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Ullah MA, Garcillán B, Whitlock E, Figgett WA, Infantino S, Eslami M, Yang S, Rahman MA, Sheng YH, Weber N, Schneider P, Tam CS, Mackay F. An unappreciated cell survival-independent role for BAFF initiating chronic lymphocytic leukemia. Front Immunol 2024; 15:1345515. [PMID: 38469292 PMCID: PMC10927009 DOI: 10.3389/fimmu.2024.1345515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/25/2024] [Indexed: 03/13/2024] Open
Abstract
Background Chronic Lymphocytic Leukemia (CLL) is characterized by the expansion of CD19+ CD5+ B cells but its origin remains debated. Mutated CLL may originate from post-germinal center B cells and unmutated CLL from CD5+ mature B cell precursors. Irrespective of precursor types, events initiating CLL remain unknown. The cytokines BAFF and APRIL each play a significant role in CLL cell survival and accumulation, but their involvement in disease initiation remains unclear. Methods We generated novel CLL models lacking BAFF or APRIL. In vivo experiments were conducted to explore the impact of BAFF or APRIL loss on leukemia initiation, progression, and dissemination. Additionally, RNA-seq and quantitative real-time PCR were performed to unveil the transcriptomic signature influenced by BAFF in CLL. The direct role of BAFF in controlling the expression of tumor-promoting genes was further assessed in patient-derived primary CLL cells ex-vivo. Results Our findings demonstrate a crucial role for BAFF, but not APRIL, in the initiation and dissemination of CLL cells. In the absence of BAFF or its receptor BAFF-R, the TCL1 transgene only increases CLL cell numbers in the peritoneal cavity, without dissemination into the periphery. While BAFF binding to BAFF-R is dispensable for peritoneal CLL cell survival, it is necessary to activate a tumor-promoting gene program, potentially linked to CLL initiation and progression. This direct role of BAFF in controlling the expression of tumor-promoting genes was confirmed in patient-derived primary CLL cells ex-vivo. Conclusions Our study, involving both mouse and human CLL cells, suggests that BAFF might initiate CLL through mechanisms independent of cell survival. Combining current CLL therapies with BAFF inhibition could offer a dual benefit by reducing peripheral tumor burden and suppressing transformed CLL cell output.
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Affiliation(s)
- Md Ashik Ullah
- Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Cancer Program, Herston, QLD, Australia
| | - Beatriz Garcillán
- The Department of Microbiology and Immunology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Eden Whitlock
- Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Cancer Program, Herston, QLD, Australia
| | - William A. Figgett
- The Department of Microbiology and Immunology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
- Garvan Institute of Medical Research, Kinghorn Centre for Clinical Genomics, Darlinghurst, NSW, Australia
| | - Simona Infantino
- The Department of Microbiology and Immunology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Mahya Eslami
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
- Department of Oncology and Children’s Research Centre, University Children’s Hospital Zürich, Zürich, Switzerland
| | - SiLing Yang
- Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Cancer Program, Herston, QLD, Australia
| | - M. Arifur Rahman
- Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Cancer Program, Herston, QLD, Australia
| | - Yong H. Sheng
- Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Cancer Program, Herston, QLD, Australia
| | - Nicholas Weber
- Cancer Care Services, Royal Brisbane and Women’s Hospital, Herston, QLD, Australia
| | - Pascal Schneider
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Constantine S. Tam
- Department of Haematology, Alfred Hospital, Melbourne, VIC, Australia
- Department of Haematology, Monash University, Melbourne, VIC, Australia
| | - Fabienne Mackay
- Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Cancer Program, Herston, QLD, Australia
- The Department of Microbiology and Immunology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
- The Department of Immunology and Pathology, Monash University, VIC, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
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2
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Deliyanti D, Figgett WA, Gebhardt T, Trapani JA, Mackay F, Wilkinson-Berka JL. CD8 + T Cells Promote Pathological Angiogenesis in Ocular Neovascular Disease. Arterioscler Thromb Vasc Biol 2023; 43:522-536. [PMID: 36794587 DOI: 10.1161/atvbaha.122.318079] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
