cardiovascular disease and reduced lifespan. Aging Cell 2021; 20:e13408. [PMID: 34096683 PMCID: PMC8282274 DOI: 10.1111/acel.13408] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 11/18/2020] [Revised: 03/17/2021] [Accepted: 05/08/2021] [Indexed: 12/25/2022] Open
Abstract
Changes in the rate and fidelity of mitochondrial protein synthesis impact the metabolic and physiological roles of mitochondria. Here we explored how environmental stress in the form of a high-fat diet modulates mitochondrial translation and affects lifespan in mutant mice with error-prone (Mrps12ep / ep ) or hyper-accurate (Mrps12ha / ha ) mitochondrial ribosomes. Intriguingly, although both mutations are metabolically beneficial in reducing body weight, decreasing circulating insulin and increasing glucose tolerance during a high-fat diet, they manifest divergent (either deleterious or beneficial) outcomes in a tissue-specific manner. In two distinct organs that are commonly affected by the metabolic disease, the heart and the liver, Mrps12ep / ep mice were protected against heart defects but sensitive towards lipid accumulation in the liver, activating genes involved in steroid and amino acid metabolism. In contrast, enhanced translational accuracy in Mrps12ha / ha mice protected the liver from a high-fat diet through activation of liver proliferation programs, but enhanced the development of severe hypertrophic cardiomyopathy and led to reduced lifespan. These findings reflect the complex transcriptional and cell signalling responses that differ between post-mitotic (heart) and highly proliferative (liver) tissues. We show trade-offs between the rate and fidelity of mitochondrial protein synthesis dictate tissue-specific outcomes due to commonly encountered stressful environmental conditions or aging.
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Affiliation(s)
- Tara R. Richman
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
| | - Judith A. Ermer
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
| | - Stefan J. Siira
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
| | - Irina Kuznetsova
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
| | - Christopher A. Brosnan
- Clem Jones Centre for Ageing Dementia Research Queensland Brain Institute The University of Queensland Brisbane Qld Australia
| | - Giulia Rossetti
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
- Telethon Kids Institute Perth Children's Hospital Nedlands WA Australia
| | - Jessica Baker
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
- Telethon Kids Institute Perth Children's Hospital Nedlands WA Australia
| | - Kara L. Perks
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
- Telethon Kids Institute Perth Children's Hospital Nedlands WA Australia
- School of Pharmacy and Biomedical Sciences Curtin University Bentley WA Australia
| | | | - Helena M. Viola
- School of Human Sciences The University of Western Australia Nedlands WA Australia
| | - Nicola Gray
- Australian National Phenome Centre Centre for Computational and Systems Medicine Health Futures Institute Murdoch University Perth WA Australia
| | - Mark Larance
- Charles Perkins Centre School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - Livia C. Hool
- School of Human Sciences The University of Western Australia Nedlands WA Australia
- Victor Chang Cardiac Research Institute Sydney NSW Australia
| | - Steven Zuryn
- Clem Jones Centre for Ageing Dementia Research Queensland Brain Institute The University of Queensland Brisbane Qld Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
- Telethon Kids Institute Perth Children's Hospital Nedlands WA Australia
- School of Pharmacy and Biomedical Sciences Curtin University Bentley WA Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
- Telethon Kids Institute Perth Children's Hospital Nedlands WA Australia
- Victor Chang Cardiac Research Institute Sydney NSW Australia
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25
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Wang S, Foster SR, Sanchez J, Corcilius L, Larance M, Canals M, Stone MJ, Payne RJ. Glycosylation Regulates N-Terminal Proteolysis and Activity of the Chemokine CCL14. ACS Chem Biol 2021; 16:973-981. [PMID: 33988967 DOI: 10.1021/acschembio.1c00006] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chemokines are secreted proteins that regulate leukocyte migration during inflammatory responses by signaling through chemokine receptors. Full length CC chemokine ligand 14, CCL14(1-74), is a weak agonist for the chemokine receptor CCR1, but its activity is substantially enhanced upon proteolytic cleavage to CCL14(9-74). CCL14 is O-glycosylated at Ser7, adjacent to the site of proteolytic activation. To determine whether glycosylation regulates the activity of CCL14, we used native chemical ligation to prepare four homogeneously glycosylated variants of CCL14(1-74). Each protein was assembled from three synthetic peptide fragments in "one-pot" using two sequential ligation reactions. We show that while glycosylation of CCL14(1-74) did not affect CCR1 binding affinity or potency of activation, sialylated variants of CCL14(1-74) exhibited reduced activity after treatment with plasmin compared to nonsialylated forms. These data indicate that glycosylation may influence the biological activity of CCL14 by regulating its conversion from the full-length to the truncated, activated form.
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Affiliation(s)
- Siyao Wang
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Simon R. Foster
- Department of Biochemistry & Molecular Biology Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Infection & Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Julie Sanchez
- Department of Biochemistry & Molecular Biology Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Infection & Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Leo Corcilius
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mark Larance
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Meritxell Canals
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham NG7 2UH, U.K
- Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, Midlands, U.K
| | - Martin J. Stone
- Department of Biochemistry & Molecular Biology Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
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26
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Premdjee B, Andersen AS, Larance M, Conde-Frieboes KW, Payne RJ. Chemical Synthesis of Phosphorylated Insulin-like Growth Factor Binding Protein 2. J Am Chem Soc 2021; 143:5336-5342. [PMID: 33797881 DOI: 10.1021/jacs.1c02280] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Chemical protein synthesis is a powerful avenue for accessing homogeneously modified proteins. While a significant number of small modified proteins bearing native post-translational modifications and non-natural modifications have been generated to date, access to larger targets has proved challenging. Herein, we describe the use of two ligation manifolds, namely, diselenide-selenoester ligation and native chemical ligation, to assemble a 31.5 kDa phosphorylated insulin-like growth factor binding protein (IGFBP-2) that comprises 290 amino acid residues, a phosphoserine post-translational modification, and nine disulfide bonds.
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Affiliation(s)
- Bhavesh Premdjee
- Department of Research Chemistry. Novo Nordisk A/S, Måløv 2760, Denmark.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Asser S Andersen
- Department of Recombinant Technologies, Novo Nordisk A/S, Måløv 2760, Denmark
| | - Mark Larance
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
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27
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Harney DJ, Cielesh M, Chu R, Cooke KC, James DE, Stöckli J, Larance M. Proteomics analysis of adipose depots after intermittent fasting reveals visceral fat preservation mechanisms. Cell Rep 2021; 34:108804. [PMID: 33657384 DOI: 10.1016/j.celrep.2021.108804] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 07/20/2020] [Revised: 01/22/2021] [Accepted: 02/05/2021] [Indexed: 12/21/2022] Open
Abstract
Intermittent fasting is a beneficial dietary treatment for obesity. But the response of each distinct adipose depot is currently poorly defined. Here we explore the response of key adipose depots to every-other-day fasting (EODF) in mice using proteomics. A key change in subcutaneous white adipose tissue (scWAT) and visceral WAT (vWAT) depots is an increase in mitochondrial protein content after EODF. This effect is correlated with increased fatty acid synthesis enzymes in both WAT depots but not in brown adipose tissue. Strikingly, EODF treatment downregulates lipolysis specifically in vWAT, mediated by a large decrease in the abundance of the catecholamine receptor (ADRB3). Together, these changes are important for preservation of the visceral lipid store during EODF. Enrichment analysis highlights downregulation of inflammatory collagen IV specifically in vWAT, allowing improved insulin sensitivity. This resource for adipose-depot-specific fasting adaptations in mice is available using a web-based interactive visualization.
