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Brand H, Fryer M, Mehdi AM, Melon A, Morcombe B, Choong K, Subedi S. Home nursing and self-administered outpatient parenteral antimicrobial treatment: a comparison of demographics and outcomes from a large regional hospital in Queensland, Australia. Intern Med J 2024. [PMID: 38591847 DOI: 10.1111/imj.16394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 03/15/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Outpatient parenteral antimicrobial treatment (OPAT) is a safe and effective therapy used in several settings across Australia. As OPAT services expand their inclusion criteria to include complex patient populations, there is an increased need for selecting appropriate patients to receive either healthcare-administered OPAT (H-OPAT) or self-administered OPAT (S-OPAT). AIMS To describe patient demographics, diagnosis, microbiology and outcomes of patients treated by H-OPAT and S-OPAT within the Sunshine Coast Hospital and Health Service, Australia. METHODS Data on demographics, diagnoses, treatment and outcomes on all patients treated by H-OPAT and S-OPAT from March 2017 to December 2019 were collected retrospectively. RESULTS One hundred and sixty-five patients (62.26%) were enrolled in H-OPAT and 100 patients (37.74%) in S-OPAT. S-OPAT patients were significantly younger. H-OPAT patients were more comorbid. Bone and joint infections were the most treated infections and were more likely to be treated by S-OPAT. There was no difference in treatment duration, cure and complication rates between S-OPAT and H-OPAT. Longer duration of therapy was associated with more complications. Treatment failure was associated with infections due to multiple organisms, number of comorbidities and treatment of surgical site, skin and soft tissue infections. CONCLUSIONS There were significant differences in demographics between H-OPAT and S-OPAT without any difference in outcomes. Overall failure and complication rates were low. Higher rates of treatment failure were predicted by the diagnosis, number of comorbidities and number of organisms treated.
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Affiliation(s)
- Holly Brand
- Griffith University School of Medicine, Gold Coast, Queensland, Australia
| | - Michael Fryer
- Sunshine Coast University Hospital, Sunshine Coast, Queensland, Australia
| | - Ahmed M Mehdi
- QCIF Bioinformatics, Queensland Cyber Infrastructure Foundation Ltd, Brisbane, Queensland, Australia
| | - Alex Melon
- Sunshine Coast University Hospital, Sunshine Coast, Queensland, Australia
| | - Bridie Morcombe
- Sunshine Coast University Hospital, Sunshine Coast, Queensland, Australia
| | - Keat Choong
- Infectious Diseases Department, Sunshine Coast University Hospital, Sunshine Coast, Queensland, Australia
- Infection Research Network, Sunshine Coast Hospital and Health Service, Sunshine Coast, Queensland, Australia
| | - Shradha Subedi
- Infectious Diseases Department, Sunshine Coast University Hospital, Sunshine Coast, Queensland, Australia
- Infection Research Network, Sunshine Coast Hospital and Health Service, Sunshine Coast, Queensland, Australia
- Microbiology, Pathology Queensland, Sunshine Coast University Hospital, Sunshine Coast, Queensland, Australia
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
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2
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Ravichandran A, Monkman J, Mehdi AM, Blick T, Snell C, Kulasinghe A, Bray LJ. The in situ transcriptomic landscape of breast tumour-associated and normal adjacent endothelial cells. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166985. [PMID: 38061601 DOI: 10.1016/j.bbadis.2023.166985] [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: 08/09/2023] [Revised: 11/17/2023] [Accepted: 12/03/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND AND AIMS Triple Negative Breast Cancer (TNBC) is associated with increased angiogenesis, which is known to aid tumour growth and metastasis. Anti-angiogenic therapies that have been developed to target this feature have mostly generated disappointing clinical results. Further research into targeted approaches is limited by a lack of understanding of the in situ molecular profile of tumour-associated vasculature. In this study, we aimed to understand the differences in the molecular profiles of tumour endothelial cells vs normal-adjacent endothelial cells in TNBC tissues. METHOD We have applied unbiased whole transcriptome spatial profiling of in situ gene expressions of endothelial cells localized in full-face patient TNBC tissues (n = 4) and normal-adjacent regions of the same patient breast tissues. RESULTS Our comparative analysis revealed that 2412 genes were differentially expressed (padj < 0.05) between the tumour endothelial cells and normal-adjacent endothelial cells. Pathway enrichment showed the enrichment of gene sets related to cell-cell, cell-ECM adhesion, chromatin organization and remodeling, and protein-DNA complex subunit organization. CONCLUSION Overall, the results revealed unique molecular profiles and signalling pathways of tumour-associated vasculature, which is a critical step towards larger cohort studies investigating potential targets for TNBC prognosis and anti-angiogenic treatments.
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Affiliation(s)
- Akhilandeshwari Ravichandran
- School of Mechanical, Medical and Process Engineering, Faculty of Engineering, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia; Centre for Biomedical Technologies, Queensland University of Technology (QUT), Brisbane, QLD 4059, Australia.
| | - James Monkman
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Ahmed M Mehdi
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia; Queensland Cyber Infrastructure Foundation Ltd, Facility for Advanced Bioinformatics, Brisbane, QLD 4072, Australia
| | - Tony Blick
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Cameron Snell
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Mater Pathology, Mater Hospital Brisbane, Mater Health Services, Brisbane, QLD 4101, Australia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia.
| | - Laura J Bray
- School of Mechanical, Medical and Process Engineering, Faculty of Engineering, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia; Centre for Biomedical Technologies, Queensland University of Technology (QUT), Brisbane, QLD 4059, Australia; Centre for the Personalised Analysis of Cancers, Queensland University of Technology, Translational Research Institute, QLD 4102, Australia; Australian Research Council (ARC) Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia.
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Chen Y, Prichard R, Mason M, Tower M, Zimmerman PA, Sparke V, Layh J, Mehdi AM, Lin FF. Barriers and facilitators to COVID-19 vaccine uptake among Australian health professional students during the pandemic: a nationwide study. J Public Health Policy 2023; 44:400-414. [PMID: 37330562 PMCID: PMC10485127 DOI: 10.1057/s41271-023-00422-9] [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] [Accepted: 05/31/2023] [Indexed: 06/19/2023]
Abstract
Using a cross-sectional online survey we investigated knowledge, attitudes, and risk perception about COVID-19 vaccination and identified factors influencing vaccine uptake among Australian health professional students from October 2021 to January 2022. We analysed data from 1114 health professional students from 17 Australian universities. Most participants were enrolled in nursing programs (n = 958, 86.8%), and 91.6% (n = 858) of the participants received COVID-19 vaccination. Approximately 27% believed COVID-19 was no more serious than seasonal influenza and that they had a low risk of acquiring COVID-19. Nearly 20% disagreed that COVID-19 vaccines in Australia were safe and perceived they were at higher-risk of acquiring COVID infection than the general population. Higher-risk perception viewing vaccination as their professional responsibility, and vaccine mandate strongly predicted vaccination behaviour. Participants consider COVID-19 information from health professionals, government websites, and World Health Organization as the most trusted information sources. The findings highlight that healthcare decision-makers and university administrators need to monitor students' hesitancy with vaccination to improve students' promotion of the vaccination to the general population.
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Affiliation(s)
- Yingyan Chen
- School of Health, University of the Sunshine Coast, Sunshine Coast, Australia
- School of Health and Human Sciences, Southern Cross University, Gold Coast, Australia
| | - Roslyn Prichard
- School of Health, University of the Sunshine Coast, Sunshine Coast, Australia
| | - Matt Mason
- School of Health, University of the Sunshine Coast, Sunshine Coast, Australia
| | - Marion Tower
- School of Nursing and Midwifery, Griffith University, Nathan, Australia
- School of Nursing, Midwifery & Social Work, The University of Queensland, Brisbane, Australia
| | | | - Vanessa Sparke
- Nursing and Midwifery, College of Healthcare Sciences, James Cook University, Cairns, Australia
| | - Janice Layh
- School of Health, University of the Sunshine Coast, Sunshine Coast, Australia
| | - Ahmed M Mehdi
- QCIF Bioinformatics, Queensland Cyber Infrastructure Foundation Ltd, Brisbane, Australia
| | - Frances Fengzhi Lin
- School of Health, University of the Sunshine Coast, Sunshine Coast, Australia.
- Sunshine Coast Health Institute, Sunshine Coast, Australia.
- College of Nursing and Health Sciences, Flinders University, Level 1, Room N103, Sturt North Sturt Road, Bedford Park, South Australia, 5042, Australia.
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Asad S, Mehdi AM, Pujhari S, Rückert C, Ebel GD, Rasgon JL. Identification of MicroRNAs in the West Nile Virus Vector Culex tarsalis (Diptera: Culicidae). J Med Entomol 2023; 60:182-293. [PMID: 36477983 DOI: 10.1093/jme/tjac182] [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] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Indexed: 05/28/2023]
Abstract
MicroRNAs (miRNAs) are a group of small noncoding RNAs that regulate gene expression during important biological processes including development and pathogen defense in most living organisms. Presently, no miRNAs have been identified in the mosquito Culex tarsalis (Diptera: Culicidae), one of the most important vectors of West Nile virus (WNV) in North America. We used small RNA sequencing data and in vitro and in vivo experiments to identify and validate a repertoire of miRNAs in Cx. tarsalis mosquitoes. Using bioinformatic approaches we analyzed small RNA sequences from the Cx. tarsalis CT embryonic cell line to discover orthologs for 86 miRNAs. Consistent with other mosquitoes such as Aedes albopictus and Culex quinquefasciatus, miR-184 was found to be the most abundant miRNA in Cx. tarsalis. We also identified 20 novel miRNAs from the recently sequenced Cx. tarsalis genome, for a total of 106 miRNAs identified in this study. The presence of selected miRNAs was biologically validated in both the CT cell line and in adult Cx. tarsalis mosquitoes using RT-qPCR and sequencing. These results will open new avenues of research into the role of miRNAs in Cx. tarsalis biology, including development, metabolism, immunity, and pathogen infection.