BACKGROUND CD4+ (cluster of differentation) and CD8+ T cells are increased in the ocular fluids of patients with neovascular retinopathy, yet their role in the disease process is unknown. METHODS We describe how CD8+ T cells migrate into the retina and contribute to pathological angiogenesis by releasing cytokines and cytotoxic factors. RESULTS In oxygen-induced retinopathy, flow cytometry revealed the numbers of CD4+ and CD8+ T cells were increased in blood, lymphoid organs, and retina throughout the development of neovascular retinopathy. Interestingly, the depletion of CD8+ T cells but not CD4+ T cells reduced retinal neovascularization and vascular leakage. Using reporter mice expressing gfp (green fluorescence protein) in CD8+ T cells, these cells were localized near neovascular tufts in the retina, confirming that CD8+ T cells contribute to the disease. Furthermore, the adoptive transfer of CD8+ T cells deficient in TNF (tumor necrosis factor), IFNγ (interferon gamma), Prf (perforin), or GzmA/B (granzymes A/B) into immunocompetent Rag1-/- mice revealed that CD8+ T cells mediate retinal vascular disease via these factors, with TNF influencing all aspects of vascular pathology. The pathway by which CD8+ T cells migrate into the retina was identified as CXCR3 (C-X-C motif chemokine receptor 3) with the CXCR3 blockade reducing the number of CD8+ T cells within the retina and retinal vascular disease. CONCLUSIONS We discovered that CXCR3 is central to the migration of CD8+ T cells into the retina as the CXCR3 blockade reduced the number of CD8+ T cells within the retina and vasculopathy. This research identified an unappreciated role for CD8+ T cells in retinal inflammation and vascular disease. Reducing CD8+ T cells via their inflammatory and recruitment pathways is a potential treatment for neovascular retinopathies.
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Affiliation(s)
- Devy Deliyanti
- Department of Anatomy and Physiology, School of Biomedical Sciences (D.D., J.L.W.-B.), University of Melbourne, Parkville, Victoria, Australia
- Department of Diabetes, Monash University, Melbourne, Victoria, Australia (D.D., J.L.W.-B.)
| | - William A Figgett
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia (W.A.F.)
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia (W.A.F., T.G.)
| | - Thomas Gebhardt
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia (W.A.F., T.G.)
| | - Joseph A Trapani
- Sir Peter MacCallum Department of Oncology (J.A.T.), University of Melbourne, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia (J.A.T.)
| | - Fabienne Mackay
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia (F.M.)
| | - Jennifer L Wilkinson-Berka
- Department of Anatomy and Physiology, School of Biomedical Sciences (D.D., J.L.W.-B.), University of Melbourne, Parkville, Victoria, Australia
- Department of Diabetes, Monash University, Melbourne, Victoria, Australia (D.D., J.L.W.-B.)
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Figgett WA, Hawson J, Lee G. Machine learning in EP research: New tools for old problems. J Cardiovasc Electrophysiol 2023; 34:1322-1323. [PMID: 36738150 DOI: 10.1111/jce.15851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Affiliation(s)
- William A Figgett
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Joshua Hawson
- Department of Cardiology, Royal Melbourne Hospital, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Victoria, Australia
| | - Geoffrey Lee
- Department of Cardiology, Royal Melbourne Hospital, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Victoria, Australia
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Quah PS, Sutton V, Whitlock E, Figgett WA, Andrews DM, Fairfax KA, Mackay F. The effects of B-cell-activating factor on the population size, maturation and function of murine natural killer cells. Immunol Cell Biol 2022; 100:761-776. [PMID: 36106449 PMCID: PMC9828838 DOI: 10.1111/imcb.12585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 08/30/2022] [Accepted: 09/13/2022] [Indexed: 01/12/2023]
Abstract
The role of B-cell-activating factor (BAFF) in B-lymphocyte biology has been comprehensively studied, but its contributions to innate immunity remain unclear. Natural killer (NK) cells form the first line of defense against viruses and tumors, and have been shown to be defective in patients with systemic lupus erythematosus (SLE). The link between BAFF and NK cells in the development and progression of SLE remains unstudied. By assessing NK cell numbers in wild-type (WT), BAFF-/- (BAFF deficient), BAFF-R-/- (BAFF receptor deficient), TACI-/- (transmembrane activator and calcium modulator and cyclophilin ligand interactor deficient), BCMA-/- (B-cell maturation antigen deficient) and BAFF transgenic (Tg) mice, we observed that BAFF signaling through BAFF-R was essential for sustaining NK cell numbers in the spleen. However, according to the cell surface expression of CD27 and CD11b on NK cells, we found that BAFF was dispensable for NK cell maturation. Ex vivo and in vivo models showed that NK cells from BAFF-/- and BAFF Tg mice produced interferon-γ and killed tumor cells at a level similar to that in WT mice. Finally, we established that NK cells do not express receptors that interact with BAFF in the steady state or in the BAFF Tg mouse model of SLE. Our findings demonstrate that BAFF has an indirect effect on NK cell homeostasis and no effect on NK cell function.