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Affiliation(s)
- Dylan J Harney
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Michelle Cielesh
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Renee Chu
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Kristen C Cooke
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, Australia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, Australia; School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Jacqueline Stöckli
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Mark Larance
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, Australia.
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28
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Ashhurst AS, Tang AH, Fajtová P, Yoon M, Aggarwal A, Stoye A, Larance M, Beretta L, Drelich A, Skinner D, Li L, Meek TD, McKerrow JH, Hook V, Tseng CTK, Turville S, Gerwick WH, O'Donoghue AJ, Payne RJ. Potent in vitro anti-SARS-CoV-2 activity by gallinamide A and analogues via inhibition of cathepsin L. bioRxiv 2020. [PMID: 33398273 DOI: 10.1101/2020a.10.23.350348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The emergence of SARS-CoV-2 in late 2019, and the subsequent COVID-19 pandemic, has led to substantial mortality, together with mass global disruption. There is an urgent need for novel antiviral drugs for therapeutic or prophylactic application. Cathepsin L is a key host cysteine protease utilized by coronaviruses for cell entry and is recognized as a promising drug target. The marine natural product, gallinamide A and several synthetic analogues, were identified as potent inhibitors of cathepsin L activity with IC 50 values in the picomolar range. Lead molecules possessed selectivity over cathepsin B and other related human cathepsin proteases and did not exhibit inhibitory activity against viral proteases Mpro and PLpro. We demonstrate that gallinamide A and two lead analogues potently inhibit SARS-CoV-2 infection in vitro , with EC 50 values in the nanomolar range, thus further highlighting the potential of cathepsin L as a COVID-19 antiviral drug target.
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29
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Ashhurst AS, Tang AH, Fajtová P, Yoon M, Aggarwal A, Stoye A, Larance M, Beretta L, Drelich A, Skinner D, Li L, Meek TD, McKerrow JH, Hook V, Tseng CTK, Turville S, Gerwick WH, O'Donoghue AJ, Payne RJ. Potent in vitro anti-SARS-CoV-2 activity by gallinamide A and analogues via inhibition of cathepsin L. bioRxiv 2020. [PMID: 33398273 DOI: 10.1101/2020.12.23.424111] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The emergence of SARS-CoV-2 in late 2019, and the subsequent COVID-19 pandemic, has led to substantial mortality, together with mass global disruption. There is an urgent need for novel antiviral drugs for therapeutic or prophylactic application. Cathepsin L is a key host cysteine protease utilized by coronaviruses for cell entry and is recognized as a promising drug target. The marine natural product, gallinamide A and several synthetic analogues, were identified as potent inhibitors of cathepsin L activity with IC 50 values in the picomolar range. Lead molecules possessed selectivity over cathepsin B and other related human cathepsin proteases and did not exhibit inhibitory activity against viral proteases Mpro and PLpro. We demonstrate that gallinamide A and two lead analogues potently inhibit SARS-CoV-2 infection in vitro , with EC 50 values in the nanomolar range, thus further highlighting the potential of cathepsin L as a COVID-19 antiviral drug target.
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30
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Martinez-Huenchullan SF, Shipsey I, Hatchwell L, Min D, Twigg SM, Larance M. Blockade of High-Fat Diet Proteomic Phenotypes Using Exercise as Prevention or Treatment. Mol Cell Proteomics 2020; 20:100027. [PMID: 33594989 PMCID: PMC7950115 DOI: 10.1074/mcp.tir120.002343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 10/29/2020] [Indexed: 11/06/2022] Open
Abstract
The increasing consumption of high-fat foods combined with a lack of exercise is a major contributor to the burden of obesity in humans. Aerobic exercise such as running is known to provide metabolic benefits, but how the overconsumption of a high-fat diet (HFD) and exercise interact is not well characterized at the molecular level. Here, we examined the plasma proteome in mice for the effects of aerobic exercise as both a treatment and as a preventative regimen for animals on either a HFD or a healthy control diet. This analysis detected large changes in the plasma proteome induced by the HFD, such as increased abundance of SERPINA7, ALDOB, and downregulation of SERPINA1E and complement factor D (CFD; adipsin). Some of these changes were significantly reverted using exercise as a preventative measure but not as a treatment regimen. To determine if either the intensity or duration of exercise influenced the outcome, we compared high-intensity interval training and endurance running. Endurance running slightly outperformed high-intensity interval training exercise, but overall, both provided similar reversion in abundance of plasma proteins modulated by the HFD, including SERPINA7, apolipoprotein E, SERPINA1E, and CFD. Finally, we compared the changes induced by overconsumption of a HFD with previous data from mice fed on an isocaloric high-saturated fatty acid or polyunsaturated fatty acid diet. This identified several common changes, including not only increased apolipoprotein C-II and apolipoprotein E but also highlighted changes specific for overconsumption of a HFD (fructose-bisphosphate aldolase B, SERPINA7, and CFD), saturated fatty acid-based diets (SERPINA1E), or polyunsaturated fatty acid-based diets (haptoglobin). Together, these data highlight the importance of early intervention with exercise to revert HFD-induced phenotypes and suggest some of the molecular mechanisms leading to the changes in the plasma proteome generated by HFD consumption. Web-based interactive visualizations are provided for this dataset (larancelab.com/hfd-exercise), which give insight into diet and exercise phenotypic interactions on the plasma proteome.
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Affiliation(s)
- Sergio F Martinez-Huenchullan
- Faculty of Science, Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia; Faculty of Medicine and Health, Central Clinical School, University of Sydney, New South Wales, Australia; Faculty of Medicine, School of Physical Therapy, Austral University of Chile, Valdivia, Chile
| | - Isaac Shipsey
- Faculty of Science, Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Luke Hatchwell
- Faculty of Science, Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Danqing Min
- Faculty of Science, Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia; Faculty of Medicine and Health, Central Clinical School, University of Sydney, New South Wales, Australia
| | - Stephen M Twigg
- Faculty of Science, Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia; Faculty of Medicine and Health, Central Clinical School, University of Sydney, New South Wales, Australia; Department of Endocrinology, Royal Prince Alfred Hospital, New South Wales, Australia.
| | - Mark Larance
- Faculty of Science, Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia.