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Affiliation(s)
- Sultan Asad
- Department of Entomology, The Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Ahmed M Mehdi
- The University of Queensland, Brisbane, Australia Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Sujit Pujhari
- Department of Entomology, The Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Pharmacology Physiology and Neuroscience, University of South Carolina School of Medicine, Columbia, SC, USA
| | - Claudia Rückert
- Department of Biochemistry and Molecular Biology, University of Nevada Reno, Reno, NV, 89557, USA
- Department of Microbiology, Immunology and Pathology, Center for Vector-borne Infectious Diseases, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USAand
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, Center for Vector-borne Infectious Diseases, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USAand
| | - Jason L Rasgon
- Department of Entomology, The Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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Bhuyan ZA, Rahman MA, Maradana MR, Mehdi AM, Bergot AS, Simone D, El-Kurdi M, Garrido-Mesa J, Cai CBB, Cameron AJ, Hanson AL, Nel HJ, Kenna T, Leo P, Rehaume L, Brown MA, Ciccia F, Thomas R. Genetically encoded Runx3 and CD4 + intestinal epithelial lymphocyte deficiencies link SKG mouse and human predisposition to spondyloarthropathy. Clin Immunol 2023; 247:109220. [PMID: 36596403 DOI: 10.1016/j.clim.2022.109220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/21/2022] [Accepted: 12/25/2022] [Indexed: 01/02/2023]
Abstract
Disturbances in immune regulation, intestinal dysbiosis and inflammation characterize ankylosing spondylitis (AS), which is associated with RUNX3 loss-of-function variants. ZAP70W163C mutant (SKG) mice have reduced ZAP70 signaling, spondyloarthritis and ileitis. In small intestine, Foxp3+ regulatory T cells (Treg) and CD4+CD8αα+TCRαβ+ intraepithelial lymphocytes (CD4-IEL) control inflammation. TGF-β and retinoic acid (RA)-producing dendritic cells and MHC-class II+ intestinal epithelial cells (IEC) are required for Treg and CD4-IEL differentiation from CD4+ conventional or Treg precursors, with upregulation of Runx3 and suppression of ThPOK. We show in SKG mouse ileum, that ZAP70W163C or ZAP70 inhibition prevented CD4-IEL but not Treg differentiation, dysregulating Runx3 and ThPOK. TGF-β/RA-mediated CD4-IEL development, T-cell IFN-γ production, MHC class-II+ IEC, tissue-resident memory T-cell and Runx3-regulated genes were reduced. In AS intestine, CD4-IEL were decreased, while in AS blood CD4+CD8+ T cells were reduced and Treg increased. Thus, genetically-encoded TCR signaling dysfunction links intestinal T-cell immunodeficiency in mouse and human spondyloarthropathy.
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Affiliation(s)
- Zaied Ahmed Bhuyan
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - M Arifur Rahman
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Muralidhara Rao Maradana
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Ahmed M Mehdi
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Anne-Sophie Bergot
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Davide Simone
- Dipartimento di Medicina di Precisione, Section of Rheumatology, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
| | - Marya El-Kurdi
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Jose Garrido-Mesa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Cheng Bang Benjamin Cai
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Amy J Cameron
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Aimee L Hanson
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Hendrik J Nel
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Tony Kenna
- Queensland University of Technology, Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland 4006, Australia
| | - Paul Leo
- Queensland University of Technology, Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland 4006, Australia
| | - Linda Rehaume
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Matthew A Brown
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom; Genomics England Ltd, Charterhouse Square, London, United Kingdom
| | - Francesco Ciccia
- Dipartimento di Medicina di Precisione, Section of Rheumatology, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
| | - Ranjeny Thomas
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia.
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Mehdi AM, Zhou C, Turrell G, Walpole E, Porceddu S, Frazer IH, Chandra J. HPV status represents dominant trait driving delineation of survival-associated gene co-expression networks in head and neck cancer. Cancer Gene Ther 2022; 30:629-640. [PMID: 36575316 PMCID: PMC10104777 DOI: 10.1038/s41417-022-00577-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 11/29/2022] [Accepted: 12/09/2022] [Indexed: 12/28/2022]
Abstract
Integration of high-dimensional tumor gene expression data with clinicopathological data can increase our understanding of disease diversity, enable retrospective patient stratification, and identify new potential biomarkers and therapeutic targets. Using a systems biology approach, we provide a holistic overview of gene co-expression networks in head and neck squamous cell carcinomas (HNSCC). Weighted gene co-expression network analysis of HNSCC RNA sequencing data from 519 patients from The Cancer Genome Atlas (TCGA) was used to determine correlates of 5-year survival, using regression tree-based optimal threshold calculations. Survival-associated gene sets were transformed to gene set scores that were assessed for correlation with clinicopathological data. We identified 8 gene co-expression modules for HNSCC tumors, each of which contained co-expressed genes associated significantly with 5-year survival. Survival-associated co-expression gene signatures correlated dominantly with tumor HPV and p16 status. Network analysis identified that survival was associated with signaling networks of infection, immunity, epithelial-mesenchymal transition (EMT), hypoxia, glycolysis, focal adhesion, extracellular matrix, MYC signaling, autophagy and transcriptional regulation. EMT-associated gene signatures were expressed dominantly in fibroblasts, and cancer-associated fibroblasts were inversely correlated with immune activity. Interestingly, a high Immune Suppression Score based on expression of 21 genes associated with immune inhibition and including immune checkpoints, cytokines and regulatory T cell factors, was also associated with increased survival probability, and was significantly higher in HPV+ HNSCC. Networks associated with HNSCC survival were further associated with survival in cervical cancer, melanoma and lung cancer. This study defines 5129 genes associated with HNSCC survival, organized into co-expressed networks, their correlation with clinicopathological data, and with gene expression data from other malignant diseases, and provides a source for the discovery of biomarkers and novel therapies for HNSCC.
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Affiliation(s)
- Ahmed M Mehdi
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, 4102, Australia.,Queensland Cyber Infrastructure Foundation Ltd, Facility for Advanced Bioinformatics, Brisbane, QLD, 4072, Australia
| | - Chenhao Zhou
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Gavin Turrell
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Euan Walpole
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, 4102, Australia.,Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
| | - Sandro Porceddu
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, 4102, Australia.,Peter MacCallum Cancer Centre, Radiation Oncology, Melbourne, VIC, 3000, Australia
| | - Ian H Frazer
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Janin Chandra
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, 4102, Australia.
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7
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Muralidharan S, Ali S, Yang L, Badshah J, Zahir SF, Ali RA, Chandra J, Frazer IH, Thomas R, Mehdi AM. Environmental pathways affecting gene expression (E.PAGE) as an R package to predict gene-environment associations. Sci Rep 2022; 12:18710. [PMID: 36333579 PMCID: PMC9636158 DOI: 10.1038/s41598-022-21988-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
The purpose of this study is to manually and semi-automatically curate a database and develop an R package that will act as a comprehensive resource to understand how biological processes are dysregulated due to interactions with environmental factors. The initial database search run on the Gene Expression Omnibus and the Molecular Signature Database retrieved a total of 90,018 articles. After title and abstract screening against pre-set criteria, a total of 237 datasets were selected and 522 gene modules were manually annotated. We then curated a database containing four environmental factors, cigarette smoking, diet, infections and toxic chemicals, along with a total of 25,789 genes that had an association with one or more of gene modules. The database and statistical analysis package was then tested with the differentially expressed genes obtained from the published literature related to type 1 diabetes, rheumatoid arthritis, small cell lung cancer, COVID-19, cobalt exposure and smoking. On testing, we uncovered statistically enriched biological processes, which revealed pathways associated with environmental factors and the genes. The curated database and enrichment tool are available as R packages at https://github.com/AhmedMehdiLab/E.PATH and https://github.com/AhmedMehdiLab/E.PAGE respectively.