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Affiliation(s)
- Pin Shie Quah
- Department of Immunology and PathologyCentral Clinical School, Monash UniversityMelbourneVICAustralia,Department of Microbiology and ImmunologyThe University of Melbourne, Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia
| | - Vivien Sutton
- Rosie Lew Cancer Immunology ProgramPeter MacCallum Cancer CentreMelbourneVICAustralia,Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVICAustralia
| | - Eden Whitlock
- Department of Microbiology and ImmunologyThe University of Melbourne, Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia,QIMR Berghofer Medical Research InstituteHerstonQLDAustralia
| | - William A Figgett
- Department of Immunology and PathologyCentral Clinical School, Monash UniversityMelbourneVICAustralia,Department of Microbiology and ImmunologyThe University of Melbourne, Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia,Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
| | - Daniel M Andrews
- Department of Immunology and PathologyCentral Clinical School, Monash UniversityMelbourneVICAustralia,Bioproperties, RingwoodMelbourneVICAustralia
| | - Kirsten A Fairfax
- Blood Cells and Blood Cancer DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia,Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTASAustralia,School of Medicine, College of Health and MedicineUniversity of TasmaniaHobartTASAustralia
| | - Fabienne Mackay
- Department of Immunology and PathologyCentral Clinical School, Monash UniversityMelbourneVICAustralia,Department of Microbiology and ImmunologyThe University of Melbourne, Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia,QIMR Berghofer Medical Research InstituteHerstonQLDAustralia,Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
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Tangye SG, Gray PE, Pillay BA, Yap JY, Figgett WA, Reeves J, Kummerfeld SK, Stoddard J, Uzel G, Jing H, Su HC, Campbell DE, Sullivan A, Burnett L, Peake J, Ma CS. Hyper-IgE Syndrome due to an Elusive Novel Intronic Homozygous Variant in DOCK8. J Clin Immunol 2022; 42:119-129. [PMID: 34657245 PMCID: PMC10461790 DOI: 10.1007/s10875-021-01152-x] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/27/2021] [Indexed: 11/29/2022]
Abstract
Rare, biallelic loss-of-function mutations in DOCK8 result in a combined immune deficiency characterized by severe and recurrent cutaneous infections, eczema, allergies, and susceptibility to malignancy, as well as impaired humoral and cellular immunity and hyper-IgE. The advent of next-generation sequencing technologies has enabled the rapid molecular diagnosis of rare monogenic diseases, including inborn errors of immunity. These advances have resulted in the implementation of gene-guided treatments, such as hematopoietic stem cell transplant for DOCK8 deficiency. However, putative disease-causing variants revealed by next-generation sequencing need rigorous validation to demonstrate pathogenicity. Here, we report the eventual diagnosis of DOCK8 deficiency in a consanguineous family due to a novel homozygous intronic deletion variant that caused aberrant exon splicing and subsequent loss of expression of DOCK8 protein. Remarkably, the causative variant was not initially detected by clinical whole-genome sequencing but was subsequently identified and validated by combining advanced genomic analysis, RNA-seq, and flow cytometry. This case highlights the need to adopt multipronged confirmatory approaches to definitively solve complex genetic cases that result from variants outside protein-coding exons and conventional splice sites.