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31
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Green ID, Pinello N, Song R, Lee Q, Halstead JM, Kwok CT, Wong ACH, Nair SS, Clark SJ, Roediger B, Schmitz U, Larance M, Hayashi R, Rasko JEJ, Wong JJL. Macrophage development and activation involve coordinated intron retention in key inflammatory regulators. Nucleic Acids Res 2020; 48:6513-6529. [PMID: 32449925 PMCID: PMC7337907 DOI: 10.1093/nar/gkaa435] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [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: 03/18/2020] [Revised: 05/04/2020] [Accepted: 05/11/2020] [Indexed: 12/31/2022] Open
Abstract
Monocytes and macrophages are essential components of the innate immune system. Herein, we report that intron retention (IR) plays an important role in the development and function of these cells. Using Illumina mRNA sequencing, Nanopore direct cDNA sequencing and proteomics analysis, we identify IR events that affect the expression of key genes/proteins involved in macrophage development and function. We demonstrate that decreased IR in nuclear-detained mRNA is coupled with increased expression of genes encoding regulators of macrophage transcription, phagocytosis and inflammatory signalling, including ID2, IRF7, ENG and LAT. We further show that this dynamic IR program persists during the polarisation of resting macrophages into activated macrophages. In the presence of proinflammatory stimuli, intron-retaining CXCL2 and NFKBIZ transcripts are rapidly spliced, enabling timely expression of these key inflammatory regulators by macrophages. Our study provides novel insights into the molecular factors controlling vital regulators of the innate immune response.
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Affiliation(s)
- Immanuel D Green
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Natalia Pinello
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Quintin Lee
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.,Immune Imaging Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - James M Halstead
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Chau-To Kwok
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Alex C H Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Shalima S Nair
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst 2010, Australia.,St. Vincent's Clinical School, UNSW, Sydney 2010, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst 2010, Australia
| | - Susan J Clark
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst 2010, Australia.,St. Vincent's Clinical School, UNSW, Sydney 2010, Australia
| | - Ben Roediger
- Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.,Immune Imaging Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Ulf Schmitz
- Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Computational Biomedicine Laboratory Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Mark Larance
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown 2006, New South Wales, Australia
| | - Rippei Hayashi
- The John Curtin School of Medical Research, The Australian National University, ACT 2601, Australia
| | - John E J Rasko
- Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
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32
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Wang X, Ashhurst AS, Dowman LJ, Watson EE, Li HY, Fairbanks AJ, Larance M, Kwan A, Payne RJ. Total Synthesis of Glycosylated Human Interferon-γ. Org Lett 2020; 22:6863-6867. [PMID: 32830985 DOI: 10.1021/acs.orglett.0c02401] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Interferon-γ (IFN-γ) is a glycoprotein that is responsible for orchestrating numerous critical immune induction and modulation processes and is used clinically for the treatment of a number of diseases. Herein, we describe the total chemical synthesis of homogeneously glycosylated variants of human IFN-γ using a tandem diselenide-selenoester ligation-deselenization strategy in the C- to N-terminal direction. The synthetic glycoproteins were successfully folded, and the structures and antiviral functions were assessed.
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Affiliation(s)
- Xiaoyi Wang
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Anneliese S Ashhurst
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Luke J Dowman
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Emma E Watson
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Henry Y Li
- School of Physical and Chemical Sciences, The University of Canterbury, Christchurch 8140, New Zealand
| | - Antony J Fairbanks
- School of Physical and Chemical Sciences, The University of Canterbury, Christchurch 8140, New Zealand
| | - Mark Larance
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ann Kwan
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, https://cipps.org.au/
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33
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Bernier M, Mitchell SJ, Wahl D, Diaz A, Singh A, Seo W, Wang M, Ali A, Kaiser T, Price NL, Aon MA, Kim EY, Petr MA, Cai H, Warren A, Di Germanio C, Di Francesco A, Fishbein K, Guiterrez V, Harney D, Koay YC, Mach J, Enamorado IN, Pulpitel T, Wang Y, Zhang J, Zhang L, Spencer RG, Becker KG, Egan JM, Lakatta EG, O'Sullivan J, Larance M, LeCouteur DG, Cogger VC, Gao B, Fernandez-Hernando C, Cuervo AM, de Cabo R. Disulfiram Treatment Normalizes Body Weight in Obese Mice. Cell Metab 2020; 32:203-214.e4. [PMID: 32413333 PMCID: PMC7957855 DOI: 10.1016/j.cmet.2020.04.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/02/2020] [Accepted: 04/24/2020] [Indexed: 02/08/2023]
Abstract
Obesity is a top public health concern, and a molecule that safely treats obesity is urgently needed. Disulfiram (known commercially as Antabuse), an FDA-approved treatment for chronic alcohol addiction, exhibits anti-inflammatory properties and helps protect against certain types of cancer. Here, we show that in mice disulfiram treatment prevented body weight gain and abrogated the adverse impact of an obesogenic diet on insulin responsiveness while mitigating liver steatosis and pancreatic islet hypertrophy. Additionally, disulfiram treatment reversed established diet-induced obesity and metabolic dysfunctions in middle-aged mice. Reductions in feeding efficiency and increases in energy expenditure were associated with body weight regulation in response to long-term disulfiram treatment. Loss of fat tissue and an increase in liver fenestrations were also observed in rats on disulfiram. Given the potent anti-obesogenic effects in rodents, repurposing disulfiram in the clinic could represent a new strategy to treat obesity and its metabolic comorbidities.