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Affiliation(s)
- Sachin Muralidharan
- grid.1003.20000 0000 9320 7537The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, 37 Kent St, Woolloongabba, QLD 4102 Australia
| | - Sarah Ali
- grid.1003.20000 0000 9320 7537Centre for Microscopy and Microanalysis, University of Queensland, St. Lucia, QLD 4072 Australia
| | - Lilin Yang
- grid.1003.20000 0000 9320 7537The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, 37 Kent St, Woolloongabba, QLD 4102 Australia
| | - Joshua Badshah
- grid.1003.20000 0000 9320 7537The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, 37 Kent St, Woolloongabba, QLD 4102 Australia
| | - Syeda Farah Zahir
- QCIF Facility for Advanced Bioinformatics, Queensland Cyber Infrastructure Foundation Ltd, Brisbane, QLD Australia
| | - Rubbiya A. Ali
- grid.1003.20000 0000 9320 7537Centre for Microscopy and Microanalysis, University of Queensland, St. Lucia, QLD 4072 Australia
| | - Janin Chandra
- grid.1003.20000 0000 9320 7537The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, 37 Kent St, Woolloongabba, QLD 4102 Australia
| | - Ian H. Frazer
- grid.1003.20000 0000 9320 7537The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, 37 Kent St, Woolloongabba, QLD 4102 Australia
| | - Ranjeny Thomas
- grid.1003.20000 0000 9320 7537The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, 37 Kent St, Woolloongabba, QLD 4102 Australia
| | - Ahmed M. Mehdi
- grid.1003.20000 0000 9320 7537The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, 37 Kent St, Woolloongabba, QLD 4102 Australia ,QCIF Facility for Advanced Bioinformatics, Queensland Cyber Infrastructure Foundation Ltd, Brisbane, QLD Australia
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Sonigra A, Nel HJ, Wehr P, Ramnoruth N, Patel S, van Schie KA, Bladen MW, Mehdi AM, Tesiram J, Talekar M, Rossjohn J, Reid HH, Stuurman FE, Roberts H, Vecchio P, Gourley I, Rigby M, Becart S, Toes RE, Scherer HU, Lê Cao KA, Campbell K, Thomas R. Randomized phase I trial of antigen-specific tolerizing immunotherapy with peptide/calcitriol liposomes in ACPA+ rheumatoid arthritis. JCI Insight 2022; 7:e160964. [PMID: 36278483 PMCID: PMC9714780 DOI: 10.1172/jci.insight.160964] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 04/11/2022] [Accepted: 09/12/2022] [Indexed: 10/11/2023] Open
Abstract
BACKGROUNDAntigen-specific regulation of autoimmune disease is a major goal. In seropositive rheumatoid arthritis (RA), T cell help to autoreactive B cells matures the citrullinated (Cit) antigen-specific immune response, generating RA-specific V domain glycosylated anti-Cit protein antibodies (ACPA VDG) before arthritis onset. Low or escalating antigen administration under "sub-immunogenic" conditions favors tolerance. We explored safety, pharmacokinetics, and immunological and clinical effects of s.c. DEN-181, comprising liposomes encapsulating self-peptide collagen II259-273 (CII) and NF-κB inhibitor 1,25-dihydroxycholecalciferol.METHODSA double-blind, placebo-controlled, exploratory, single-ascending-dose, phase I trial assessed the impact of low, medium, and high DEN-181 doses on peripheral blood CII-specific and bystander Cit64vimentin59-71-specific (Cit-Vim-specific) autoreactive T cell responses, cytokines, and ACPA in 17 HLA-DRB1*04:01+ or *01:01+ ACPA+ RA patients on methotrexate.RESULTSDEN-181 was well tolerated. Relative to placebo and normalized to baseline values, Cit-Vim-specific T cells decreased in patients administered medium and high doses of DEN-181. Relative to placebo, percentage of CII-specific programmed cell death 1+ T cells increased within 28 days of DEN-181. Exploratory analysis in DEN-181-treated patients suggested improved RA disease activity was associated with expansion of CII-specific and Cit-Vim-specific T cells; reduction in ACPA VDG, memory B cells, and inflammatory myeloid populations; and enrichment in CCR7+ and naive T cells. Single-cell sequencing identified T cell transcripts associated with tolerogenic TCR signaling and exhaustion after low or medium doses of DEN-181.CONCLUSIONThe safety and immunomodulatory activity of low/medium DEN-181 doses provide rationale to further assess antigen-specific immunomodulatory therapy in ACPA+ RA.TRIAL REGISTRATIONAnzctr.org.au identifier ACTRN12617001482358, updated September 8, 2022.FUNDINGInnovative Medicines Initiative 2 Joint Undertaking (grant agreement 777357), supported by European Union's Horizon 2020 research and innovation programme and European Federation of Pharmaceutical Industries and Associations; Arthritis Queensland; National Health and Medical Research Council (NHMRC) Senior Research Fellowship; and NHMRC grant 2008287.
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Affiliation(s)
- Amee Sonigra
- Department of Rheumatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Hendrik J. Nel
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Pascale Wehr
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Nishta Ramnoruth
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Swati Patel
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Karin A. van Schie
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Maxwell W. Bladen
- Melbourne Integrative Genomics and School of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia
| | - Ahmed M. Mehdi
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Joanne Tesiram
- Department of Rheumatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Meghna Talekar
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Hugh H. Reid
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Frederik E. Stuurman
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Helen Roberts
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
- Dendright Pty Ltd, Brisbane, Queensland, Australia
| | - Phillip Vecchio
- Department of Rheumatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Ian Gourley
- Immunology Clinical Development, Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Mark Rigby
- Immunology Clinical Development, Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Stephane Becart
- Discovery Immunology, Janssen Research & Development, LLC, La Jolla, California, USA
| | - Rene E.M. Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Hans Ulrich Scherer
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics and School of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia
| | - Kim Campbell
- Immunology Translational Medicine, Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Ranjeny Thomas
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
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9
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Kanaan C, Layoun H, Kondoleon N, Mirzai S, Fadel R, Schold J, Arrigain S, Mehdi AM, Taliercio JT, Unai S, Kapadia S, Harb S, Nakhoul G. Comparison of CT acquired valvular calcification scores in hemodialysis vs peritoneal dialysis patients undergoing open heart surgery. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.2613] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Several factors have been identified as independent risk factors for cardiac valvular calcification (CVC), including but not limited to age, inflammatory conditions, loss of calcification inhibitors, and dysregulated bone mineral metabolism. However, data is scarce regarding which dialysis modality portends more severe CVC.
Purpose
Our aim was to compare the degree of valvular calcification in hemodialysis (HD) and peritoneal dialysis (PD) patients prior to open heart surgery (OHS) using a computed CT calcium score.
Methods
Dialysis patients who underwent OHS at our institution from 2009–2019 who had a pre-surgical cardiac CT were grouped according to duration of dialysis modality prior to their surgical date. There were two study cohorts to evaluate outcomes of interest: mitral and aortic calcification. We included the first surgical record per patient for patients undergoing isolated CABG, or CABG+valve surgery (repair or replacement), or valve-only surgery (repair or replacement). To evaluate mitral calcification, we excluded any patients undergoing any mitral valve surgery (repair or replacement). We also excluded patients with a history of mitral valve repair/replacement. To evaluate aortic calcification, we excluded any patients undergoing any aortic valve surgery (repair or replacement). We also excluded patients with a history of aortic valve repair/replacement. Mitral annular and aortic valvular calcification were assessed using the Agatston score. Logistic regression was performed to test for the association of PD and HD cumulative dialysis duration with presence of valvular calcification.
Results
A total of 296 patients met inclusion criteria for at least one of the strata in our study. Of those, 214 met inclusion for the mitral strata, and 166 met criteria for the aortic strata (Table 1). In the logistic regression model for the mitral strata, age and female sex were associated with higher odds of presence of mitral calcification (Figure 1). Cumulative years on PD and cumulative years on HD were not significantly associated with presence of mitral calcification. In the logistic regression model for the aortic strata, age was associated with higher odds of presence of aortic calcification, while female sex was associated with lower odds (Figure 1). Cumulative years on PD and cumulative years on HD were not significantly associated with presence of aortic calcification.
Conclusion
Presence of mitral and aortic calcification for patients undergoing OHS was not significantly associated with cumulative length of PD or HD after adjusting for age and gender, suggesting that there may be more factors at play in the progression of valvular calcification in end stage renal disease patients than what was previously thought.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- C Kanaan
- Cleveland Clinic Foundation , Cleveland , United States of America
| | - H Layoun
- Cleveland Clinic Foundation , Cleveland , United States of America
| | - N Kondoleon
- Cleveland Clinic Foundation , Cleveland , United States of America
| | - S Mirzai
- Cleveland Clinic Foundation , Cleveland , United States of America
| | - R Fadel
- Cleveland Clinic Foundation , Cleveland , United States of America
| | - J Schold
- Cleveland Clinic Foundation , Cleveland , United States of America
| | - S Arrigain
- Cleveland Clinic Foundation , Cleveland , United States of America
| | - A M Mehdi
- Cleveland Clinic Foundation , Cleveland , United States of America
| | - J T Taliercio
- Cleveland Clinic Foundation , Cleveland , United States of America
| | - S Unai
- Cleveland Clinic Foundation , Cleveland , United States of America
| | - S Kapadia
- Cleveland Clinic Foundation , Cleveland , United States of America
| | - S Harb
- Cleveland Clinic Foundation , Cleveland , United States of America
| | - G Nakhoul
- Cleveland Clinic Foundation , Cleveland , United States of America
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10
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Sadeghirad H, Monkman J, Mehdi AM, Ladwa R, O’Byrne K, Hughes BGM, Kulasinghe A. Dissecting Tissue Compartment-Specific Protein Signatures in Primary and Metastatic Oropharyngeal Squamous Cell Carcinomas. Front Immunol 2022; 13:895513. [PMID: 35651606 PMCID: PMC9149425 DOI: 10.3389/fimmu.2022.895513] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) often presents with locoregional or distant disease, despite multimodal therapeutic approaches, which include surgical resection, chemoradiotherapy, and more recently, immunotherapy for metastatic or recurrent HNSCC. Therapies often target the primary and nodal regional HNSCC sites, and their efficacy at controlling occult distant sites remains poor. While our understanding of the tumor microenvironment conducive to effective therapies is increasing, the biology underpinning locoregional sites remains unclear. Here, we applied targeted spatial proteomic approaches to primary and lymph node metastasis from an oropharyngeal SCC (OPSCC) cohort to understand the expression of proteins within tumors, and stromal compartments of the respective sites in samples of both matched and unmatched patients. In unmatched analyses of n = 43 primary and 11 nodal metastases, our data indicated that tumor cells in nodal metastases had higher levels of Ki-67, PARP, BAD, and cleaved caspase 9, suggesting a role for increased proliferation, DNA repair, and apoptosis within these metastatic cells. Conversely, in matched analyses (n = 7), pro-apoptotic markers BIM and BAD were enriched in the stroma of primary tumors. Univariate, overall survival (OS) analysis indicated CD25 in tumor regions of primary tumors to be associated with reduced survival (HR = 3.3, p = 0.003), while progesterone receptor (PR) was associated with an improved OS (HR = 0.33, p = 0.015). This study highlights the utility of spatial proteomics for delineating the tumor and stromal compartment composition, and utility toward understanding these properties in locoregional metastasis. These findings indicate unique biological properties of lymph node metastases that may elucidate further understanding of distant metastatic in OPSCC.