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Affiliation(s)
- Stuart G Tangye
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- Clinical Immunogenomics Research Consortium of Australasia (CIRCA), Sydney, New South Wales, Australia
| | - Paul E Gray
- Clinical Immunogenomics Research Consortium of Australasia (CIRCA), Sydney, New South Wales, Australia
- Department of Immunology and Infectious Diseases, Sydney Children's Hospital, Sydney, New South Wales, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Bethany A Pillay
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Jin Yan Yap
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia
- Clinical Immunogenomics Research Consortium of Australasia (CIRCA), Sydney, New South Wales, Australia
| | - William A Figgett
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia
| | - John Reeves
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Sarah K Kummerfeld
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia
| | - Jennifer Stoddard
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, MD, USA
| | - Gulbu Uzel
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Huie Jing
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dianne E Campbell
- Department of Allergy and Immunology, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Anna Sullivan
- Clinical Immunogenomics Research Consortium of Australasia (CIRCA), Sydney, New South Wales, Australia
- Queensland Children's Hospital and University of Queensland, South Brisbane, Queensland, Australia
| | - Leslie Burnett
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- Clinical Immunogenomics Research Consortium of Australasia (CIRCA), Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Jane Peake
- Clinical Immunogenomics Research Consortium of Australasia (CIRCA), Sydney, New South Wales, Australia
- Queensland Children's Hospital and University of Queensland, South Brisbane, Queensland, Australia
| | - Cindy S Ma
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales, 2010, Australia.
- St Vincent's Clinical School, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia.
- Clinical Immunogenomics Research Consortium of Australasia (CIRCA), Sydney, New South Wales, Australia.
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6
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Bakhuraysah MM, Theotokis P, Lee JY, Alrehaili AA, Aui PM, Figgett WA, Azari MF, Abou-Afech JP, Mackay F, Siatskas C, Alderuccio F, Strittmatter SM, Grigoriadis N, Petratos S. B-cells expressing NgR1 and NgR3 are localized to EAE-induced inflammatory infiltrates and are stimulated by BAFF. Sci Rep 2021; 11:2890. [PMID: 33536561 PMCID: PMC7858582 DOI: 10.1038/s41598-021-82346-6] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 01/14/2021] [Indexed: 02/01/2023] Open
Abstract
We have previously reported evidence that Nogo-A activation of Nogo-receptor 1 (NgR1) can drive axonal dystrophy during the neurological progression of experimental autoimmune encephalomyelitis (EAE). However, the B-cell activating factor (BAFF/BlyS) may also be an important ligand of NgR during neuroinflammation. In the current study we define that NgR1 and its homologs may contribute to immune cell signaling during EAE. Meningeal B-cells expressing NgR1 and NgR3 were identified within the lumbosacral spinal cords of ngr1+/+ EAE-induced mice at clinical score 1. Furthermore, increased secretion of immunoglobulins that bound to central nervous system myelin were shown to be generated from isolated NgR1- and NgR3-expressing B-cells of ngr1+/+ EAE-induced mice. In vitro BAFF stimulation of NgR1- and NgR3-expressing B cells, directed them into the cell cycle DNA synthesis phase. However, when we antagonized BAFF signaling by co-incubation with recombinant BAFF-R, NgR1-Fc, or NgR3 peptides, the B cells remained in the G0/G1 phase. The data suggest that B cells express NgR1 and NgR3 during EAE, being localized to infiltrates of the meninges and that their regulation is governed by BAFF signaling.