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Affiliation(s)
- Michel Bernier
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Sarah J Mitchell
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Devin Wahl
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia; Ageing and Alzheimer's Institute, ANZAC Research Institute, Concord Clinical School/Sydney Medical School, Concord, NSW 2139, Australia
| | - Antonio Diaz
- Department of Developmental and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Abhishek Singh
- Vascular Biology and Therapeutics Program, Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine, Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Wonhyo Seo
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mingy Wang
- Laboratory of Cardiovascular Science, Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Ahmed Ali
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Tamzin Kaiser
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Nathan L Price
- Vascular Biology and Therapeutics Program, Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine, Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Miguel A Aon
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; Laboratory of Cardiovascular Science, Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Eun-Young Kim
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; Functional Genomics Research Center, KRIBB, Daejeon 305-806, Republic of Korea
| | - Michael A Petr
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Huan Cai
- Laboratory of Clinical Investigation, Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Alessa Warren
- Ageing and Alzheimer's Institute, ANZAC Research Institute, Concord Clinical School/Sydney Medical School, Concord, NSW 2139, Australia
| | - Clara Di Germanio
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Andrea Di Francesco
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ken Fishbein
- Laboratory of Clinical Investigation, Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Vince Guiterrez
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Dylan Harney
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Yen Chin Koay
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia; Heart Research Institute, The University of Sydney, Sydney, NSW 2042, Australia
| | - John Mach
- Kolling Institute of Medical Research and Sydney Medical School, University of Sydney, Sydney, NSW 2065, Australia
| | - Ignacio Navas Enamorado
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Tamara Pulpitel
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia; Ageing and Alzheimer's Institute, ANZAC Research Institute, Concord Clinical School/Sydney Medical School, Concord, NSW 2139, Australia
| | - Yushi Wang
- Laboratory of Cardiovascular Science, Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Jing Zhang
- Laboratory of Cardiovascular Science, Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Li Zhang
- Laboratory of Cardiovascular Science, Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Richard G Spencer
- Laboratory of Clinical Investigation, Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Kevin G Becker
- Laboratory of Genetics, Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Josephine M Egan
- Laboratory of Clinical Investigation, Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Edward G Lakatta
- Laboratory of Cardiovascular Science, Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - John O'Sullivan
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia; Heart Research Institute, The University of Sydney, Sydney, NSW 2042, Australia
| | - Mark Larance
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - David G LeCouteur
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia; Ageing and Alzheimer's Institute, ANZAC Research Institute, Concord Clinical School/Sydney Medical School, Concord, NSW 2139, Australia
| | - Victoria C Cogger
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia; Ageing and Alzheimer's Institute, ANZAC Research Institute, Concord Clinical School/Sydney Medical School, Concord, NSW 2139, Australia
| | - Bin Gao
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carlos Fernandez-Hernando
- Vascular Biology and Therapeutics Program, Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine, Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Rafael de Cabo
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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34
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Bernier M, Harney D, Koay YC, Diaz A, Singh A, Wahl D, Pulpitel T, Ali A, Guiterrez V, Mitchell SJ, Kim EY, Mach J, Price NL, Aon MA, LeCouteur DG, Cogger VC, Fernandez-Hernando C, O’Sullivan J, Larance M, Cuervo AM, de Cabo R. Elucidating the mechanisms by which disulfiram protects against obesity and metabolic syndrome. NPJ Aging Mech Dis 2020; 6:8. [PMID: 32714562 PMCID: PMC7374720 DOI: 10.1038/s41514-020-0046-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/16/2020] [Indexed: 12/25/2022] Open
Abstract
There is an unmet need and urgency to find safe and effective anti-obesity interventions. Our recent study in mice fed on obesogenic diet found that treatment with the alcohol aversive drug disulfiram reduced feeding efficiency and led to a decrease in body weight and an increase in energy expenditure. The intervention with disulfiram improved glucose tolerance and insulin sensitivity, and mitigated metabolic dysfunctions in various organs through poorly defined mechanisms. Here, integrated analysis of transcriptomic and proteomic data from mouse and rat livers unveiled comparable signatures in response to disulfiram, revealing pathways associated with lipid and energy metabolism, redox, and detoxification. In cell culture, disulfiram was found to be a potent activator of autophagy, the malfunctioning of which has negative consequences on metabolic regulation. Thus, repurposing disulfiram may represent a potent strategy to combat obesity.
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Affiliation(s)
- Michel Bernier
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224 USA
| | - Dylan Harney
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006 Australia
| | - Yen Chin Koay
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006 Australia
- Heart Research Institute, The University of Sydney, Sydney, NSW 2042 Australia
| | - Antonio Diaz
- Department of Developmental and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY 10461 USA
| | - Abhishek Singh
- Vascular Biology and Therapeutics Program, Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine, Department of Pathology, Yale University School of Medicine, New Haven, CT 06510 USA
| | - Devin Wahl
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224 USA
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006 Australia
- Ageing and Alzheimer’s Institute, ANZAC Research Institute, Concord Clinical School/Sydney Medical School, Concord, NSW 2139 Australia
| | - Tamara Pulpitel
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006 Australia
- Ageing and Alzheimer’s Institute, ANZAC Research Institute, Concord Clinical School/Sydney Medical School, Concord, NSW 2139 Australia
| | - Ahmed Ali
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224 USA
| | - Vince Guiterrez
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224 USA
| | - Sarah J. Mitchell
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224 USA
| | - Eun-Young Kim
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224 USA
- Functional Genomics Research Center, KRIBB, Daejeon, 305-806 Republic of Korea
| | - John Mach
- Kolling Institute of Medical Research and Sydney Medical School, University of Sydney, Sydney, NSW 2064 Australia
| | - Nathan L. Price
- Vascular Biology and Therapeutics Program, Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine, Department of Pathology, Yale University School of Medicine, New Haven, CT 06510 USA
| | - Miguel A. Aon
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224 USA
| | - David G. LeCouteur
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006 Australia
- Ageing and Alzheimer’s Institute, ANZAC Research Institute, Concord Clinical School/Sydney Medical School, Concord, NSW 2139 Australia
| | - Victoria C. Cogger
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006 Australia
- Ageing and Alzheimer’s Institute, ANZAC Research Institute, Concord Clinical School/Sydney Medical School, Concord, NSW 2139 Australia
| | - Carlos Fernandez-Hernando
- Vascular Biology and Therapeutics Program, Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine, Department of Pathology, Yale University School of Medicine, New Haven, CT 06510 USA
| | - John O’Sullivan
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006 Australia
- Heart Research Institute, The University of Sydney, Sydney, NSW 2042 Australia
| | - Mark Larance
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006 Australia
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY 10461 USA
| | - Rafael de Cabo
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224 USA
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Freire T, Senior AM, Perks R, Pulpitel T, Clark X, Brandon AE, Wahl D, Hatchwell L, Le Couteur DG, Cooney GJ, Larance M, Simpson SJ, Solon-Biet SM. Sex-specific metabolic responses to 6 hours of fasting during the active phase in young mice. J Physiol 2020; 598:2081-2092. [PMID: 32198893 DOI: 10.1113/jp278806] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 08/23/2019] [Accepted: 03/04/2020] [Indexed: 02/06/2023] Open
Abstract
KEY POINTS Night time/active phase food restriction for 6 h impaired glucose intolerance in young male and female mice. Females displayed increased capacity for lipogenesis and triglyceride storage in response to a short daily fast. Females had lower fasting insulin levels and an increased potential for utilizing fat for energy through β-oxidation compared to males. The need for the inclusion of both sexes, and the treatment of sex as an independent variable, is emphasized within the context of this fasting regime. ABSTRACT There is growing interest in understanding the mechanistic significance and benefits of fasting physiology in combating obesity. Increasing the fasting phase of a normal day can promote restoration and repair mechanisms that occur during the post-absorptive period. Most studies exploring the effect of restricting food access on mitigating obesity have done so with a large bias towards the use of male mice. Here, we disentangle the roles of sex, food intake and food withdrawal in the response to a short-term daily fasting intervention, in which food was removed for 6 h in the dark/active phase of young, 8-week-old mice. We showed that the removal of food during the dark phase impaired glucose tolerance in males and females, possibly due to the circadian disruption induced by this feeding protocol. Although both sexes demonstrated similar patterns of food intake, body composition and various metabolic markers, there were clear sex differences in the magnitude and extent of these responses. While females displayed enhanced capacity for lipogenesis and triglyceride storage, they also had low fasting insulin levels and an increased potential for utilizing available energy sources such as fat for energy through β-oxidation. Our results highlight the intrinsic biological and metabolic disparities between male and female mice, emphasizing the growing need for the inclusion of both sexes in scientific research. Furthermore, our results illustrate sex-specific metabolic pathways that regulate lipogenesis, obesity and overall metabolic health.