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Affiliation(s)
- Habib Sadeghirad
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - James Monkman
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Ahmed M. Mehdi
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
- Queensland Cyber Infrastructure Foundation Ltd., QCIF Facility for Advanced Bioinformatics, Brisbane, QLD, Australia
| | - Rahul Ladwa
- Princess Alexandra Hospital, Woolloongabba, QLD, Australia
- Faculty of Medicine, University of Queensland, Herston, QLD, Australia
| | - Ken O’Byrne
- Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Brett G. M. Hughes
- Faculty of Medicine, University of Queensland, Herston, QLD, Australia
- Cancer Care Services, Royal Brisbane and Women’s Hospital, Herston, QLD, Australia
| | - Arutha Kulasinghe
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
- Faculty of Medicine, University of Queensland, Herston, QLD, Australia
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11
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Rødahl I, Gotley J, Andersen SB, Yu M, Mehdi AM, Christ AN, Hamilton-Williams EE, Frazer IH, Lukowski SW, Chandra J. Acquisition of murine splenic myeloid cells for protein and gene expression profiling by advanced flow cytometry and CITE-seq. STAR Protoc 2021; 2:100842. [PMID: 34585169 PMCID: PMC8456112 DOI: 10.1016/j.xpro.2021.100842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Indexed: 11/30/2022] Open
Abstract
Here, we outline detailed protocols to isolate and profile murine splenic dendritic cells (DCs) through advanced flow cytometry of the myeloid compartment and single-cell transcriptomic profiling with integrated cell surface protein expression through CITE-seq. This protocol provides a general transferrable road map for different tissues and species. For complete details on the use and execution of this protocol, please refer to Lukowski et al. (2021). Protocol to obtain integrated single-cell gene and protein expression data Optimized flow cytometry panel for confident delineation of six main myeloid lineages Gating strategy identifies large cell state heterogeneity within each lineage
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Affiliation(s)
- Inga Rødahl
- Center for Infectious Medicine, Department of Medicine, Karolinska Institute, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden.,The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - James Gotley
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Stacey B Andersen
- The Institute for Molecular Bioscience, The University of Queensland, Woolloongabba, QLD 4067, Australia
| | - Meihua Yu
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Ahmed M Mehdi
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Angelika N Christ
- The Institute for Molecular Bioscience, The University of Queensland, Woolloongabba, QLD 4067, Australia
| | - Emma E Hamilton-Williams
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Ian H Frazer
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Samuel W Lukowski
- The Institute for Molecular Bioscience, The University of Queensland, Woolloongabba, QLD 4067, Australia
| | - Janin Chandra
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
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12
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Koller-Smith L, Mehdi AM, March L, Tooth L, Mishra G, Thomas R. Rheumatoid arthritis is a preventable disease: 11 ways to reduce your patients' risk. Intern Med J 2021; 52:711-716. [PMID: 34553824 DOI: 10.1111/imj.15537] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/09/2021] [Accepted: 09/12/2021] [Indexed: 11/30/2022]
Abstract
New evidence shows that up to 40% of rheumatoid arthritis (RA) cases are attributable to exposure to potentially modifiable factors. We can now identify people at higher risk of RA (pre-RA) through their family history, risk factors, autoantibodies and symptoms. Counselling these patients to act to modify factors known to be associated with RA risk could prevent the development of RA, and evidence shows that informing individuals of their risk and of ways to reduce it leads to positive behavioural change and is not harmful. This consumer-focused narrative review is targeted at primary care providers and physicians to describe 11 changes that can be made, based on current evidence linking potentially modifiable factors to RA risk. These evidence-based recommendations are: Cease smoking Reduce exposure to inhaled silica, dusts and occupational risks Maintain a healthy weight Increase leisure time physical activity Maintain good dental hygiene Maximise breastfeeding if able Maximise dietary quality, and avoid high salt diets Consume high levels of Omega-3 fatty acids and fish Reduce consumption of sugar-sweetened soft drinks Consume moderate levels of alcohol Remain Vitamin D replete This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Louise Koller-Smith
- The University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland.,School of Medicine, The University of Newcastle, Newcastle, New South Wales
| | - Ahmed M Mehdi
- The University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland
| | - Lyn March
- Florance and Cope Professorial Department of Rheumatology, Royal North Shore Hospital and Institute of Bone and Joint Research, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales
| | - Leigh Tooth
- School of Public Health, The University of Queensland, Herston, Queensland
| | - Gita Mishra
- School of Public Health, The University of Queensland, Herston, Queensland
| | - Ranjeny Thomas
- The University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland
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13
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Musthaffa Y, Hamilton-Williams EE, Nel HJ, Bergot AS, Mehdi AM, Harris M, Thomas R. Proinsulin-specific T-cell responses correlate with estimated c-peptide and predict partial remission duration in type 1 diabetes. Clin Transl Immunology 2021; 10:e1315. [PMID: 34336205 PMCID: PMC8312239 DOI: 10.1002/cti2.1315] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/20/2021] [Accepted: 06/27/2021] [Indexed: 12/11/2022] Open
Abstract
Objective Type 1 diabetes (T1D) is an autoimmune disorder in which autoreactive T cells destroy insulin-producing β-cells. Interventions that preserve β-cell function represent a fundamental therapeutic goal in T1D and biomarkers that predict and monitor β-cell function, and changes in islet autoantigenic signatures are needed. As proinsulin and neoantigens derived from proinsulin peptides (hybrid insulin peptides, HIPs) are important T1D autoantigens, we analysed peripheral blood CD4+ T-cell autoantigen-specific proliferative responses and their relationship to estimated β-cell function. Methods We recruited 72 people with and 42 without T1D, including 17 pre-diabetic islet antibody-positive and 9 antibody-negative first-degree relatives and 16 unrelated healthy controls with T1D-risk HLA types. We estimated C-peptide level at 3-month intervals for 2 years post-diagnosis and measured CD4+ T-cell proliferation to proinsulin epitopes and HIPs using an optimised bioassay. Results We show that CD4+ T-cell proliferation to any islet peptide and to multiple epitopes were significantly more frequent in pre-diabetic islet antibody-positive siblings and participants with T1D ≤ 3 months of duration, than in participants with T1D > 3 months or healthy controls. Among participants with T1D and first-degree relatives, CD4+ T-cell proliferation occurred most frequently in response to proinsulin33-63 (full-length C-peptide). Proinsulin33-63-specific responses were associated with HLA-DR3-DQ2 and/or HLA-DR4/DQ8. In children with T1D, proinsulin33-63-specific T-cell proliferation positively associated with concurrent estimated C-peptide and predicted survival in honeymoon. Conclusion CD4+ T-cell proliferative responses to proinsulin-containing autoantigens are common before and immediately after diagnosis of T1D but decline thereafter. Proinsulin33-63-specific CD4+ T-cell response is a novel marker of estimated residual endogenous β-cell function and predicts a better 2-year disease outcome.
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Affiliation(s)
- Yassmin Musthaffa
- Department of Endocrinology and Diabetes Queensland Children's Hospital South Brisbane QLD Australia.,The University of Queensland Diamantina Institute The University of Queensland Brisbane QLD Australia
| | - Emma E Hamilton-Williams
- The University of Queensland Diamantina Institute The University of Queensland Brisbane QLD Australia
| | - Hendrik J Nel
- The University of Queensland Diamantina Institute The University of Queensland Brisbane QLD Australia
| | - Anne-Sophie Bergot
- The University of Queensland Diamantina Institute The University of Queensland Brisbane QLD Australia
| | - Ahmed M Mehdi
- The University of Queensland Diamantina Institute The University of Queensland Brisbane QLD Australia
| | - Mark Harris
- Department of Endocrinology and Diabetes Queensland Children's Hospital South Brisbane QLD Australia.,The University of Queensland Diamantina Institute The University of Queensland Brisbane QLD Australia
| | - Ranjeny Thomas
- The University of Queensland Diamantina Institute The University of Queensland Brisbane QLD Australia
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14
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Budhwani M, Turrell G, Yu M, Frazer IH, Mehdi AM, Chandra J. Immune-Inhibitory Gene Expression is Positively Correlated with Overall Immune Activity and Predicts Increased Survival Probability of Cervical and Head and Neck Cancer Patients. Front Mol Biosci 2021; 8:622643. [PMID: 33834038 PMCID: PMC8021786 DOI: 10.3389/fmolb.2021.622643] [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] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 02/05/2021] [Indexed: 01/04/2023] Open
Abstract
Background: Limited immunotherapy options are approved for the treatment of cervical cancer and only 10-25% of patients respond effectively to checkpoint inhibition monotherapy. To aid the development of novel therapeutic immune targets, we aimed to explore survival-associated immune biomarkers and co-expressed immune networks in cervical cancer. Methods: Using The Cancer Genome Atlas (TCGA) Cervical Squamous Cell Carcinoma (CESC) data (n = 304), we performed weighted gene co-expression network analysis (WGCNA), and determined which co-expressed immune-related genes and networks are associated with survival probability in CESC patients under conventional therapy. A "Pan-Immune Score" and "Immune Suppression Score" was generated based on expression of survival-associated co-expressed immune networks and immune suppressive genes, which were subsequently tested for association with survival probablity using the TCGA Head Neck Squamous Cell Carcinoma (HNSCC) data (n = 528), representing a second SCC cancer type. Results: In CESC, WGCNA identified a co-expression module enriched in immune response related genes, including 462 genes where high expression was associated with increased survival probability, and enriched for genes associated with T cell receptor, cytokine and chemokine signaling. However, a high level of expression of 43 of the genes in this module was associated with decreased survival probability but were not enriched in particular pathways. Separately, we identified 20 genes associated with immune suppression including inhibitory immune checkpoint and regulatory T cell-related genes, where high expression was associated with increased survival probability. Expression of these 20 immune suppressive genes (represented as "Immune Suppression Score") was highly correlated with expression of overall survival-associated immune genes (represented as "Pan-Immune Score"). However, high expression of seven immune suppression genes, including TWEAK-R, CD73, IL1 family and TGFb family genes, was significantly associated with decreased survival probability. Both scores also significantly associated with survival probability in HNSCC, and correlated with the previously established "Immunophenoscore." Conclusion: CESC and HNSCC tumors expressing genes predictive of T cell infiltrates (hot tumors) have a better prognosis, despite simultaneous expression of many immune inhibitory genes, than tumors lacking expression of genes associated with T cell infiltrates (cold tumors) whether or not these tumor express immune inhibitory genes.