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Affiliation(s)
- Maha M Bakhuraysah
- Department of Neuroscience, Central Clinical School, Monash University, Prahran, VIC, 3004, Australia.,Faculty of Applied Medical Sciences, Taif University, Taif, 26521, Kingdom of Saudi Arabia
| | - Paschalis Theotokis
- Laboratory of Experimental Neurology and Neuroimmunology, Department of Neurology, AHEPA University Hospital, 54636, Thessaloniki, Macedonia, Greece
| | - Jae Young Lee
- Department of Neuroscience, Central Clinical School, Monash University, Prahran, VIC, 3004, Australia.,Toolgen Inc., Gasan Digital-Ro, 08594, Geumcheon, Seoul, Korea
| | - Amani A Alrehaili
- Department of Neuroscience, Central Clinical School, Monash University, Prahran, VIC, 3004, Australia.,Faculty of Applied Medical Sciences, Taif University, Taif, 26521, Kingdom of Saudi Arabia
| | - Pei-Mun Aui
- Department of Neuroscience, Central Clinical School, Monash University, Prahran, VIC, 3004, Australia
| | - William A Figgett
- Department of Microbiology and Immunology, School of Biomedical Science, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Michael F Azari
- Department of Neuroscience, Central Clinical School, Monash University, Prahran, VIC, 3004, Australia
| | - John-Paul Abou-Afech
- Department of Neuroscience, Central Clinical School, Monash University, Prahran, VIC, 3004, Australia
| | - Fabienne Mackay
- Department of Microbiology and Immunology, School of Biomedical Science, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia.,QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | | | - Frank Alderuccio
- Department of Immunology and Pathology, Central Clinical School, Monash University, Prahran, VIC, 3004, Australia
| | - Stephen M Strittmatter
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, 06536, USA
| | - Nikolaos Grigoriadis
- Laboratory of Experimental Neurology and Neuroimmunology, Department of Neurology, AHEPA University Hospital, 54636, Thessaloniki, Macedonia, Greece
| | - Steven Petratos
- Department of Neuroscience, Central Clinical School, Monash University, Prahran, VIC, 3004, Australia.
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7
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Figgett WA, Monaghan K, Ng M, Alhamdoosh M, Maraskovsky E, Wilson NJ, Hoi AY, Morand EF, Mackay F. Machine learning applied to whole-blood RNA-sequencing data uncovers distinct subsets of patients with systemic lupus erythematosus. Clin Transl Immunology 2019; 8:e01093. [PMID: 31921420 PMCID: PMC6946916 DOI: 10.1002/cti2.1093] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 08/28/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022] Open
Abstract
Objectives Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease that is difficult to treat. There is currently no optimal stratification of patients with SLE, and thus, responses to available treatments are unpredictable. Here, we developed a new stratification scheme for patients with SLE, based on the computational analysis of patients’ whole‐blood transcriptomes. Methods We applied machine learning approaches to RNA‐sequencing (RNA‐seq) data sets to stratify patients with SLE into four distinct clusters based on their gene expression profiles. A meta‐analysis on three recently published whole‐blood RNA‐seq data sets was carried out, and an additional similar data set of 30 patients with SLE and 29 healthy donors was incorporated in this study; a total of 161 patients with SLE and 57 healthy donors were analysed. Results Examination of SLE clusters, as opposed to unstratified SLE patients, revealed underappreciated differences in the pattern of expression of disease‐related genes relative to clinical presentation. Moreover, gene signatures correlated with flare activity were successfully identified. Conclusion Given that SLE disease heterogeneity is a key challenge hindering the design of optimal clinical trials and the adequate management of patients, our approach opens a new possible avenue addressing this limitation via a greater understanding of SLE heterogeneity in humans. Stratification of patients based on gene expression signatures may be a valuable strategy allowing the identification of separate molecular mechanisms underpinning disease in SLE. Further, this approach may have a use in understanding the variability in responsiveness to therapeutics, thereby improving the design of clinical trials and advancing personalised therapy.
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Affiliation(s)
- William A Figgett
- Department of Microbiology and Immunology University of Melbourne at the Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia
| | | | | | | | | | | | - Alberta Y Hoi
- Centre for Inflammatory Diseases School of Clinical Sciences Monash University Clayton VIC Australia
| | - Eric F Morand
- Centre for Inflammatory Diseases School of Clinical Sciences Monash University Clayton VIC Australia
| | - Fabienne Mackay
- Department of Microbiology and Immunology University of Melbourne at the Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia.,Department of Immunology and Pathology Central Clinical School Monash University Melbourne VIC Australia
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Garcillán B, Figgett WA, Infantino S, Lim EX, Mackay F. Molecular control of B-cell homeostasis in health and malignancy. Immunol Cell Biol 2018; 96:453-462. [PMID: 29499091 DOI: 10.1111/imcb.12030] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 02/26/2018] [Accepted: 02/26/2018] [Indexed: 12/19/2022]
Abstract
Altered B-cell homeostasis underlies a wide range of pathologies, from cancers to autoimmunity and immunodeficiency. The molecular safeguards against those disorders, which also allow effective immune responses, are therefore particularly critical. Here, we review recent findings detailing the fine control of B-cell homeostasis, during B-cell development, maturation in the periphery and during activation and differentiation into antibody-producing cells.
