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Bertuzzi M, Howell GJ, Thomson DD, Fortune-Grant R, Möslinger A, Dancer P, Van Rhijn N, Motsi N, Codling A, Bignell EM. Epithelial uptake leads to fungal killing in vivo and is aberrant in COPD-derived epithelial cells. iScience 2024; 27:109939. [PMID: 38846001 PMCID: PMC11154633 DOI: 10.1016/j.isci.2024.109939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/07/2023] [Accepted: 05/06/2024] [Indexed: 06/09/2024] Open
Abstract
Hundreds of spores of Aspergillus fumigatus (Af) are inhaled daily by human beings, representing a constant, possibly fatal, threat to respiratory health. The small size of Af spores suggests that interactions with alveolar epithelial cells (AECs) are frequent; thus, we hypothesized that spore uptake by AECs is important for driving fungal killing and susceptibility to Aspergillus-related disease. Using single-cell approaches to measure spore uptake and its outcomes in vivo, we demonstrate that Af spores are internalized and killed by AECs during whole-animal infection. Moreover, comparative analysis of primary human AECs from healthy and chronic obstructive pulmonary disease (COPD) donors revealed significant alterations in the uptake and killing of spores in COPD-derived AECs. We conclude that AECs contribute to the killing of Af spores and that dysregulation of curative AEC responses in COPD may represent a driver of Aspergillus-related diseases.
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Affiliation(s)
- Margherita Bertuzzi
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
| | - Gareth J. Howell
- Flow Cytometry Core Facility, Faculty of Biology, Medicine and Health, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
| | - Darren D. Thomson
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
| | - Rachael Fortune-Grant
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
| | - Anna Möslinger
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
| | - Patrick Dancer
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
| | - Norman Van Rhijn
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
| | - Natasha Motsi
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
| | - Alice Codling
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
| | - Elaine M. Bignell
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
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2
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Guruceaga X, Perez-Cuesta U, Martin-Vicente A, Pelegri-Martinez E, Thorn HI, Cendon-Sanchez S, Xie J, Nywening AV, Ramirez-Garcia A, Fortwendel JR, Rementeria A. The Aspergillus fumigatus maiA gene contributes to cell wall homeostasis and fungal virulence. Front Cell Infect Microbiol 2024; 14:1327299. [PMID: 38343890 PMCID: PMC10853476 DOI: 10.3389/fcimb.2024.1327299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
In this study, two distinct in vitro infection models of Aspergillus fumigatus, using murine macrophages (RAW264.7) and human lung epithelial cells (A549), were employed to identify the genes important for fungal adaptation during infection. Transcriptomic analyses of co-incubated A. fumigatus uncovered 140 fungal genes up-regulated in common between both models that, when compared with a previously published in vivo transcriptomic study, allowed the identification of 13 genes consistently up-regulated in all three infection conditions. Among them, the maiA gene, responsible for a critical step in the L-phenylalanine degradation pathway, was identified. Disruption of maiA resulted in a mutant strain unable to complete the Phe degradation pathway, leading to an excessive production of pyomelanin when this amino acid served as the sole carbon source. Moreover, the disruption mutant exhibited noticeable cell wall abnormalities, with reduced levels of β-glucans within the cell wall but did not show lack of chitin or mannans. The maiA-1 mutant strain induced reduced inflammation in primary macrophages and displayed significantly lower virulence in a neutropenic mouse model of infection. This is the first study linking the A. fumigatus maiA gene to fungal cell wall homeostasis and virulence.