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Affiliation(s)
- Megha Budhwani
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Gavin Turrell
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Meihua Yu
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Ian H Frazer
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Ahmed M Mehdi
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Janin Chandra
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
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15
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García-González PA, Maggi J, Schinnerling K, Sepúlveda-Gutiérrez A, Soto L, Neira O, Mehdi AM, Nel HJ, Pesce B, Aravena O, Molina MC, Catalán D, Thomas R, Verdugo RA, Aguillón JC. Regulation of Tolerogenic Features on Dexamethasone-Modulated MPLA-Activated Dendritic Cells by MYC. Front Immunol 2019; 10:1171. [PMID: 31191540 PMCID: PMC6547838 DOI: 10.3389/fimmu.2019.01171] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/08/2019] [Indexed: 01/05/2023] Open
Abstract
The potential of tolerogenic dendritic cells (tolDCs) to shape immune responses and restore tolerance has turn them into a promising therapeutic tool for cellular therapies directed toward immune regulation in autoimmunity. Although the cellular mechanisms by which these cells can exert their regulatory function are well-known, the mechanisms driving their differentiation and function are still poorly known, and the variety of stimuli and protocols applied to differentiate DCs toward a tolerogenic phenotype makes it even more complex to underpin the molecular features involved in their function. Through transcriptional profiling analysis of monocyte-derived tolDCs modulated with dexamethasone (Dex) and activated with monophosphoryl lipid A (MPLA), known as DM-DCs, we were able to identify MYC as one of the transcriptional regulators of several genes differentially expressed on DM-DCs compared to MPLA-matured DCs (M-DCs) and untreated/immature DCs (DCs) as revealed by Ingenuity Pathway Analysis (IPA) upstream regulators evaluation. Additionally, MYC was also amidst the most upregulated genes in DM-DCs, finding that was confirmed at a transcriptional as well as at a protein level. Blockade of transactivation of MYC target genes led to the downregulation of tolerance-related markers IDO1 and JAG1. MYC blockade also led to downregulation of PLZF and STAT3, transcription factors associated with immune regulation and inhibition of DC maturation, further supporting a role of MYC as an upstream regulator contributing to the regulatory phenotype of DM-DCs. On the other hand, we had previously shown that fatty acid oxidation, oxidative metabolism and zinc homeostasis are amongst the main biological functions represented in DM-DCs, and here we show that DM-DCs exhibit higher intracellular expression of ROS and Zinc compared to mature M-DCs and DCs. Taken together, these findings suggest that the regulatory profile of DM-DCs is partly shaped by the effect of the transcriptional regulation of tolerance-inducing genes by MYC and the modulation of oxidative metabolic processes and signaling mediators such as Zinc and ROS.
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Affiliation(s)
- Paulina A García-González
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Jaxaira Maggi
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Katina Schinnerling
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | | | - Lilian Soto
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile.,Unidad de Dolor, Departamento de Medicina, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Oscar Neira
- Sección de Reumatología, Hospital del Salvador, Santiago, Chile
| | - Ahmed M Mehdi
- Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, University of Queensland, Brisbane, QLD, Australia
| | - Hendrik J Nel
- Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, University of Queensland, Brisbane, QLD, Australia
| | - Bárbara Pesce
- MED.UCHILE-FACS Laboratorio, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Octavio Aravena
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - María Carmen Molina
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Diego Catalán
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Ranjeny Thomas
- Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, University of Queensland, Brisbane, QLD, Australia
| | - Ricardo A Verdugo
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Juan Carlos Aguillón
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
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16
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Zahir SF, Griffin A, Veerman JL, Magliano DJ, Shaw JE, Cao KAL, Mehdi AM. Exploring the association between BMI and mortality in Australian women and men with and without diabetes: the AusDiab study. Diabetologia 2019; 62:754-758. [PMID: 30809715 PMCID: PMC6450848 DOI: 10.1007/s00125-019-4830-4] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/22/2019] [Indexed: 01/04/2023]
Abstract
AIMS/HYPOTHESIS There is conflicting evidence about the obesity paradox-the counterintuitive survival advantage of obesity among certain subpopulations of individuals with chronic conditions. It is believed that results supporting the obesity paradox are due to methodological flaws, such as collider bias. The aim of this study was to examine the association between obesity and mortality in Australian men and women. In addition, we explored whether obesity would appear to be protective if the analysis was restricted to a subpopulation with disease, and to discuss the potential role of collider bias in producing such a result. METHODS The examined cohort included 10,575 Australian adults (4844 men and 5731 women) aged 25-91 years who were recruited for the AusDiab baseline survey in 1999 and followed-up through 2014. The main predictor variable was BMI categorised as normal weight (18.5 to <25 kg/m2), overweight (25 to <30 kg/m2) and obese (≥30 kg/m2), and the outcome of interest was all-cause mortality. Hazard ratios were estimated from Cox proportional hazards regression models in the entire cohort and then in subpopulations with and without diabetes. RESULTS A total of 1477 deaths occurred during 145,384 person-years (median 14.6 years) of follow-up. Mortality was higher in obese than in normal-weight individuals for the full population (HR 1.18; 95% CI 1.05, 1.32). When an interaction between diabetes status and BMI category was added to the model, there was no evidence of an interaction between BMI and diabetes status (p = 0.92). When participants with and without diabetes were analysed separately, there was no evidence of an association between obesity and mortality in those with diabetes (HR 0.91; 95% CI 0.62, 1.33). CONCLUSIONS/INTERPRETATION In the entire AusDiab cohort, we found a significantly higher mortality among obese participants as compared with their normal-weight counterparts. We found no difference in the obesity-mortality association between individuals with and without diabetes.
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Affiliation(s)
- Syeda F Zahir
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Level 6, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.
| | | | | | | | - Jonathan E Shaw
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia
| | - Ahmed M Mehdi
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Level 6, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.
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17
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Buchanan K, Mehdi AM, Hughes I, Cotterill A, Le Cao KA, Thomas R, Harris M. An improved clinical model to predict stimulated C-peptide in children with recent-onset type 1 diabetes. Pediatr Diabetes 2019; 20:166-171. [PMID: 30556344 DOI: 10.1111/pedi.12808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 04/23/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Stimulated C-peptide measurement after a mixed meal tolerance test (MMTT) is the accepted gold standard for assessing residual beta-cell function in type 1 diabetes (T1D); however, this approach is impractical outside of clinical trials. OBJECTIVE To develop an improved estimate of residual beta-cell function in children with T1D using commonly measured clinical variables. SUBJECTS/METHODS A clinical model to predict 90-minute MMTT stimulated C-peptide in children with recent-onset T1D was developed from the combined AbATE, START, and TIDAL placebo subjects (n = 46) 6 months post-recruitment using multiple linear regression. This model was then validated in a clinical cohort (Hvidoere study group, n = 262). RESULTS A model of estimated C-peptide at 6 months post-diagnosis, which included age, gender, body mass index (BMI), hemoglobin A1c (HbA1c), and insulin dose predicted 90-minute stimulated C-peptide measurements (adjusted R2 = 0.63, P < 0.0001). The predictive value of insulin dose and HbA1c alone (IDAA1c) for 90-minute stimulated C-peptide was significantly lower (R2 = 0.37, P < 0.0001). The slopes of linear regression lines of the estimated and stimulated 90-minute C-peptide levels obtained at 6 and 12 months post diagnosis in the Hvidoere clinical cohort were R2 = 0.36, P < 0.0001 at 6 months and R2 = 0.37, P < 0.0001 at 12 months. CONCLUSIONS A clinical model including age, gender, BMI, HbA1c, and insulin dose predicts stimulated C-peptide levels in children with recent-onset T1D. Estimated C-peptide is an improved surrogate to monitor residual beta-cell function outside clinical trial settings.