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Affiliation(s)
- Therese Freire
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Alistair M Senior
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Ruth Perks
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Tamara Pulpitel
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Ximonie Clark
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Amanda E Brandon
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Health and Medicine, University of Sydney, Sydney, NSW, Australia
| | - Devin Wahl
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Health and Medicine, University of Sydney, Sydney, NSW, Australia
| | - Luke Hatchwell
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - David G Le Couteur
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,Ageing and Alzheimer's Institute and Centre for Education and Research on Ageing, Concord Hospital, Concord, NSW, Australia
| | - Gregory J Cooney
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Health and Medicine, University of Sydney, Sydney, NSW, Australia
| | - Mark Larance
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Stephen J Simpson
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Samantha M Solon-Biet
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Health and Medicine, University of Sydney, Sydney, NSW, Australia
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36
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Hatchwell L, Harney DJ, Cielesh M, Young K, Koay YC, O’Sullivan JF, Larance M. Multi-omics Analysis of the Intermittent Fasting Response in Mice Identifies an Unexpected Role for HNF4α. Cell Rep 2020; 30:3566-3582.e4. [DOI: 10.1016/j.celrep.2020.02.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/24/2020] [Accepted: 02/11/2020] [Indexed: 12/21/2022] Open
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37
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Woodhouse RM, Buchmann G, Hoe M, Harney DJ, Low JKK, Larance M, Boag PR, Ashe A. Chromatin Modifiers SET-25 and SET-32 Are Required for Establishment but Not Long-Term Maintenance of Transgenerational Epigenetic Inheritance. Cell Rep 2019; 25:2259-2272.e5. [PMID: 30463020 DOI: 10.1016/j.celrep.2018.10.085] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [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: 01/28/2018] [Revised: 09/25/2018] [Accepted: 10/24/2018] [Indexed: 12/24/2022] Open
Abstract
Some epigenetic modifications are inherited from one generation to the next, providing a potential mechanism for the inheritance of environmentally acquired traits. Transgenerational inheritance of RNAi phenotypes in Caenorhabditis elegans provides an excellent model to study this phenomenon, and although studies have implicated both chromatin modifications and small RNA pathways in heritable silencing, their relative contributions remain unclear. Here, we demonstrate that the putative histone methyltransferases SET-25 and SET-32 are required for establishment of a transgenerational silencing signal but not for long-term maintenance of this signal between subsequent generations, suggesting that transgenerational epigenetic inheritance is a multi-step process with distinct genetic requirements for establishment and maintenance of heritable silencing. Furthermore, small RNA sequencing reveals that the abundance of secondary siRNAs (thought to be the effector molecules of heritable silencing) does not correlate with silencing phenotypes. Together, our results suggest that the current mechanistic models of epigenetic inheritance are incomplete.
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Affiliation(s)
- Rachel M Woodhouse
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Gabriele Buchmann
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Matthew Hoe
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Dylan J Harney
- The University of Sydney, Charles Perkins Centre, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Jason K K Low
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Mark Larance
- The University of Sydney, Charles Perkins Centre, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Peter R Boag
- Monash University, Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Clayton, VIC 3800, Australia
| | - Alyson Ashe
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia; The University of Wollongong, School of Biological Sciences and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
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38
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Byrne FL, Olzomer EM, Marriott GR, Quek LE, Katen A, Su J, Nelson ME, Hart-Smith G, Larance M, Sebesfi VF, Cuff J, Martyn GE, Childress E, Alexopoulos SJ, Poon IK, Faux MC, Burgess AW, Reid G, McCarroll JA, Santos WL, Quinlan KG, Turner N, Fazakerley DJ, Kumar N, Hoehn KL. Phenotypic screen for oxygen consumption rate identifies an anti-cancer naphthoquinone that induces mitochondrial oxidative stress. Redox Biol 2019; 28:101374. [PMID: 31743887 PMCID: PMC6861633 DOI: 10.1016/j.redox.2019.101374] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 07/31/2019] [Revised: 10/07/2019] [Accepted: 11/04/2019] [Indexed: 11/09/2022] Open
Abstract
A hallmark of cancer cells is their ability to reprogram nutrient metabolism. Thus, disruption to this phenotype is a potential avenue for anti-cancer therapy. Herein we used a phenotypic chemical library screening approach to identify molecules that disrupted nutrient metabolism (by increasing cellular oxygen consumption rate) and were toxic to cancer cells. From this screen we discovered a 1,4-Naphthoquinone (referred to as BH10) that is toxic to a broad range of cancer cell types. BH10 has improved cancer-selective toxicity compared to doxorubicin, 17-AAG, vitamin K3, and other known anti-cancer quinones. BH10 increases glucose oxidation via both mitochondrial and pentose phosphate pathways, decreases glycolysis, lowers GSH:GSSG and NAPDH/NAPD+ ratios exclusively in cancer cells, and induces necrosis. BH10 targets mitochondrial redox defence as evidenced by increased mitochondrial peroxiredoxin 3 oxidation and decreased mitochondrial aconitase activity, without changes in markers of cytosolic or nuclear damage. Over-expression of mitochondria-targeted catalase protects cells from BH10-mediated toxicity, while the thioredoxin reductase inhibitor auranofin synergistically enhances BH10-induced peroxiredoxin 3 oxidation and cytotoxicity. Overall, BH10 represents a 1,4-Naphthoquinone with an improved cancer-selective cytotoxicity profile via its mitochondrial specificity. Phenotypic screen identifies a 1,4-Naphthoquinone BH10 with improved cancer-selective cytotoxicity BH10 decreases glycolysis and increases glucose oxidation BH10-mediated cytotoxicity is linked to mitochondrial oxidative stress
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Affiliation(s)
- Frances L Byrne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
| | - Ellen M Olzomer
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Gabriella R Marriott
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Lake-Ee Quek
- School of Mathematics and Statistics, The University of Sydney, Sydney, Australia
| | - Alice Katen
- School of Chemistry, University of New South Wales, Sydney, NSW, Australia
| | - Jacky Su
- School of Chemistry, University of New South Wales, Sydney, NSW, Australia
| | - Marin E Nelson
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Australia
| | - Gene Hart-Smith
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mark Larance
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Australia
| | - Veronica F Sebesfi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jeff Cuff
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Gabriella E Martyn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Elizabeth Childress
- Department of Chemistry and VT Center for Drug Discovery, Virginia Tech, Blacksburg, VA, USA
| | - Stephanie J Alexopoulos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Ivan K Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Maree C Faux
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Antony W Burgess
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Glen Reid
- Concord Medical School, Asbestos Disease Research Institute, University of Sydney, Australia
| | - Joshua A McCarroll
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales Sydney, New South Wales, Australia
| | - Webster L Santos
- Department of Chemistry and VT Center for Drug Discovery, Virginia Tech, Blacksburg, VA, USA
| | - Kate Gr Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Nigel Turner
- School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel J Fazakerley
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Australia
| | - Naresh Kumar
- School of Chemistry, University of New South Wales, Sydney, NSW, Australia
| | - Kyle L Hoehn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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39
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Harney DJ, Hutchison AT, Su Z, Hatchwell L, Heilbronn LK, Hocking S, James DE, Larance M. Small-protein Enrichment Assay Enables the Rapid, Unbiased Analysis of Over 100 Low Abundance Factors from Human Plasma. Mol Cell Proteomics 2019; 18:1899-1915. [PMID: 31308252 PMCID: PMC6731089 DOI: 10.1074/mcp.tir119.001562] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 05/17/2019] [Revised: 07/08/2019] [Indexed: 12/15/2022] Open
Abstract
Unbiased and sensitive quantification of low abundance small proteins in human plasma (e.g. hormones, immune factors, metabolic regulators) remains an unmet need. These small protein factors are typically analyzed individually and using antibodies that can lack specificity. Mass spectrometry (MS)-based proteomics has the potential to address these problems, however the analysis of plasma by MS is plagued by the extremely large dynamic range of this body fluid, with protein abundances spanning at least 13 orders of magnitude. Here we describe an enrichment assay (SPEA), that greatly simplifies the plasma dynamic range problem by enriching small-proteins of 2-10 kDa, enabling the rapid, specific and sensitive quantification of >100 small-protein factors in a single untargeted LC-MS/MS acquisition. Applying this method to perform deep-proteome profiling of human plasma we identify C5ORF46 as a previously uncharacterized human plasma protein. We further demonstrate the reproducibility of our workflow for low abundance protein analysis using a stable-isotope labeled protein standard of insulin spiked into human plasma. SPEA provides the ability to study numerous important hormones in a single rapid assay, which we applied to study the intermittent fasting response and observed several unexpected changes including decreased plasma abundance of the iron homeostasis regulator hepcidin.