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Affiliation(s)
- Xabier Guruceaga
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Uxue Perez-Cuesta
- Department of Immunology, Microbiology, and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Adela Martin-Vicente
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Eduardo Pelegri-Martinez
- Department of Immunology, Microbiology, and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Harrison I. Thorn
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, United States
- Graduate Program in Pharmaceutical Science, College of Graduate Health Sciences, University of Tennessee Healths Science Center, Memphis, TN, United States
| | - Saioa Cendon-Sanchez
- Department of Immunology, Microbiology, and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jinhong Xie
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, United States
- Graduate Program in Pharmaceutical Science, College of Graduate Health Sciences, University of Tennessee Healths Science Center, Memphis, TN, United States
| | - Ashley V. Nywening
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, United States
- Integrated Program in Biomedical Sciences, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Andoni Ramirez-Garcia
- Department of Immunology, Microbiology, and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jarrod R. Fortwendel
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Aitor Rementeria
- Department of Immunology, Microbiology, and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
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Thakur R, Shishodia SK, Sharma A, Chauhan A, Kaur S, Shankar J. Accelerating the understanding of Aspergillus terreus: Epidemiology, physiology, immunology and advances. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100220. [PMID: 38303967 PMCID: PMC10831165 DOI: 10.1016/j.crmicr.2024.100220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
Aspergillus species encompass a variety of infections, ranging from invasive aspergillosis to allergic conditions, contingent upon the immune status of the host. In this spectrum, Aspergillus terreus stands out due to its emergence as a notable pathogen and its intrinsic resistance to amphotericin-B. The significance of Aspergillus-associated infections has witnessed a marked increase in the past few decades, particularly with the increasing number of immunocompromised individuals. The exploration of epidemiology, morphological transitions, immunopathology, and novel treatment approaches such as new antifungal drugs (PC945, olorofim) and combinational therapy using antifungal drugs and phytochemicals (Phytochemicals: quercetin, shikonin, artemisinin), also using immunotherapies to modulate immune response has resulted in better outcomes. Furthermore, in the context COVID-19 era and its aftermath, fungal infections have emerged as a substantial challenge for both immunocompromised and immunocompetent individuals. This is attributed to the use of immune-suppressing therapies during COVID-19 infections and the increase in transplant cases. Consequently, this review aims to provide an updated overview encompassing the epidemiology, germination events, immunopathology, and novel drug treatment strategies against Aspergillus terreus-associated infections.
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Affiliation(s)
- Raman Thakur
- Department of Medical Laboratory Science, Lovely Professional University, Jalandhar, Punjab, India
| | | | - Ananya Sharma
- Genomic Laboratory, Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat Solan, Himachal Pradesh, India
| | - Arjun Chauhan
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura, Uttar Pradesh, India
| | - Sumanpreet Kaur
- Department of Medical Laboratory Science, Lovely Professional University, Jalandhar, Punjab, India
| | - Jata Shankar
- Genomic Laboratory, Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat Solan, Himachal Pradesh, India
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Novel Treatment Approach for Aspergilloses by Targeting Germination. J Fungi (Basel) 2022; 8:jof8080758. [PMID: 35893126 PMCID: PMC9331470 DOI: 10.3390/jof8080758] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/03/2022] [Accepted: 07/19/2022] [Indexed: 12/24/2022] Open
Abstract
Germination of conidia is an essential process within the Aspergillus life cycle and plays a major role during the infection of hosts. Conidia are able to avoid detection by the majority of leukocytes when dormant. Germination can cause severe health problems, specifically in immunocompromised people. Aspergillosis is most often caused by Aspergillus fumigatus (A. fumigatus) and affects neutropenic patients, as well as people with cystic fibrosis (CF). These patients are often unable to effectively detect and clear the conidia or hyphae and can develop chronic non-invasive and/or invasive infections or allergic inflammatory responses. Current treatments with (tri)azoles can be very effective to combat a variety of fungal infections. However, resistance against current azoles has emerged and has been increasing since 1998. As a consequence, patients infected with resistant A. fumigatus have a reported mortality rate of 88% to 100%. Especially with the growing number of patients that harbor azole-resistant Aspergilli, novel antifungals could provide an alternative. Aspergilloses differ in defining characteristics, but germination of conidia is one of the few common denominators. By specifically targeting conidial germination with novel antifungals, early intervention might be possible. In this review, we propose several morphotypes to disrupt conidial germination, as well as potential targets. Hopefully, new antifungals against such targets could contribute to disturbing the ability of Aspergilli to germinate and grow, resulting in a decreased fungal burden on patients.
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Brown A, Mead ME, Steenwyk JL, Goldman GH, Rokas A. Extensive non-coding sequence divergence between the major human pathogen Aspergillus fumigatus and its relatives. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:802494. [PMID: 36866034 PMCID: PMC9977105 DOI: 10.3389/ffunb.2022.802494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/09/2022] [Indexed: 11/13/2022]
Abstract
Invasive aspergillosis is a deadly fungal disease; more than 400,000 patients are infected worldwide each year and the mortality rate can be as high as 50-95%. Of the ~450 species in the genus Aspergillus only a few are known to be clinically relevant, with the major pathogen Aspergillus fumigatus being responsible for ~50% of all invasive mold infections. Genomic comparisons between A. fumigatus and other Aspergillus species have historically focused on protein-coding regions. However, most A. fumigatus genes, including those that modulate its virulence, are also present in other pathogenic and non-pathogenic closely related species. Our hypothesis is that differential gene regulation - mediated through the non-coding regions upstream of genes' first codon - contributes to A. fumigatus pathogenicity. To begin testing this, we compared non-coding regions upstream of the first codon of single-copy orthologous genes from the two A. fumigatus reference strains Af293 and A1163 and eight closely related Aspergillus section Fumigati species. We found that these non-coding regions showed extensive sequence variation and lack of homology across species. By examining the evolutionary rates of both protein-coding and non-coding regions in a subset of orthologous genes with highly conserved non-coding regions across the phylogeny, we identified 418 genes, including 25 genes known to modulate A. fumigatus virulence, whose non-coding regions exhibit a different rate of evolution in A. fumigatus. Examination of sequence alignments of these non-coding regions revealed numerous instances of insertions, deletions, and other types of mutations of at least a few nucleotides in A. fumigatus compared to its close relatives. These results show that closely related Aspergillus species that vary greatly in their pathogenicity exhibit extensive non-coding sequence variation and identify numerous changes in non-coding regions of A. fumigatus genes known to contribute to virulence.