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Affiliation(s)
- Kerry Buchanan
- The University of Queensland, Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia.,Queensland Children's Hospital, Department of Paediatric Endocrinology, Queensland Children's Hospital, South Brisbane, Queensland, Australia
| | - Ahmed M Mehdi
- The University of Queensland, Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Ian Hughes
- The University of Queensland, Mater Research Institute, Translational Research Institute, Brisbane, Australia
| | - Andrew Cotterill
- Queensland Children's Hospital, Department of Paediatric Endocrinology, Queensland Children's Hospital, South Brisbane, Queensland, Australia
| | - Kim-Anh Le Cao
- The University of Queensland, Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia.,The University of Melbourne, Melbourne Integrative Genomics and School of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ranjeny Thomas
- The University of Queensland, Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Mark Harris
- The University of Queensland, Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia.,Queensland Children's Hospital, Department of Paediatric Endocrinology, Queensland Children's Hospital, South Brisbane, Queensland, Australia
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18
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Rehaume LM, Matigian N, Mehdi AM, Lachner N, Bowerman KL, Daly J, Lê Cao KA, Hugenholtz P, Thomas R. IL-23 favours outgrowth of spondyloarthritis-associated pathobionts and suppresses host support for homeostatic microbiota. Ann Rheum Dis 2019; 78:494-503. [DOI: 10.1136/annrheumdis-2018-214381] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 12/14/2022]
Abstract
ObjectivesCertain gut bacterial families, including Bacteroidaceae, Porphyromonadaceae and Prevotellaceae, are increased in people suffering from spondyloarthropathy (SpA), a disease group associated with IL23R signalling variants. To understand the relationship between host interleukin (IL)-23 signalling and gut bacterial dysbiosis in SpA, we inhibited IL-23 in dysbiotic ZAP-70-mutant SKG mice that develop IL-23-dependent SpA-like arthritis, psoriasis-like skin inflammation and Crohn’s-like ileitis in response to microbial beta 1,3-glucan (curdlan).MethodsWe treated SKG mice weekly with anti-IL-23 or isotype mAb for 3 weeks, rested them for 3 weeks, then administered curdlan or saline. We collected faecal samples longitudinally, assessed arthritis, spondylitis, psoriasis and ileitis histologically, and analysed the microbiota community profiles using next-generation sequencing. We used multivariate sparse partial least squares discriminant analysis to identify operational taxonomic unit (OTU) signatures best classifying treatment groups and linear regression to develop a predictive model of disease severity.ResultsIL-23p19 inhibition in naïve SKG mice decreased Bacteroidaceae, Porphyromonadaceae and Prevotellaceae. Abundance of Clostridiaceae and Lachnospiraceae families concomitantly increased, and curdlan-mediated SpA development decreased. Abundance of Enterobacteriaceae and Porphyromonadaceae family and reduction in Lachnospiraceae Dorea genus OTUs early in disease course were associated with disease severity in affected tissues.ConclusionsDysbiosis in SKG mice reflects human SpA and is IL-23p19 dependent. In genetically susceptible hosts, IL-23p19 favours outgrowth of SpA-associated pathobionts and reduces support for homeostatic-inducing microbiota. The relative abundance of specific pathobionts is associated with disease severity.
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19
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O’Sullivan BJ, Yekollu S, Ruscher R, Mehdi AM, Maradana MR, Chidgey AP, Thomas R. Autoimmune-Mediated Thymic Atrophy Is Accelerated but Reversible in RelB-Deficient Mice. Front Immunol 2018; 9:1092. [PMID: 29872433 PMCID: PMC5972300 DOI: 10.3389/fimmu.2018.01092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 01/15/2018] [Accepted: 05/01/2018] [Indexed: 01/28/2023] Open
Abstract
Polymorphisms impacting thymic function may decrease peripheral tolerance and hasten autoimmune disease. The NF-κB transcription factor subunit, RelB, is essential for the development and differentiation of medullary thymic epithelial cells (mTECs): RelB-deficient mice have reduced thymic cellularity and markedly fewer mTECs, lacking AIRE. The precise mechanism of this mTEC reduction in the absence of RelB is unclear. To address this, we studied mTECs and dendritic cells (DCs), which critically regulate negative selection, and thymic regulatory T-cells (tTreg) in RelB-/- mice, which have spontaneous multiorgan autoimmune disease. RelB-/- thymi were organized, with medullary structures containing AIRE- mTECs, DCs, and CD4+ thymocytes, but fewer tTreg. Granulocytes infiltrated the RelB-/- thymic cortex, capsule, and medulla, producing inflammatory thymic medullary atrophy, which could be treated by granulocyte depletion or RelB+ DC immunotherapy, with concomitant recovery of mTEC and tTreg numbers. These data indicate that central tolerance defects may be accelerated by autoimmune thymic inflammation where impaired RelB signaling impairs the medullary niche, and may be reversible by therapies enhancing peripheral Treg or suppressing inflammation.
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Affiliation(s)
- Brendan J. O’Sullivan
- Diamantina Institute, Translational Research Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Suman Yekollu
- Diamantina Institute, Translational Research Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Roland Ruscher
- Diamantina Institute, Translational Research Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Ahmed M. Mehdi
- Diamantina Institute, Translational Research Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Muralidhara Rao Maradana
- Diamantina Institute, Translational Research Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Ann P. Chidgey
- Stem Cells and Immune Regeneration Laboratory, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Ranjeny Thomas
- Diamantina Institute, Translational Research Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia
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20
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Mehdi AM, Hamilton-Williams EE, Cristino A, Ziegler A, Bonifacio E, Le Cao KA, Harris M, Thomas R. A peripheral blood transcriptomic signature predicts autoantibody development in infants at risk of type 1 diabetes. JCI Insight 2018. [PMID: 29515040 DOI: 10.1172/jci.insight.98212] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Autoimmune-mediated destruction of pancreatic islet β cells results in type 1 diabetes (T1D). Serum islet autoantibodies usually develop in genetically susceptible individuals in early childhood before T1D onset, with multiple islet autoantibodies predicting diabetes development. However, most at-risk children remain islet-antibody negative, and no test currently identifies those likely to seroconvert. We sought a genomic signature predicting seroconversion risk by integrating longitudinal peripheral blood gene expression profiles collected in high-risk children included in the BABYDIET and DIPP cohorts, of whom 50 seroconverted. Subjects were followed for 10 years to determine time of seroconversion. Any cohort effect and the time of seroconversion were corrected to uncover genes differentially expressed (DE) in seroconverting children. Gene expression signatures associated with seroconversion were evident during the first year of life, with 67 DE genes identified in seroconverting children relative to those remaining antibody negative. These genes contribute to T cell-, DC-, and B cell-related immune responses. Near-birth expression of ADCY9, PTCH1, MEX3B, IL15RA, ZNF714, TENM1, and PLEKHA5, along with HLA risk score predicted seroconversion (AUC 0.85). The ubiquitin-proteasome pathway linked DE genes and T1D susceptibility genes. Therefore, a gene expression signature in infancy predicts risk of seroconversion. Ubiquitination may play a mechanistic role in diabetes progression.
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Affiliation(s)
- Ahmed M Mehdi
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, Australia
| | - Emma E Hamilton-Williams
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, Australia
| | - Alexandre Cristino
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, Australia
| | - Anette Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum Munchen, Neuherberg, and Forschergruppe Diabetes, Klinikum rechts der Isar, Institut für Diabetesforschung, Neuherberg, Germany
| | - Ezio Bonifacio
- CRTD-DFG Research Center for Regenerative Therapies Dresden, Medical Faculty Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Kim-Anh Le Cao
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, Australia
| | - Mark Harris
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, Australia.,Lady Cilento Children's Hospital, South Brisbane, Australia
| | - Ranjeny Thomas
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Woolloongabba, Australia
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21
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García-González PA, Schinnerling K, Sepúlveda-Gutiérrez A, Maggi J, Mehdi AM, Nel HJ, Pesce B, Larrondo ML, Aravena O, Molina MC, Catalán D, Thomas R, Verdugo RA, Aguillón JC. Dexamethasone and Monophosphoryl Lipid A Induce a Distinctive Profile on Monocyte-Derived Dendritic Cells through Transcriptional Modulation of Genes Associated With Essential Processes of the Immune Response. Front Immunol 2017; 8:1350. [PMID: 29109727 PMCID: PMC5660598 DOI: 10.3389/fimmu.2017.01350] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 09/06/2017] [Accepted: 10/03/2017] [Indexed: 02/02/2023] Open
Abstract
There is growing interest in the use of tolerogenic dendritic cells (tolDCs) as a potential target for immunotherapy. However, the molecular bases that drive the differentiation of monocyte-derived DCs (moDCs) toward a tolerogenic state are still poorly understood. Here, we studied the transcriptional profile of moDCs from healthy subjects, modulated with dexamethasone (Dex) and activated with monophosphoryl lipid A (MPLA), referred to as Dex-modulated and MPLA-activated DCs (DM-DCs), as an approach to identify molecular regulators and pathways associated with the induction of tolerogenic properties in tolDCs. We found that DM-DCs exhibit a distinctive transcriptional profile compared to untreated (DCs) and MPLA-matured DCs. Differentially expressed genes downregulated by DM included MMP12, CD1c, IL-1B, and FCER1A involved in DC maturation/inflammation and genes upregulated by DM included JAG1, MERTK, IL-10, and IDO1 involved in tolerance. Genes related to chemotactic responses, cell-to-cell signaling and interaction, fatty acid oxidation, metal homeostasis, and free radical scavenging were strongly enriched, predicting the activation of alternative metabolic processes than those driven by counterpart DCs. Furthermore, we identified a set of genes that were regulated exclusively by the combined action of Dex and MPLA, which are mainly involved in the control of zinc homeostasis and reactive oxygen species production. These data further support the important role of metabolic processes on the control of the DC-driven regulatory immune response. Thus, Dex and MPLA treatments modify gene expression in moDCs by inducing a particular transcriptional profile characterized by the activation of tolerance-associated genes and suppression of the expression of inflammatory genes, conferring the potential to exert regulatory functions and immune response modulation.