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Affiliation(s)
- Dylan J Harney
- ‡Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Amy T Hutchison
- ¶Discipline of Medicine, University of Adelaide, Adelaide, Australia
| | - Zhiduan Su
- ‡Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Luke Hatchwell
- ‡Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | | | - Samantha Hocking
- §Central Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - David E James
- ‡Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Mark Larance
- ‡Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.
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40
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Harney DJ, Hutchison AT, Hatchwell L, Humphrey SJ, James DE, Hocking S, Heilbronn LK, Larance M. Proteomic Analysis of Human Plasma during Intermittent Fasting. J Proteome Res 2019; 18:2228-2240. [PMID: 30892045 PMCID: PMC6503536 DOI: 10.1021/acs.jproteome.9b00090] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Intermittent fasting (IF) increases lifespan and decreases metabolic disease phenotypes and cancer risk in model organisms, but the health benefits of IF in humans are less clear. Human plasma derived from clinical trials is one of the most difficult sample sets to analyze using mass spectrometry-based proteomics due to the extensive sample preparation required and the need to process many samples to achieve statistical significance. Here, we describe an optimized and accessible device (Spin96) to accommodate up to 96 StageTips, a widely used sample preparation medium enabling efficient and consistent processing of samples prior to LC-MS/MS. We have applied this device to the analysis of human plasma from a clinical trial of IF. In this longitudinal study employing 8-weeks IF, we identified significant abundance differences induced by the IF intervention, including increased apolipoprotein A4 (APOA4) and decreased apolipoprotein C2 (APOC2) and C3 (APOC3). These changes correlated with a significant decrease in plasma triglycerides after the IF intervention. Given that these proteins have a role in regulating apolipoprotein particle metabolism, we propose that IF had a positive effect on lipid metabolism through modulation of HDL particle size and function. In addition, we applied a novel human protein variant database to detect common protein variants across the participants. We show that consistent detection of clinically relevant peptides derived from both alleles of many proteins is possible, including some that are associated with human metabolic phenotypes. Together, these findings illustrate the power of accessible workflows for proteomics analysis of clinical samples to yield significant biological insight.
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Affiliation(s)
- Dylan J Harney
- Charles Perkins Centre, School of Life and Environmental Sciences , University of Sydney , Sydney , NSW 2006 , Australia
| | - Amy T Hutchison
- Discipline of Medicine , University of Adelaide , Adelaide , SA 5005 , Australia
| | - Luke Hatchwell
- Charles Perkins Centre, School of Life and Environmental Sciences , University of Sydney , Sydney , NSW 2006 , Australia
| | - Sean J Humphrey
- Charles Perkins Centre, School of Life and Environmental Sciences , University of Sydney , Sydney , NSW 2006 , Australia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences , University of Sydney , Sydney , NSW 2006 , Australia
| | - Samantha Hocking
- Central Clinical School, Faculty of Medicine and Health , University of Sydney , Sydney , NSW 2006 , Australia
| | - Leonie K Heilbronn
- Discipline of Medicine , University of Adelaide , Adelaide , SA 5005 , Australia
| | - Mark Larance
- Charles Perkins Centre, School of Life and Environmental Sciences , University of Sydney , Sydney , NSW 2006 , Australia
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41
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Yoshikawa H, Larance M, Harney DJ, Sundaramoorthy R, Ly T, Owen-Hughes T, Lamond AI. Efficient analysis of mammalian polysomes in cells and tissues using Ribo Mega-SEC. eLife 2018; 7:36530. [PMID: 30095066 PMCID: PMC6086667 DOI: 10.7554/elife.36530] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 03/09/2018] [Accepted: 07/28/2018] [Indexed: 12/14/2022] Open
Abstract
We describe Ribo Mega-SEC, a powerful approach for the separation and biochemical analysis of mammalian polysomes and ribosomal subunits using Size Exclusion Chromatography and uHPLC. Using extracts from either cells, or tissues, polysomes can be separated within 15 min from sample injection to fraction collection. Ribo Mega-SEC shows translating ribosomes exist predominantly in polysome complexes in human cell lines and mouse liver tissue. Changes in polysomes are easily quantified between treatments, such as the cellular response to amino acid starvation. Ribo Mega-SEC is shown to provide an efficient, convenient and highly reproducible method for studying functional translation complexes. We show that Ribo Mega-SEC is readily combined with high-throughput MS-based proteomics to characterize proteins associated with polysomes and ribosomal subunits. It also facilitates isolation of complexes for electron microscopy and structural studies.
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Affiliation(s)
- Harunori Yoshikawa
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mark Larance
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Dylan J Harney
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | | | - Tony Ly
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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42
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Crozier TWM, Tinti M, Larance M, Lamond AI, Ferguson MAJ. Prediction of Protein Complexes in Trypanosoma brucei by Protein Correlation Profiling Mass Spectrometry and Machine Learning. Mol Cell Proteomics 2017; 16:2254-2267. [PMID: 29042480 PMCID: PMC5724185 DOI: 10.1074/mcp.o117.068122] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 03/06/2017] [Revised: 08/04/2017] [Indexed: 01/10/2023] Open
Abstract
A disproportionate number of predicted proteins from the genome sequence of the protozoan parasite Trypanosoma brucei, an important human and animal pathogen, are hypothetical proteins of unknown function. This paper describes a protein correlation profiling mass spectrometry approach, using two size exclusion and one ion exchange chromatography systems, to derive sets of predicted protein complexes in this organism by hierarchical clustering and machine learning methods. These hypothesis-generating proteomic data are provided in an open access online data visualization environment (http://134.36.66.166:8083/complex_explorer). The data can be searched conveniently via a user friendly, custom graphical interface. We provide examples of both potential new subunits of known protein complexes and of novel trypanosome complexes of suggested function, contributing to improving the functional annotation of the trypanosome proteome. Data are available via ProteomeXchange with identifier PXD005968.