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Affiliation(s)
- Alec Brown
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Matthew E. Mead
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
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Barros BCSC, Almeida BR, Barros DTL, Toledo MS, Suzuki E. Respiratory Epithelial Cells: More Than Just a Physical Barrier to Fungal Infections. J Fungi (Basel) 2022; 8:jof8060548. [PMID: 35736031 PMCID: PMC9225092 DOI: 10.3390/jof8060548] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/12/2022] [Accepted: 05/21/2022] [Indexed: 02/06/2023] Open
Abstract
The respiratory epithelium is highly complex, and its composition varies along the conducting airways and alveoli. In addition to their primary function in maintaining the respiratory barrier and lung homeostasis for gas exchange, epithelial cells interact with inhaled pathogens, which can manipulate cell signaling pathways, promoting adhesion to these cells or hosting tissue invasion. Moreover, pathogens (or their products) can induce the secretion of chemokines and cytokines by epithelial cells, and in this way, these host cells communicate with the immune system, modulating host defenses and inflammatory outcomes. This review will focus on the response of respiratory epithelial cells to two human fungal pathogens that cause systemic mycoses: Aspergillus and Paracoccidioides. Some of the host epithelial cell receptors and signaling pathways, in addition to fungal adhesins or other molecules that are responsible for fungal adhesion, invasion, or induction of cytokine secretion will be addressed in this review.
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Affiliation(s)
- Bianca C. S. C. Barros
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo 05503-900, SP, Brazil;
| | - Bruna R. Almeida
- Department of Microbiology, Immunology, and Parasitology, Escola Paulista de Medicina, Universidade Federal de São Paulo, Ed. Antonio C. M. Paiva, São Paulo 04023-062, SP, Brazil; (B.R.A.); (D.T.L.B.)
| | - Debora T. L. Barros
- Department of Microbiology, Immunology, and Parasitology, Escola Paulista de Medicina, Universidade Federal de São Paulo, Ed. Antonio C. M. Paiva, São Paulo 04023-062, SP, Brazil; (B.R.A.); (D.T.L.B.)
| | - Marcos S. Toledo
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, Ed. Leal Prado, São Paulo 04023-062, SP, Brazil;
| | - Erika Suzuki
- Department of Microbiology, Immunology, and Parasitology, Escola Paulista de Medicina, Universidade Federal de São Paulo, Ed. Antonio C. M. Paiva, São Paulo 04023-062, SP, Brazil; (B.R.A.); (D.T.L.B.)
- Correspondence:
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Tiew PY, Thng KX, Chotirmall SH. Clinical Aspergillus Signatures in COPD and Bronchiectasis. J Fungi (Basel) 2022; 8:jof8050480. [PMID: 35628736 PMCID: PMC9146266 DOI: 10.3390/jof8050480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022] Open
Abstract
Pulmonary mycoses remain a global threat, causing significant morbidity and mortality. Patients with airways disease, including COPD and bronchiectasis, are at increased risks of pulmonary mycoses and its associated complications. Frequent use of antibiotics and corticosteroids coupled with impaired host defenses predispose patients to fungal colonization and airway persistence, which are associated with negative clinical consequences. Notably, Aspergillus species remain the best-studied fungal pathogen and induce a broad spectrum of clinical manifestations in COPD and bronchiectasis ranging from colonization and sensitization to more invasive disease. Next-generation sequencing (NGS) has gained prominence in the field of respiratory infection, and in some cases is beginning to act as a viable alternative to traditional culture. NGS has revolutionized our understanding of airway microbiota and in particular fungi. In this context, it permits the identification of the previously unculturable, fungal composition, and dynamic change within microbial communities of the airway, including potential roles in chronic respiratory disease. Furthermore, inter-kingdom microbial interactions, including fungi, in conjunction with host immunity have recently been shown to have important clinical roles in COPD and bronchiectasis. In this review, we provide an overview of clinical Aspergillus signatures in COPD and bronchiectasis and cover the current advances in the understanding of the mycobiome in these disease states. The challenges and limitations of NGS will be addressed.