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Affiliation(s)
- Paulina A García-González
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Katina Schinnerling
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Alejandro Sepúlveda-Gutiérrez
- Programa de Genética Humana, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile
| | - Jaxaira Maggi
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Ahmed M Mehdi
- Translational Research Institute, University of Queensland Diamantina Institute, Woolloongabba, QLD, Australia
| | - Hendrik J Nel
- Translational Research Institute, University of Queensland Diamantina Institute, Woolloongabba, QLD, Australia
| | - Bárbara Pesce
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile
| | - Milton L Larrondo
- Banco de Sangre, Hospital Clínico de la Universidad de Chile, Santiago, Chile
| | - Octavio Aravena
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile
| | - María C Molina
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile
| | - Diego Catalán
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Ranjeny Thomas
- Translational Research Institute, University of Queensland Diamantina Institute, Woolloongabba, QLD, Australia
| | - Ricardo A Verdugo
- Programa de Genética Humana, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile
| | - Juan C Aguillón
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
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22
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Ali RA, Mehdi AM, Rothnagel R, Hamilton NA, Gerle C, Landsberg MJ, Hankamer B. RAZA: A Rapid 3D z-crossings algorithm to segment electron tomograms and extract organelles and macromolecules. J Struct Biol 2017; 200:73-86. [PMID: 29032142 DOI: 10.1016/j.jsb.2017.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 04/12/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 11/30/2022]
Abstract
Resolving the 3D architecture of cells to atomic resolution is one of the most ambitious challenges of cellular and structural biology. Central to this process is the ability to automate tomogram segmentation to identify sub-cellular components, facilitate molecular docking and annotate detected objects with associated metadata. Here we demonstrate that RAZA (Rapid 3D z-crossings algorithm) provides a robust, accurate, intuitive, fast, and generally applicable segmentation algorithm capable of detecting organelles, membranes, macromolecular assemblies and extrinsic membrane protein domains. RAZA defines each continuous contour within a tomogram as a discrete object and extracts a set of 3D structural fingerprints (major, middle and minor axes, surface area and volume), enabling selective, semi-automated segmentation and object extraction. RAZA takes advantage of the fact that the underlying algorithm is a true 3D edge detector, allowing the axes of a detected object to be defined, independent of its random orientation within a cellular tomogram. The selectivity of object segmentation and extraction can be controlled by specifying a user-defined detection tolerance threshold for each fingerprint parameter, within which segmented objects must fall and/or by altering the number of search parameters, to define morphologically similar structures. We demonstrate the capability of RAZA to selectively extract subgroups of organelles (mitochondria) and macromolecular assemblies (ribosomes) from cellular tomograms. Furthermore, the ability of RAZA to define objects and their contours, provides a basis for molecular docking and rapid tomogram annotation.
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Affiliation(s)
- Rubbiya A Ali
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Ahmed M Mehdi
- Translational Research Institute, University of Queensland Diamantina Institute, Brisbane, QLD, Australia; Department of Electrical Engineering, University of Engineering and Technology, Lahore, Punjab, Pakistan
| | - Rosalba Rothnagel
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Nicholas A Hamilton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Christoph Gerle
- Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Michael J Landsberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Ben Hankamer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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23
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García-González PA, Schinnerling K, Sepúlveda-Gutiérrez A, Maggi J, Hoyos L, Morales RA, Mehdi AM, Nel HJ, Soto L, Pesce B, Molina MC, Cuchacovich M, Larrondo ML, Neira Ó, Catalán DF, Hilkens CM, Thomas R, Verdugo RA, Aguillón JC. Treatment with Dexamethasone and Monophosphoryl Lipid A Removes Disease-Associated Transcriptional Signatures in Monocyte-Derived Dendritic Cells from Rheumatoid Arthritis Patients and Confers Tolerogenic Features. Front Immunol 2016; 7:458. [PMID: 27826300 PMCID: PMC5078319 DOI: 10.3389/fimmu.2016.00458] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 07/16/2016] [Accepted: 10/12/2016] [Indexed: 01/27/2023] Open
Abstract
Tolerogenic dendritic cells (TolDCs) are promising tools for therapy of autoimmune diseases, such as rheumatoid arthritis (RA). Here, we characterize monocyte-derived TolDCs from RA patients modulated with dexamethasone and activated with monophosphoryl lipid A (MPLA), referred to as MPLA-tDCs, in terms of gene expression, phenotype, cytokine profile, migratory properties, and T cell-stimulatory capacity in order to explore their suitability for cellular therapy. MPLA-tDCs derived from RA patients displayed an anti-inflammatory profile with reduced expression of co-stimulatory molecules and high IL-10/IL-12 ratio, but were capable of migrating toward the lymphoid chemokines CXCL12 and CCL19. These MPLA-tDCs induced hyporesponsiveness of autologous CD4+ T cells specific for synovial antigens in vitro. Global transcriptome analysis confirmed a unique transcriptional profile of MPLA-tDCs and revealed that RA-associated genes, which were upregulated in untreated DCs from RA patients, returned to expression levels of healthy donor-derived DCs after treatment with dexamethasone and MPLA. Thus, monocyte-derived DCs from RA patients have the capacity to develop tolerogenic features at transcriptional as well as at translational level, when modulated with dexamethasone and MPLA, overcoming disease-related effects. Furthermore, the ability of MPLA-tDCs to impair T cell responses to synovial antigens validates their potential as cellular treatment for RA.
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Affiliation(s)
- Paulina A García-González
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Katina Schinnerling
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | | | - Jaxaira Maggi
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Lorena Hoyos
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Rodrigo A Morales
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Ahmed M Mehdi
- Translational Research Institute, University of Queensland Diamantina Institute , Woolloongabba, QLD , Australia
| | - Hendrik J Nel
- Translational Research Institute, University of Queensland Diamantina Institute , Woolloongabba, QLD , Australia
| | - Lilian Soto
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile; Unidad de Dolor, Hospital Clínico de la Universidad de Chile, Santiago, Chile
| | - Bárbara Pesce
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - María Carmen Molina
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile , Santiago , Chile
| | - Miguel Cuchacovich
- Departamento de Medicina, Hospital Clínico de la Universidad de Chile , Santiago , Chile
| | - Milton L Larrondo
- Banco de Sangre, Hospital Clínico de la Universidad de Chile , Santiago , Chile
| | - Óscar Neira
- Sección de Reumatología, Hospital del Salvador , Santiago , Chile
| | - Diego Francisco Catalán
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Catharien M Hilkens
- Musculoskeletal Research Group, Faculty of Medical Sciences, Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne , UK
| | - Ranjeny Thomas
- Translational Research Institute, University of Queensland Diamantina Institute , Woolloongabba, QLD , Australia
| | - Ricardo A Verdugo
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile , Santiago , Chile
| | - Juan C Aguillón
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas (ICBM), Universidad de Chile, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
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24
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Benham H, Nel HJ, Law SC, Mehdi AM, Street S, Ramnoruth N, Pahau H, Lee BT, Ng J, Brunck MEG, Hyde C, Trouw LA, Dudek NL, Purcell AW, O'Sullivan BJ, Connolly JE, Paul SK, Lê Cao KA, Thomas R. Citrullinated peptide dendritic cell immunotherapy in HLA risk genotype-positive rheumatoid arthritis patients. Sci Transl Med 2016; 7:290ra87. [PMID: 26041704 DOI: 10.1126/scitranslmed.aaa9301] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In animals, immunomodulatory dendritic cells (DCs) exposed to autoantigen can suppress experimental arthritis in an antigen-specific manner. In rheumatoid arthritis (RA), disease-specific anti-citrullinated peptide autoantibodies (ACPA or anti-CCP) are found in the serum of about 70% of RA patients and are strongly associated with HLA-DRB1 risk alleles. This study aimed to explore the safety and biological and clinical effects of autologous DCs modified with a nuclear factor κB (NF-κB) inhibitor exposed to four citrullinated peptide antigens, designated "Rheumavax," in a single-center, open-labeled, first-in-human phase 1 trial. Rheumavax was administered once intradermally at two progressive dose levels to 18 human leukocyte antigen (HLA) risk genotype-positive RA patients with citrullinated peptide-specific autoimmunity. Sixteen RA patients served as controls. Rheumavax was well tolerated: adverse events were grade 1 (of 4) severity. At 1 month after treatment, we observed a reduction in effector T cells and an increased ratio of regulatory to effector T cells; a reduction in serum interleukin-15 (IL-15), IL-29, CX3CL1, and CXCL11; and reduced T cell IL-6 responses to vimentin(447-455)-Cit450 relative to controls. Rheumavax did not induce disease flares in patients recruited with minimal disease activity, and DAS28 decreased within 1 month in Rheumavax-treated patients with active disease. This exploratory study demonstrates safety and biological activity of a single intradermal injection of autologous modified DCs exposed to citrullinated peptides, and provides rationale for further studies to assess clinical efficacy and antigen-specific effects of autoantigen immunomodulatory therapy in RA.