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Affiliation(s)
- Thomas W M Crozier
- From the ‡Division of Biological Chemistry and Drug Discovery and.,§Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD2 1NW, UK
| | - Michele Tinti
- From the ‡Division of Biological Chemistry and Drug Discovery and
| | - Mark Larance
- §Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD2 1NW, UK
| | - Angus I Lamond
- §Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD2 1NW, UK
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43
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Akay A, Di Domenico T, Suen KM, Nabih A, Parada GE, Larance M, Medhi R, Berkyurek AC, Zhang X, Wedeles CJ, Rudolph KLM, Engelhardt J, Hemberg M, Ma P, Lamond AI, Claycomb JM, Miska EA. The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription. Dev Cell 2017; 42:241-255.e6. [PMID: 28787591 PMCID: PMC5554785 DOI: 10.1016/j.devcel.2017.07.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [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: 12/21/2016] [Revised: 05/14/2017] [Accepted: 07/05/2017] [Indexed: 02/02/2023]
Abstract
Small RNAs play a crucial role in genome defense against transposable elements and guide Argonaute proteins to nascent RNA transcripts to induce co-transcriptional gene silencing. However, the molecular basis of this process remains unknown. Here, we identify the conserved RNA helicase Aquarius/EMB-4 as a direct and essential link between small RNA pathways and the transcriptional machinery in Caenorhabditis elegans. Aquarius physically interacts with the germline Argonaute HRDE-1. Aquarius is required to initiate small-RNA-induced heritable gene silencing. HRDE-1 and Aquarius silence overlapping sets of genes and transposable elements. Surprisingly, removal of introns from a target gene abolishes the requirement for Aquarius, but not HRDE-1, for small RNA-dependent gene silencing. We conclude that Aquarius allows small RNA pathways to compete for access to nascent transcripts undergoing co-transcriptional splicing in order to detect and silence transposable elements. Thus, Aquarius and HRDE-1 act as gatekeepers coordinating gene expression and genome defense.
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Affiliation(s)
- Alper Akay
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Tomas Di Domenico
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Kin M Suen
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Amena Nabih
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Guillermo E Parada
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Mark Larance
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Ragini Medhi
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Ahmet C Berkyurek
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Xinlian Zhang
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Christopher J Wedeles
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Konrad L M Rudolph
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Jan Engelhardt
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Haertelstraße 16-18, Leipzig 04107, Germany
| | - Martin Hemberg
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Ping Ma
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Eric A Miska
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK.
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44
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Harvald EB, Sprenger RR, Dall KB, Ejsing CS, Nielsen R, Mandrup S, Murillo AB, Larance M, Gartner A, Lamond AI, Færgeman NJ. Multi-omics Analyses of Starvation Responses Reveal a Central Role for Lipoprotein Metabolism in Acute Starvation Survival in C. elegans. Cell Syst 2017; 5:38-52.e4. [PMID: 28734827 DOI: 10.1016/j.cels.2017.06.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 11/15/2016] [Revised: 03/03/2017] [Accepted: 06/08/2017] [Indexed: 12/21/2022]
Abstract
Starvation causes comprehensive metabolic changes, which are still not fully understood. Here, we used quantitative proteomics and RNA sequencing to examine the temporal starvation responses in wild-type Caenorhabditis elegans and animals lacking the transcription factor HLH-30. Our findings show that starvation alters the abundance of hundreds of proteins and mRNAs in a temporal manner, many of which are involved in central metabolic pathways, including lipoprotein metabolism. We demonstrate that premature death of hlh-30 animals under starvation can be prevented by knockdown of either vit-1 or vit-5, encoding two different lipoproteins. We further show that the size and number of intestinal lipid droplets under starvation are altered in hlh-30 animals, which can be rescued by knockdown of vit-1. Taken together, this indicates that survival of hlh-30 animals under starvation is closely linked to regulation of intestinal lipid stores. We provide the most detailed poly-omic analysis of starvation responses to date, which serves as a resource for further mechanistic studies of starvation.
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Affiliation(s)
- Eva Bang Harvald
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Richard R Sprenger
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Kathrine Brændgaard Dall
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Ronni Nielsen
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Alejandro Brenes Murillo
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Mark Larance
- Centre for Gene Regulation and Expression, College of Life Science, University of Dundee, Dow Street, Dundee, UK
| | - Anton Gartner
- Centre for Gene Regulation and Expression, College of Life Science, University of Dundee, Dow Street, Dundee, UK
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, College of Life Science, University of Dundee, Dow Street, Dundee, UK
| | - Nils J Færgeman
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark.
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45
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Larance M, Kirkwood KJ, Tinti M, Brenes Murillo A, Ferguson MAJ, Lamond AI. Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling. Mol Cell Proteomics 2016; 15:2476-90. [PMID: 27114452 PMCID: PMC4937518 DOI: 10.1074/mcp.o115.055467] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 03/11/2016] [Indexed: 12/30/2022] Open
Abstract
We present a methodology using in vivo crosslinking combined with HPLC-MS for the global analysis of endogenous protein complexes by protein correlation profiling. Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility during chromatographic separation. We show this efficiently detects both integral membrane and membrane-associated protein complexes,in addition to soluble complexes, allowing identification and analysis of complexes not accessible in native extracts. We compare the protein complexes detected by HPLC-MS protein correlation profiling in both native and formaldehyde crosslinked U2OS cell extracts. These proteome-wide data sets of both in vivo crosslinked and native protein complexes from U2OS cells are freely available via a searchable online database (www.peptracker.com/epd). Raw data are also available via ProteomeXchange (identifier PXD003754).
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Affiliation(s)
- Mark Larance
- From the ‡Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Kathryn J Kirkwood
- From the ‡Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michele Tinti
- §Biological Chemistry and Drug Discovery Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Alejandro Brenes Murillo
- From the ‡Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michael A J Ferguson
- §Biological Chemistry and Drug Discovery Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Angus I Lamond
- From the ‡Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom;
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46
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Hammond CM, Sundaramoorthy R, Larance M, Lamond A, Stevens MA, El-Mkami H, Norman DG, Owen-Hughes T. The histone chaperone Vps75 forms multiple oligomeric assemblies capable of mediating exchange between histone H3-H4 tetramers and Asf1-H3-H4 complexes. Nucleic Acids Res 2016; 44:6157-72. [PMID: 27036862 PMCID: PMC5291247 DOI: 10.1093/nar/gkw209] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [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: 12/21/2015] [Accepted: 03/17/2016] [Indexed: 11/14/2022] Open
Abstract
Vps75 is a histone chaperone that has been historically characterized as homodimer by X-ray crystallography. In this study, we present a crystal structure containing two related tetrameric forms of Vps75 within the crystal lattice. We show Vps75 associates with histones in multiple oligomers. In the presence of equimolar H3–H4 and Vps75, the major species is a reconfigured Vps75 tetramer bound to a histone H3–H4 tetramer. However, in the presence of excess histones, a Vps75 dimer bound to a histone H3–H4 tetramer predominates. We show the Vps75–H3–H4 interaction is compatible with the histone chaperone Asf1 and deduce a structural model of the Vps75–Asf1-H3–H4 (VAH) co-chaperone complex using the Pulsed Electron-electron Double Resonance (PELDOR) technique and cross-linking MS/MS distance restraints. The model provides a molecular basis for the involvement of both Vps75 and Asf1 in Rtt109 catalysed histone H3 K9 acetylation. In the absence of Asf1 this model can be used to generate a complex consisting of a reconfigured Vps75 tetramer bound to a H3–H4 tetramer. This provides a structural explanation for many of the complexes detected biochemically and illustrates the ability of Vps75 to interact with dimeric or tetrameric H3–H4 using the same interaction surface.