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Affiliation(s)
- Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore 168753, Singapore;
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore 308433, Singapore
- Correspondence:
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Ortiz SC, Pennington K, Thomson DD, Bertuzzi M. Novel Insights into Aspergillus fumigatus Pathogenesis and Host Response from State-of-the-Art Imaging of Host-Pathogen Interactions during Infection. J Fungi (Basel) 2022; 8:264. [PMID: 35330266 PMCID: PMC8954776 DOI: 10.3390/jof8030264] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/21/2022] [Accepted: 03/01/2022] [Indexed: 12/03/2022] Open
Abstract
Aspergillus fumigatus spores initiate more than 3,000,000 chronic and 300,000 invasive diseases annually, worldwide. Depending on the immune status of the host, inhalation of these spores can lead to a broad spectrum of disease, including invasive aspergillosis, which carries a 50% mortality rate overall; however, this mortality rate increases substantially if the infection is caused by azole-resistant strains or diagnosis is delayed or missed. Increasing resistance to existing antifungal treatments is becoming a major concern; for example, resistance to azoles (the first-line available oral drug against Aspergillus species) has risen by 40% since 2006. Despite high morbidity and mortality, the lack of an in-depth understanding of A. fumigatus pathogenesis and host response has hampered the development of novel therapeutic strategies for the clinical management of fungal infections. Recent advances in sample preparation, infection models and imaging techniques applied in vivo have addressed important gaps in fungal research, whilst questioning existing paradigms. This review highlights the successes and further potential of these recent technologies in understanding the host-pathogen interactions that lead to aspergillosis.
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Affiliation(s)
- Sébastien C. Ortiz
- Manchester Academic Health Science Centre, Core Technology Facility, Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Grafton Street, Manchester M13 9NT, UK; (S.C.O.); (K.P.)
| | - Katie Pennington
- Manchester Academic Health Science Centre, Core Technology Facility, Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Grafton Street, Manchester M13 9NT, UK; (S.C.O.); (K.P.)
| | - Darren D. Thomson
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK;
| | - Margherita Bertuzzi
- Manchester Academic Health Science Centre, Core Technology Facility, Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Grafton Street, Manchester M13 9NT, UK; (S.C.O.); (K.P.)
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Arunachalam D, Ramanathan SM, Menon A, Madhav L, Ramaswamy G, Namperumalsamy VP, Prajna L, Kuppamuthu D. Expression of immune response genes in human corneal epithelial cells interacting with Aspergillus flavus conidia. BMC Genomics 2022; 23:5. [PMID: 34983375 PMCID: PMC8728928 DOI: 10.1186/s12864-021-08218-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/18/2021] [Indexed: 12/19/2022] Open
Abstract
Background Aspergillus flavus, one of the causative agents of human fungal keratitis, can be phagocytosed by human corneal epithelial (HCE) cells and the conidia containing phagosomes mature into phagolysosomes. But the immunological responses of human corneal epithelial cells interacting with A. flavus are not clear. In this study, we report the expression of immune response related genes of HCE cells exposed to A. flavus spores using targeted transcriptomics. Methods Human corneal epithelial cell line and primary cultures were grown in a six-well plate and used for coculture experiments. Internalization of the conidia was confirmed by immunofluorescence microscopy of the colocalized endosomal markers CD71 and LAMP1. Total RNA was isolated, and the quantity and quality of the isolated RNA were assessed using Qubit and Bioanalyzer. NanoString nCounter platform was used for the analysis of mRNA abundance using the Human Immunology panel. R-package and nSolver software were used for data analysis. KEGG and FunRich 3.1.3 tools were used to analyze the differentially expressed genes. Results Different morphotypes of conidia were observed after 6 h of coculture with human corneal epithelial cells and found to be internalized by epithelial cells. NanoString profiling showed more than 20 differentially expressed genes in immortalized human corneal epithelial cell line and more than ten differentially expressed genes in primary corneal epithelial cells. Distinct set of genes were altered in their expression in cell line and primary corneal epithelial cells. KEGG pathway analysis revealed that genes associated with TNF signaling, NF-KB signaling, and Th17 signaling were up-regulated, and genes associated with chemokine signaling and B cell receptor signaling were down regulated. FunRich pathway analysis showed that pathways such as CDC42 signaling, PI3K signaling, and Arf6 trafficking events were activated by the clinical isolates CI1123 and CI1698 in both type of cells. Conclusions Combining the transcript analysis data from cell lines and primary cultures, we showed the up regulation of immune defense genes in A. flavus infected cells. At the same time, chemokine signaling and B cell signaling pathways are downregulated. The variability in the expression levels in the immortalized cell line and the primary cultures is likely due to the variable epigenetic reprogramming in the immortalized cells and primary cultures in the absence of any changes in the genome. It highlights the importance of using both cell types in host-pathogen interaction studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08218-5.