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Affiliation(s)
- Helen Benham
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia. University of Queensland School of Medicine, Brisbane, Queensland 4102, Australia
| | - Hendrik J Nel
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Soi Cheng Law
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Ahmed M Mehdi
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Shayna Street
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Nishta Ramnoruth
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Helen Pahau
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Bernett T Lee
- Singapore Immunology Network, Agency for Science, Technology and Research, 8A Biomedical Grove, Immunos Building, Level 3, Biopolis, 138673 Singapore, Singapore
| | - Jennifer Ng
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Marion E G Brunck
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Claire Hyde
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Leendert A Trouw
- Department of Rheumatology, Leiden University Medical Center, Leiden 2333, Netherlands
| | - Nadine L Dudek
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Brendan J O'Sullivan
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - John E Connolly
- Singapore Immunology Network, Agency for Science, Technology and Research, 8A Biomedical Grove, Immunos Building, Level 3, Biopolis, 138673 Singapore, Singapore
| | - Sanjoy K Paul
- Queensland Clinical Trials & Biostatistics Centre, School of Population Health, The University of Queensland, Brisbane, Queensland 4006, Australia
| | - Kim-Anh Lê Cao
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Ranjeny Thomas
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia.
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Róna G, Borsos M, Ellis JJ, Mehdi AM, Christie M, Környei Z, Neubrandt M, Tóth J, Bozóky Z, Buday L, Madarász E, Bodén M, Kobe B, Vértessy BG. Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation. Cell Cycle 2015; 13:3551-64. [PMID: 25483092 DOI: 10.4161/15384101.2014.960740] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Phosphorylation by the cyclin-dependent kinase 1 (Cdk1) adjacent to nuclear localization signals (NLSs) is an important mechanism of regulation of nucleocytoplasmic transport. However, no systematic survey has yet been performed in human cells to analyze this regulatory process, and the corresponding cell-cycle dynamics have not yet been investigated. Here, we focused on the human proteome and found that numerous proteins, previously not identified in this context, are associated with Cdk1-dependent phosphorylation sites adjacent to their NLSs. Interestingly, these proteins are involved in key regulatory events of DNA repair, epigenetics, or RNA editing and splicing. This finding indicates that cell-cycle dependent events of genome editing and gene expression profiling may be controlled by nucleocytoplasmic trafficking. For in-depth investigations, we selected a number of these proteins and analyzed how point mutations, expected to modify the phosphorylation ability of the NLS segments, perturb nucleocytoplasmic localization. In each case, we found that mutations mimicking hyper-phosphorylation abolish nuclear import processes. To understand the mechanism underlying these phenomena, we performed a video microscopy-based kinetic analysis to obtain information on cell-cycle dynamics on a model protein, dUTPase. We show that the NLS-adjacent phosphorylation by Cdk1 of human dUTPase, an enzyme essential for genomic integrity, results in dynamic cell cycle-dependent distribution of the protein. Non-phosphorylatable mutants have drastically altered protein re-import characteristics into the nucleus during the G1 phase. Our results suggest a dynamic Cdk1-driven mechanism of regulation of the nuclear proteome composition during the cell cycle.
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Key Words
- Cdc28, cyclin-dependent protein kinase (Cdk) encoded by CDC28
- Cdk1, cyclin-dependent kinase 1
- GO, gene ontology
- NES, nuclear export signal
- NLS, nuclear localization signal
- SNP, single nucleotide polymorphisms
- SV40, Simian virus 40
- UBA1, Ubiquitin-activating enzyme E1
- UNG2, Human Uracil-DNA glycosylase 2
- cNLS, classical nuclear localization signal
- cell cycle
- dNTP, deoxyribonucleotide triphosphate
- dTTP, deoxythymidine triphosphate
- dUMP, deoxyuridine monophosphate
- dUTP, deoxyuridine triphosphate
- dUTPase
- importin
- phosphorylation
- trafficking
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Affiliation(s)
- Gergely Róna
- a Institute of Enzymology; RCNS; Hungarian Academy of Sciences ; Budapest , Hungary
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26
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Abstract
Protein synthesis is finely regulated across all organisms, from bacteria to humans, and its integrity underpins many important processes. Emerging evidence suggests that the dynamic range of protein abundance is greater than that observed at the transcript level. Technological breakthroughs now mean that sequencing-based measurement of mRNA levels is routine, but protocols for measuring protein abundance remain both complex and expensive. This paper introduces a Bayesian network that integrates transcriptomic and proteomic data to predict protein abundance and to model the effects of its determinants. We aim to use this model to follow a molecular response over time, from condition-specific data, in order to understand adaptation during processes such as the cell cycle. With microarray data now available for many conditions, the general utility of a protein abundance predictor is broad. Whereas most quantitative proteomics studies have focused on higher organisms, we developed a predictive model of protein abundance for both Saccharomyces cerevisiae and Schizosaccharomyces pombe to explore the latitude at the protein level. Our predictor primarily relies on mRNA level, mRNA-protein interaction, mRNA folding energy and half-life, and tRNA adaptation. The combination of key features, allowing for the low certainty and uneven coverage of experimental observations, gives comparatively minor but robust prediction accuracy. The model substantially improved the analysis of protein regulation during the cell cycle: predicted protein abundance identified twice as many cell-cycle-associated proteins as experimental mRNA levels. Predicted protein abundance was more dynamic than observed mRNA expression, agreeing with experimental protein abundance from a human cell line. We illustrate how the same model can be used to predict the folding energy of mRNA when protein abundance is available, lending credence to the emerging view that mRNA folding affects translation efficiency. The software and data used in this research are available at http://bioinf.scmb.uq.edu.au/proteinabundance/.
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Affiliation(s)
- Ahmed M Mehdi
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
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27
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Mehdi AM, Sehgal MSB, Kobe B, Bailey TL, Bodén M. DLocalMotif: a discriminative approach for discovering local motifs in protein sequences. ACTA ACUST UNITED AC 2012; 29:39-46. [PMID: 23142965 DOI: 10.1093/bioinformatics/bts654] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION Local motifs are patterns of DNA or protein sequences that occur within a sequence interval relative to a biologically defined anchor or landmark. Current protein motif discovery methods do not adequately consider such constraints to identify biologically significant motifs that are only weakly over-represented but spatially confined. Using negatives, i.e. sequences known to not contain a local motif, can further increase the specificity of their discovery. RESULTS This article introduces the method DLocalMotif that makes use of positional information and negative data for local motif discovery in protein sequences. DLocalMotif combines three scoring functions, measuring degrees of motif over-representation, entropy and spatial confinement, specifically designed to discriminatively exploit the availability of negative data. The method is shown to outperform current methods that use only a subset of these motif characteristics. We apply the method to several biological datasets. The analysis of peroxisomal targeting signals uncovers several novel motifs that occur immediately upstream of the dominant peroxisomal targeting signal-1 signal. The analysis of proline-tyrosine nuclear localization signals uncovers multiple novel motifs that overlap with C2H2 zinc finger domains. We also evaluate the method on classical nuclear localization signals and endoplasmic reticulum retention signals and find that DLocalMotif successfully recovers biologically relevant sequence properties. AVAILABILITY http://bioinf.scmb.uq.edu.au/dlocalmotif/
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Affiliation(s)
- Ahmed M Mehdi
- Institute for Molecular Bioscience, The University of Queensland, Australia
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Abstract
MOTIVATION Nucleo-cytoplasmic trafficking of proteins is a core regulatory process that sustains the integrity of the nuclear space of eukaryotic cells via an interplay between numerous factors. Despite progress on experimentally characterizing a number of nuclear localization signals, their presence alone remains an unreliable indicator of actual translocation. RESULTS This article introduces a probabilistic model that explicitly recognizes a variety of nuclear localization signals, and integrates relevant amino acid sequence and interaction data for any candidate nuclear protein. In particular, we develop and incorporate scoring functions based on distinct classes of classical nuclear localization signals. Our empirical results show that the model accurately predicts whether a protein is imported into the nucleus, surpassing the classification accuracy of similar predictors when evaluated on the mouse and yeast proteomes (area under the receiver operator characteristic curve of 0.84 and 0.80, respectively). The model also predicts the sequence position of a nuclear localization signal and whether it interacts with importin-α. AVAILABILITY http://pprowler.itee.uq.edu.au/NucImport
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Affiliation(s)
- Ahmed M Mehdi
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
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Marfori M, Mynott A, Ellis JJ, Mehdi AM, Saunders NFW, Curmi PM, Forwood JK, Bodén M, Kobe B. Molecular basis for specificity of nuclear import and prediction of nuclear localization. Biochim Biophys Acta 2010; 1813:1562-77. [PMID: 20977914 DOI: 10.1016/j.bbamcr.2010.10.013] [Citation(s) in RCA: 303] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 10/15/2010] [Accepted: 10/19/2010] [Indexed: 01/03/2023]
Abstract
Although proteins are translated on cytoplasmic ribosomes, many of these proteins play essential roles in the nucleus, mediating key cellular processes including but not limited to DNA replication and repair as well as transcription and RNA processing. Thus, understanding how these critical nuclear proteins are accurately targeted to the nucleus is of paramount importance in biology. Interaction and structural studies in the recent years have jointly revealed some general rules on the specificity determinants of the recognition of nuclear targeting signals by their specific receptors, at least for two nuclear import pathways: (i) the classical pathway, which involves the classical nuclear localization sequences (cNLSs) and the receptors importin-α/karyopherin-α and importin-β/karyopherin-β1; and (ii) the karyopherin-β2 pathway, which employs the proline-tyrosine (PY)-NLSs and the receptor transportin-1/karyopherin-β2. The understanding of specificity rules allows the prediction of protein nuclear localization. We review the current understanding of the molecular determinants of the specificity of nuclear import, focusing on the importin-α•cargo recognition, as well as the currently available databases and predictive tools relevant to nuclear localization. This article is part of a Special Issue entitled: Regulation of Signaling and Cellular Fate through Modulation of Nuclear Protein Import.
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Affiliation(s)
- Mary Marfori
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
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