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Affiliation(s)
- Beatriz Garcillán
- The Department of Microbiology and Immunology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - William A Figgett
- The Department of Microbiology and Immunology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Simona Infantino
- The Department of Microbiology and Immunology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Ee Xin Lim
- The Department of Microbiology and Immunology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Fabienne Mackay
- The Department of Microbiology and Immunology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
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9
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Figgett WA, Deliyanti D, Fairfax KA, Quah PS, Wilkinson-Berka JL, Mackay F. Deleting the BAFF receptor TACI protects against systemic lupus erythematosus without extensive reduction of B cell numbers. J Autoimmun 2015; 61:9-16. [DOI: 10.1016/j.jaut.2015.04.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 04/21/2015] [Accepted: 04/26/2015] [Indexed: 01/06/2023]
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10
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Tan SM, Deliyanti D, Figgett WA, Talia DM, de Haan JB, Wilkinson-Berka JL. Ebselen by modulating oxidative stress improves hypoxia-induced macroglial Müller cell and vascular injury in the retina. Exp Eye Res 2015; 136:1-8. [PMID: 25912997 DOI: 10.1016/j.exer.2015.04.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 03/31/2015] [Accepted: 04/22/2015] [Indexed: 01/08/2023]
Abstract
Oxidative stress is an important contributor to glial and vascular cell damage in ischemic retinopathies. We hypothesized that ebselen via its ability to reduce reactive oxygen species (ROS) and augment nuclear factor-like 2 (Nrf2) anti-oxidants would attenuate hypoxia-induced damage to macroglial Müller cells and also lessen retinal vasculopathy. Primary cultures of rat Müller cells were exposed to normoxia (21% O2), hypoxia (0.5% O2) and ebselen (2.5 μM) for up to 72 h. Oxygen-induced retinopathy (OIR) was induced in C57BL/6J mice while control mice were housed in room air. Mice received vehicle (saline, 5% dimethyl sulfoxide) or ebselen (10 mg/kg) each day between postnatal days 6-18. In cultured Müller cells, flow cytometry for dihydroethidium revealed that ebselen reduced the hypoxia-induced increase in ROS levels, whilst increasing the expression of Nrf2-regulated anti-oxidant genes, heme oxygenase 1, glutathione peroxidase-1, NAD(P)H dehydrogenase quinone oxidoreductase 1 and glutamate-cysteine ligase. Moreover, in Müller cells, ebselen reduced the hypoxia-induced increase in protein levels of pro-angiogenic and pro-inflammatory factors including vascular endothelial growth factor, interleukin-6, monocyte chemoattractant-protein 1 and intercellular adhesion molecule-1, and the mRNA levels of glial fibrillary acidic protein (GFAP), a marker of Müller cell injury. Ebselen improved OIR by attenuating capillary vaso-obliteration and neovascularization and a concomitant reduction in Müller cell gliosis and GFAP. We conclude that ebselen protects against hypoxia-induced injury of retinal Müller cells and the microvasculature, which is linked to its ability to reduce oxidative stress, vascular damaging factors and inflammation. Agents such as ebselen may be potential treatments for retinopathies that feature oxidative stress-mediated damage to glia and the microvasculature.