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Affiliation(s)
- Divya Arunachalam
- Proteomics Department, Aravind Medical Research Foundation, Dr. G. Venkataswamy Eye Research Institute, Aravind Eye Care System, Madurai, Tamil Nadu, India.,Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Shruthi Mahalakshmi Ramanathan
- Proteomics Department, Aravind Medical Research Foundation, Dr. G. Venkataswamy Eye Research Institute, Aravind Eye Care System, Madurai, Tamil Nadu, India
| | - Athul Menon
- Theracues Innovations Private Limited, Bangalore, India, Karnataka
| | - Lekshmi Madhav
- Theracues Innovations Private Limited, Bangalore, India, Karnataka
| | | | | | - Lalitha Prajna
- Department of Ocular Microbiology, Aravind Eye Hospital, Aravind Eye Care System, Madurai, Tamil Nadu, India
| | - Dharmalingam Kuppamuthu
- Proteomics Department, Aravind Medical Research Foundation, Dr. G. Venkataswamy Eye Research Institute, Aravind Eye Care System, Madurai, Tamil Nadu, India. .,Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India. .,Aravind Medical Research Foundation, Dr. G.Venkataswamy Eye Research Institute, Aravind Eye Care System, No.1 Anna Nagar, Madurai, Tamil Nadu, India.
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Archer M, Xu J. Current Practices for Reference Gene Selection in RT-qPCR of Aspergillus: Outlook and Recommendations for the Future. Genes (Basel) 2021; 12:genes12070960. [PMID: 34202507 PMCID: PMC8307107 DOI: 10.3390/genes12070960] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022] Open
Abstract
Aspergillus is a genus of filamentous fungi with vast geographic and ecological distributions. Species within this genus are clinically, agriculturally and biotechnologically relevant, leading to increasing interest in elucidating gene expression dynamics of key metabolic and physiological processes. Reverse-transcription quantitative Polymerase Chain Reaction (RT-qPCR) is a sensitive and specific method of quantifying gene expression. A crucial step for comparing RT-qPCR results between strains and experimental conditions is normalisation to experimentally validated reference gene(s). In this review, we provide a critical analysis of current reference gene selection and validation practices for RT-qPCR gene expression analyses of Aspergillus. Of 90 primary research articles obtained through our PubMed query, 17 experimentally validated the reference gene(s) used. Twenty reference genes were used across the 90 studies, with beta-tubulin being the most used reference gene, followed by actin, 18S rRNA and glyceraldehyde 3-phosphate dehydrogenase. Sixteen of the 90 studies used multiple reference genes for normalisation. Failing to experimentally validate the stability of reference genes can lead to conflicting results, as was the case for four studies. Overall, our review highlights the need to experimentally validate reference genes in RT-qPCR studies of Aspergillus.
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Affiliation(s)
| | - Jianping Xu
- Correspondence: ; Tel.: +1-905-525-9140 (ext. 27934); Fax: +1-905-522-6066
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11
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Rowley J, Namvar S, Gago S, Labram B, Bowyer P, Richardson MD, Herrick SE. Differential Proinflammatory Responses to Aspergillus fumigatus by Airway Epithelial Cells In Vitro Are Protease Dependent. J Fungi (Basel) 2021; 7:468. [PMID: 34200666 PMCID: PMC8228831 DOI: 10.3390/jof7060468] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/29/2021] [Accepted: 06/03/2021] [Indexed: 12/05/2022] Open
Abstract
Aspergillus fumigatus is an important human respiratory mould pathogen. In addition to a barrier function, airway epithelium elicits a robust defence against inhaled A. fumigatus by initiating an immune response. The manner by which A. fumigatus initiates this response and the reasons for the immunological heterogeneity with different isolates are unclear. Both direct fungal cell wall-epithelial cell interaction and secretion of soluble proteases have been proposed as possible mechanisms. Our aim was to determine the contribution of fungal proteases to the induction of epithelial IL-6 and IL-8 in response to different A. fumigatus isolates. Airway epithelial cells were exposed to conidia from a low or high protease-producing strain of A. fumigatus, and IL-6 and IL-8 gene expression and protein production were quantified. The role of proteases in cytokine production was further determined using specific protease inhibitors. The proinflammatory cytokine response correlated with conidia germination and hyphal extension. IL-8 induction was significantly reduced in the presence of matrix metalloprotease or cysteine protease inhibitors. With a high protease-producing strain of A. fumigatus, IL-6 release was metalloprotease dependent. Dectin-1 antagonism also inhibited the production of both cytokines. In conclusion, A. fumigatus-secreted proteases mediate a proinflammatory response by airway epithelial cells in a strain-dependent manner.