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Affiliation(s)
- Colin M Hammond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | - Mark Larance
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Angus Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Michael A Stevens
- Nucleic Acids Structure Research Group, University of Dundee, Dundee DD1 5EH, UK
| | - Hassane El-Mkami
- School of Physics and Astronomy, University of St Andrews, St Andrews, KY16 9SS, UK
| | - David G Norman
- Nucleic Acids Structure Research Group, University of Dundee, Dundee DD1 5EH, UK
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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47
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Larance M, Pourkarimi E, Wang B, Brenes Murillo A, Kent R, Lamond AI, Gartner A. Global Proteomics Analysis of the Response to Starvation in C. elegans. Mol Cell Proteomics 2015; 14:1989-2001. [PMID: 25963834 PMCID: PMC4587315 DOI: 10.1074/mcp.m114.044289] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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: 09/02/2014] [Indexed: 12/31/2022] Open
Abstract
Periodic starvation of animals induces large shifts in metabolism but may also influence many other cellular systems and can lead to adaption to prolonged starvation conditions. To date, there is limited understanding of how starvation affects gene expression, particularly at the protein level. Here, we have used mass-spectrometry-based quantitative proteomics to identify global changes in the Caenorhabditis elegans proteome due to acute starvation of young adult animals. Measuring changes in the abundance of over 5,000 proteins, we show that acute starvation rapidly alters the levels of hundreds of proteins, many involved in central metabolic pathways, highlighting key regulatory responses. Surprisingly, we also detect changes in the abundance of chromatin-associated proteins, including specific linker histones, histone variants, and histone posttranslational modifications associated with the epigenetic control of gene expression. To maximize community access to these data, they are presented in an online searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/).
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Affiliation(s)
- Mark Larance
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Ehsan Pourkarimi
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Bin Wang
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Alejandro Brenes Murillo
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Robert Kent
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Angus I Lamond
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Anton Gartner
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
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48
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Bailly A, Perrin A, Bou Malhab LJ, Pion E, Larance M, Nagala M, Smith P, O'Donohue MF, Gleizes PE, Zomerdijk J, Lamond AI, Xirodimas DP. The NEDD8 inhibitor MLN4924 increases the size of the nucleolus and activates p53 through the ribosomal-Mdm2 pathway. Oncogene 2015; 35:415-26. [PMID: 25867069 DOI: 10.1038/onc.2015.104] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 02/10/2015] [Accepted: 03/03/2015] [Indexed: 12/19/2022]
Abstract
The ubiquitin-like molecule NEDD8 is essential for viability, growth and development, and is a potential target for therapeutic intervention. We found that the small molecule inhibitor of NEDDylation, MLN4924, alters the morphology and increases the surface size of the nucleolus in human and germline cells of Caenorhabditis elegans in the absence of nucleolar fragmentation. SILAC proteomics and monitoring of rRNA production, processing and ribosome profiling shows that MLN4924 changes the composition of the nucleolar proteome but does not inhibit RNA Pol I transcription. Further analysis demonstrates that MLN4924 activates the p53 tumour suppressor through the RPL11/RPL5-Mdm2 pathway, with characteristics of nucleolar stress. The study identifies the nucleolus as a target of inhibitors of NEDDylation and provides a mechanism for p53 activation upon NEDD8 inhibition. It also indicates that targeting the nucleolar proteome without affecting nucleolar transcription initiates the required signalling events for the control of cell cycle regulators.
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Affiliation(s)
- A Bailly
- Centre de Recherche de Biochimie Macromoléculaire-UMR 5237, CNRS, Montpellier, France
| | - A Perrin
- Centre de Recherche de Biochimie Macromoléculaire-UMR 5237, CNRS, Montpellier, France
| | - L J Bou Malhab
- Centre de Recherche de Biochimie Macromoléculaire-UMR 5237, CNRS, Montpellier, France
| | - E Pion
- Centre de Recherche de Biochimie Macromoléculaire-UMR 5237, CNRS, Montpellier, France
| | - M Larance
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland/UK
| | - M Nagala
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland/UK
| | - P Smith
- Millennium Pharmaceuticals Inc., Cambridge, MA, USA
| | - M-F O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, UMR CNRS 5099, Bâtiment IBCG, Toulouse, France
| | - P-E Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, UMR CNRS 5099, Bâtiment IBCG, Toulouse, France
| | - J Zomerdijk
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland/UK
| | - A I Lamond
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland/UK
| | - D P Xirodimas
- Centre de Recherche de Biochimie Macromoléculaire-UMR 5237, CNRS, Montpellier, France
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50
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Akay A, Craig A, Lehrbach N, Larance M, Pourkarimi E, Wright JE, Lamond A, Miska E, Gartner A. RNA-binding protein GLD-1/quaking genetically interacts with the mir-35 and the let-7 miRNA pathways in Caenorhabditis elegans. Open Biol 2013; 3:130151. [PMID: 24258276 PMCID: PMC3843822 DOI: 10.1098/rsob.130151] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [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] [Indexed: 12/30/2022] Open
Abstract
Messenger RNA translation is regulated by RNA-binding proteins and small non-coding RNAs called microRNAs. Even though we know the majority of RNA-binding proteins and microRNAs that regulate messenger RNA expression, evidence of interactions between the two remain elusive. The role of the RNA-binding protein GLD-1 as a translational repressor is well studied during Caenorhabditis elegans germline development and maintenance. Possible functions of GLD-1 during somatic development and the mechanism of how GLD-1 acts as a translational repressor are not known. Its human homologue, quaking (QKI), is essential for embryonic development. Here, we report that the RNA-binding protein GLD-1 in C. elegans affects multiple microRNA pathways and interacts with proteins required for microRNA function. Using genome-wide RNAi screening, we found that nhl-2 and vig-1, two known modulators of miRNA function, genetically interact with GLD-1. gld-1 mutations enhance multiple phenotypes conferred by mir-35 and let-7 family mutants during somatic development. We used stable isotope labelling with amino acids in cell culture to globally analyse the changes in the proteome conferred by let-7 and gld-1 during animal development. We identified the histone mRNA-binding protein CDL-1 to be, in part, responsible for the phenotypes observed in let-7 and gld-1 mutants. The link between GLD-1 and miRNA-mediated gene regulation is further supported by its biochemical interaction with ALG-1, CGH-1 and PAB-1, proteins implicated in miRNA regulation. Overall, we have uncovered genetic and biochemical interactions between GLD-1 and miRNA pathways.
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Affiliation(s)
- Alper Akay
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK
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