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Affiliation(s)
- Sih Min Tan
- Oxidative Stress Laboratory, Diabetic Complications Division, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Devy Deliyanti
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - William A Figgett
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Dean M Talia
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Judy B de Haan
- Oxidative Stress Laboratory, Diabetic Complications Division, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia.
| | - Jennifer L Wilkinson-Berka
- Oxidative Stress Laboratory, Diabetic Complications Division, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
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Deliyanti D, Armani R, Casely D, Figgett WA, Agrotis A, Wilkinson-Berka JL. Retinal vasculopathy is reduced by dietary salt restriction: involvement of Glia, ENaCα, and the renin-angiotensin-aldosterone system. Arterioscler Thromb Vasc Biol 2014; 34:2033-41. [PMID: 25012132 DOI: 10.1161/atvbaha.114.303792] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
OBJECTIVE Neovascularization and vaso-obliteration are vision-threatening events that develop by interactions between retinal vascular and glial cells. A high-salt diet is causal in cardiovascular and renal disease, which is linked to modulation of the renin-angiotensin-aldosterone system. However, it is not known whether dietary salt influences retinal vasculopathy and if the renin-angiotensin-aldosterone system is involved. We examined whether a low-salt (LS) diet influenced vascular and glial cell injury and the renin-angiotensin-aldosterone system in ischemic retinopathy. APPROACH AND RESULTS Pregnant Sprague Dawley rats were fed LS (0.03% NaCl) or normal salt (0.3% NaCl) diets, and ischemic retinopathy was induced in the offspring. An LS diet reduced retinal neovascularization and vaso-obliteration, the mRNA and protein levels of the angiogenic factors, vascular endothelial growth factor, and erythropoietin. Microglia, which influence vascular remodeling in ischemic retinopathy, were reduced by LS as was tumor necrosis factor-α. Macroglial Müller cells maintain the integrity of the blood-retinal barrier, and in ischemic retinopathy, LS reduced their gliosis and also vascular leakage. In retina, LS reduced mineralocorticoid receptor, angiotensin type 1 receptor, and renin mRNA levels, whereas, as expected, plasma levels of aldosterone and renin were increased. The aldosterone/mineralocorticoid receptor-sensitive epithelial sodium channel alpha (ENaCα), which is expressed in Müller cells, was increased in ischemic retinopathy and reduced by LS. In cultured Müller cells, high salt increased ENaCα, which was prevented by mineralocorticoid receptor and angiotensin type 1 receptor blockade. Conversely, LS reduced ENaCα, angiotensin type 1 receptor, and mineralocorticoid receptor expression. CONCLUSIONS An LS diet reduced retinal vasculopathy, by modulating glial cell function and the retinal renin-angiotensin-aldosterone system.
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Affiliation(s)
- Devy Deliyanti
- From the Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia (D.D., R.A., W.A.F., A.A., J.L.W.-B.); and Prosearch International, Malvern, Victoria, Australia (D.C.)
| | - Roksana Armani
- From the Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia (D.D., R.A., W.A.F., A.A., J.L.W.-B.); and Prosearch International, Malvern, Victoria, Australia (D.C.)
| | - David Casely
- From the Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia (D.D., R.A., W.A.F., A.A., J.L.W.-B.); and Prosearch International, Malvern, Victoria, Australia (D.C.)
| | - William A Figgett
- From the Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia (D.D., R.A., W.A.F., A.A., J.L.W.-B.); and Prosearch International, Malvern, Victoria, Australia (D.C.)
| | - Alex Agrotis
- From the Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia (D.D., R.A., W.A.F., A.A., J.L.W.-B.); and Prosearch International, Malvern, Victoria, Australia (D.C.)
| | - Jennifer L Wilkinson-Berka
- From the Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia (D.D., R.A., W.A.F., A.A., J.L.W.-B.); and Prosearch International, Malvern, Victoria, Australia (D.C.).
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Figgett WA, Vincent FB, Saulep-Easton D, Mackay F. Roles of ligands from the TNF superfamily in B cell development, function, and regulation. Semin Immunol 2014; 26:191-202. [PMID: 24996229 DOI: 10.1016/j.smim.2014.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [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: 06/05/2014] [Accepted: 06/09/2014] [Indexed: 01/01/2023]
Abstract
Most ligands from the tumour necrosis factor (TNF) superfamily play very important roles in the immune system, and particularly so in B lymphocyte biology. TNF ligands are essential to many aspects of normal B cell biology from development in the bone marrow to maturation in the periphery as well as for activation and differentiation into germinal centre, memory or plasma cells. TNF ligands also influence other aspects of B cell biology such as their ability to present antigens or regulate immune responses. Importantly, inadequate regulation of many TNF ligands is associated with B cell disorders including autoimmunity and cancers. As a result, inhibitors of a number of TNF ligands have been tested in the clinic, with some becoming very successful approved treatments alleviating B cell-mediated pathologies.