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Affiliation(s)
- Jessica Rowley
- School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester and Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (J.R.); (S.N.); (S.G.); (B.L.); (P.B.); (M.D.R.)
| | - Sara Namvar
- School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester and Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (J.R.); (S.N.); (S.G.); (B.L.); (P.B.); (M.D.R.)
- School of Science, Engineering and Environment, University of Salford, Salford M5 4WT, UK
| | - Sara Gago
- School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester and Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (J.R.); (S.N.); (S.G.); (B.L.); (P.B.); (M.D.R.)
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester M13 9NT, UK
- NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester M23 9LT, UK
| | - Briony Labram
- School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester and Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (J.R.); (S.N.); (S.G.); (B.L.); (P.B.); (M.D.R.)
| | - Paul Bowyer
- School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester and Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (J.R.); (S.N.); (S.G.); (B.L.); (P.B.); (M.D.R.)
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester M13 9NT, UK
| | - Malcolm D. Richardson
- School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester and Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (J.R.); (S.N.); (S.G.); (B.L.); (P.B.); (M.D.R.)
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester M13 9NT, UK
- NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester M23 9LT, UK
- Mycology Reference Centre, ECMM Excellence Centre of Medical Mycology, Manchester University NHS Foundation Trust, Manchester M23 9LT, UK
| | - Sarah E. Herrick
- School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester and Manchester Academic Health Science Centre, Manchester M13 9PT, UK; (J.R.); (S.N.); (S.G.); (B.L.); (P.B.); (M.D.R.)
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12
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Characterisation of Aspergillus fumigatus Endocytic Trafficking within Airway Epithelial Cells Using High-Resolution Automated Quantitative Confocal Microscopy. J Fungi (Basel) 2021; 7:jof7060454. [PMID: 34200399 PMCID: PMC8229978 DOI: 10.3390/jof7060454] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/15/2022] Open
Abstract
The precise characterization of the mechanisms modulating Aspergillus fumigatus survival within airway epithelial cells has been impaired by the lack of live-cell imaging technologies and user-friendly quantification approaches. Here we described the use of an automated image analysis pipeline to estimate the proportion of A. fumigatus spores taken up by airway epithelial cells, those contained within phagolysosomes or acidified phagosomes, along with the fungal factors contributing to these processes. Coupling the use of fluorescent A. fumigatus strains and fluorescent epithelial probes targeting lysosomes, acidified compartments and cell membrane, we found that both the efficacy of lysosome recruitment to phagosomes and phagosome acidification determines the capacity of airway epithelial cells to contain A. fumigatus growth. Overall, the capability of the airway epithelium to prevent A. fumigatus survival was higher in bronchial epithelial than alveolar epithelial cells. Certain A. fumigatus cell wall mutants influenced phagosome maturation in airway epithelial cells. Taken together, this live-cell 4D imaging approach allows observation and measurement of the very early processes of A. fumigatus interaction within live airway epithelial monolayers.
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13
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Fungal Infection and Inflammation in Cystic Fibrosis. Pathogens 2021; 10:pathogens10050618. [PMID: 34069863 PMCID: PMC8157353 DOI: 10.3390/pathogens10050618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/14/2022] Open
Abstract
Fungi are frequently recovered from lower airway samples from people with cystic fibrosis (CF), yet the role of fungi in the progression of lung disease is debated. Recent studies suggest worsening clinical outcomes associated with airway fungal detection, although most studies to date are retrospective or observational. The presence of fungi can elicit a T helper cell type 2 (Th-2) mediated inflammatory reaction known as allergic bronchopulmonary aspergillosis (ABPA), particularly in those with a genetic atopic predisposition. In this review, we discuss the epidemiology of fungal infections in people with CF, risk factors associated with development of fungal infections, and microbiologic approaches for isolation and identification of fungi. We review the spectrum of fungal disease presentations, clinical outcomes after isolation of fungi from airway samples, and the importance of considering airway co-infections. Finally, we discuss the association between fungi and airway inflammation highlighting gaps in knowledge and future research questions that may further elucidate the role of fungus in lung disease progression.
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14
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Kim JC, Lee MR, Kim S, Park SE, Lee SJ, Shin TY, Kim WJ, Kim J. Transcriptome Analysis of the Japanese Pine Sawyer Beetle, Monochamus alternatus, Infected with the Entomopathogenic Fungus Metarhizium anisopliae JEF-197. J Fungi (Basel) 2021; 7:jof7050373. [PMID: 34068801 PMCID: PMC8151162 DOI: 10.3390/jof7050373] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/16/2021] [Accepted: 05/08/2021] [Indexed: 12/13/2022] Open
Abstract
The Japanese pine sawyer (JPS) beetle, Monochamus alternatus Hope (Coleoptera: Cerambycidae), damages pine trees and transmits the pine wilt nematode, Bursaphelenchus xylophilus Nickle. Chemical agents have been used to control JPS beetle, but due to various issues, efforts are being made to replace these chemical agents with entomopathogenic fungi. We investigated the expression of immune-related genes in JPS beetle in response to infection with JEF-197, a Metarhizium anisopliae isolate, using RNA-seq. RNA samples were obtained from JEF-197, JPS adults treated with JEF-197, and non-treated JPS adults on the 8th day after fungal treatment, and RNA-seq was performed using Illumina sequencing. JPS beetle transcriptome was assembled de novo and differentially expressed gene (DEG) analysis was performed. There were 719 and 1953 up- and downregulated unigenes upon JEF-197 infection, respectively. Upregulated contigs included genes involved in RNA transport, ribosome biogenesis in eukaryotes, spliceosome-related genes, and genes involved in immune-related signaling pathways such as the Toll and Imd pathways. Forty-two fungal DEGs related to energy and protein metabolism were upregulated, and genes involved in the stress response were also upregulated in the infected JPS beetles. Together, our results indicate that infection of JPS beetles by JEF-197 induces the expression of immune-related genes.
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Affiliation(s)
- Jong-Cheol Kim
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Korea; (J.-C.K.); (M.-R.L.); (S.K.); (S.-E.P.); (T.-Y.S.)
| | - Mi-Rong Lee
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Korea; (J.-C.K.); (M.-R.L.); (S.K.); (S.-E.P.); (T.-Y.S.)
| | - Sihyeon Kim
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Korea; (J.-C.K.); (M.-R.L.); (S.K.); (S.-E.P.); (T.-Y.S.)
| | - So-Eun Park
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Korea; (J.-C.K.); (M.-R.L.); (S.K.); (S.-E.P.); (T.-Y.S.)
| | - Se-Jin Lee
- Department of Agricultural Life Science, Sunchon National University, Suncheon 57922, Korea;
| | - Tae-Young Shin
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Korea; (J.-C.K.); (M.-R.L.); (S.K.); (S.-E.P.); (T.-Y.S.)
| | - Woo-Jin Kim
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Korea; (J.-C.K.); (M.-R.L.); (S.K.); (S.-E.P.); (T.-Y.S.)
- Correspondence: (W.-J.K.); (J.K.); Tel.: +82-63-270-2525 (J.K.)
| | - Jaesu Kim
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Korea; (J.-C.K.); (M.-R.L.); (S.K.); (S.-E.P.); (T.-Y.S.)
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54596, Korea
- Correspondence: (W.-J.K.); (J.K.); Tel.: +82-63-270-2525 (J.K.)