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Affiliation(s)
- William A Figgett
- Department of Immunology, Monash University, Central Clinical School, Alfred Medical Research and Education Precinct (AMREP), Commercial Road, Melbourne, Victoria 3004, Australia
| | - Fabien B Vincent
- Department of Immunology, Monash University, Central Clinical School, Alfred Medical Research and Education Precinct (AMREP), Commercial Road, Melbourne, Victoria 3004, Australia
| | - Damien Saulep-Easton
- Department of Immunology, Monash University, Central Clinical School, Alfred Medical Research and Education Precinct (AMREP), Commercial Road, Melbourne, Victoria 3004, Australia
| | - Fabienne Mackay
- Department of Immunology, Monash University, Central Clinical School, Alfred Medical Research and Education Precinct (AMREP), Commercial Road, Melbourne, Victoria 3004, Australia.
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Figgett WA, Fairfax K, Vincent FB, Le Page MA, Katik I, Deliyanti D, Quah PS, Verma P, Grumont R, Gerondakis S, Hertzog P, O'Reilly LA, Strasser A, Mackay F. The TACI receptor regulates T-cell-independent marginal zone B cell responses through innate activation-induced cell death. Immunity 2013; 39:573-83. [PMID: 24012421 DOI: 10.1016/j.immuni.2013.05.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 05/20/2013] [Indexed: 11/30/2022]
Abstract
Activation-induced cell death (AICD) plays a critical role in immune homeostasis and tolerance. In T-cell-dependent humoral responses, AICD of B cells is initiated by Fas ligand (FasL) on T cells, stimulating the Fas receptor on B cells. In contrast, T-cell-independent B cell responses involve innate-type B lymphocytes, such as marginal zone (MZ) B cells, and little is known about the mechanisms that control AICD during innate B cell responses to Toll-like receptor (TLR) activation. Here, we show that MZ B cells undergo AICD in response to TLR4 activation in vivo. The transmembrane activator, calcium modulator, and cyclophilin ligand interactor (TACI) receptor and TLR4 cooperate to upregulate expression of both FasL and Fas on MZ B cells and also to repress inhibitors of Fas-induced apoptosis signaling. These findings demonstrate an unappreciated role for TACI and its ligands in the regulation of AICD during T-cell-independent B cell responses.
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Affiliation(s)
- William A Figgett
- Department of Immunology, Monash University, Melbourne, VIC 3004, Australia; Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
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Abstract
The BAFF system plays a key role in the development of autoimmunity, especially in systemic lupus erythematosus (SLE). This often leads to the assumption that BAFF is mostly a B cell factor with a specific role in autoimmunity. Focus on BAFF and autoimmunity, driven by pharmaceutical successes with the recent approval of a novel targeted therapy Belimumab, has relegated other potential roles of BAFF to the background. Far from being SLE-specific, the BAFF system has a much broader relevance in infection, cancer and allergy. In this review, we provide the latest views on additional roles of the BAFF system in health and diseases, as well as an update on BAFF and autoimmunity, with particular focus on current clinical trials.
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Affiliation(s)
| | | | | | | | - Fabienne Mackay
- Corresponding author at: Department of Immunology, Monash University, Central Clinical School, Alfred Hospital, 89 Commercial Road, Melbourne, Victoria 3004, Australia. Tel.: +61 3 99030713; fax: +61 3 99030038.
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Mackay F, Figgett WA, Saulep D, Lepage M, Hibbs ML. B-cell stage and context-dependent requirements for survival signals from BAFF and the B-cell receptor. Immunol Rev 2010; 237:205-25. [DOI: 10.1111/j.1600-065x.2010.00944.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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