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15
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Dysregulation of Key Proteinases in Aspergillus fumigatus Induced by Blood Platelets. Rep Biochem Mol Biol 2021; 10:95-104. [PMID: 34277873 DOI: 10.52547/rbmb.10.1.95] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 12/13/2020] [Indexed: 11/18/2022]
Abstract
Background Aspergillus fumigatus is the most common species causing invasive aspergillosis (IA), a life-threatening infection with more than 80% mortality. Interactions between A. fumigatus and human blood platelets lead to intravascular thrombosis and localized infarcts. To better understand A. fumigatus pathogenesis, we aimed to analyze the genetic basis of interactions between the pathogen and blood platelets. Methods A bioinformatic pipeline on microarray gene expression dataset, including analysis of differentially expressed genes (DEGs) using Limma R package and their molecular function, as well as biological pathways identification, was conducted to find the effective genes involved in IA. In the wet phase, the gene expression patterns following fungal exposure to blood platelets at 15, 30, 60, and 180 min were evaluated by quantitative reverse transcriptase-PCR analysis. Results Three genes encoding aspartic endopeptidases including (Pep1), (Asp f 13), and (β-glucanase) were the standing candidates. The invasion-promoting fungal proteinase-encoding genes were down-regulated after 30 min of hyphal incubation with blood platelets, and then up-regulated at 60 and 180 min, although only Pep1 was greater than the control at the 60and 180 min time points. Also, the same genes were downregulated in more the clinical isolates relative to the standard strain CBS 144.89. Conclusion Our findings delineate the possible induction of fungal-encoded proteinases by blood platelets. This provides a new research line into A. fumigatus' molecular pathogenesis. Such insight into IA pathogenesis might also guide researchers toward novel platelet-based therapies that involve molecular interventions, especially in IA patients.
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16
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Bertuzzi M, Howell GJ. Single-Cell Analysis of Fungal Uptake in Cultured Airway Epithelial Cells Using Differential Fluorescent Staining and Imaging Flow Cytometry. Methods Mol Biol 2021; 2260:83-109. [PMID: 33405032 DOI: 10.1007/978-1-0716-1182-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The respiratory epithelium is the initial point of host contact for inhaled particles, leading to orchestrated, but highly heterogeneous, responses. Human airway epithelial cells (AECs) play a crucial role in host defense by promoting uptake and killing of inhaled microorganisms and concomitant cytokine production in order to recruit professional phagocytes to the site of infection. However, inhaled pathogens can also reside and replicate intracellularly to evade host immune defenses or circulating antimicrobial drugs, ultimately causing apoptosis or cell death of the infected AECs. Imaging flow cytometry (IFC) combines flow cytometry, fluorescent microscopy, and advanced data-processing algorithms to dissect the heterogeneity of the interaction of AECs and inhaled microorganisms and its outcomes at the single-cell level. Here, we describe a novel single-cell approach based on differential fluorescent staining and state-of-the-art IFC to identify, quantify, and analyze individual host-pathogen complexes from cultured AECs infected with spores of the major human fungal pathogen Aspergillus fumigatus.
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Affiliation(s)
- Margherita Bertuzzi
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Core Technology Facility Building, The University of Manchester, Manchester, UK.
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
| | - Gareth J Howell
- Flow Cytometry Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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17
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Keizer EM, Wösten HAB, de Cock H. EphA2-Dependent Internalization of A. fumigatus Conidia in A549 Lung Cells Is Modulated by DHN-Melanin. Front Microbiol 2020; 11:534118. [PMID: 33123097 PMCID: PMC7573251 DOI: 10.3389/fmicb.2020.534118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 09/18/2020] [Indexed: 12/15/2022] Open
Abstract
Dectin-1 and ephrin type-A receptor 2 (EphA2) receptors recognize β-glucan present in the fungal cell wall. Inhibition of Dectin-1 with the monoclonal 2a11 antibody was shown to reduce internalization of conidia of the human pathogen Aspergillus fumigatus into epithelial cells. In this study, we investigated the role of the EphA2 receptor present on A549 epithelial type II lung cells in the interaction with A. fumigatus conidia. We assessed whether EphA2 is involved in association and internalization of conidia by receptor inhibition by an antibody or by using the kinase inhibitor dasatinib. A 50% reduction of internalization of conidia was observed when this receptor was blocked with either the EphA2-specific monoclonal antibody or dasatinib, which was similar when Dectin-1 was inhibited with the 2a11 monoclonal antibody. Inhibition of both receptors reduced the internalization to 40%. EphA2 inhibition was also assessed in a hydrophobin deletion strain (ΔrodA) that exposes more β-glucan and a dihydroxynaphthalene (DHN)-melanin deletion strain (ΔpksP) that exposes more glucosamine and glycoproteins. The ΔrodA strain behaved similar to the wild-type strain with or without EphA2 inhibition. In contrast, the ΔpksP mutant showed an increase in association to the A549 cells and a decrease in internalization. Internalization was not further decreased by EphA2 inhibition. Taken together, the presence of DHN-melanin in the spore cell wall results in an EphA2-dependent internalization of conidia of A. fumigatus into A549 cells.
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Affiliation(s)
- Esther M Keizer
- Microbiology & Institute of Biomembranes, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Han A B Wösten
- Microbiology & Institute of Biomembranes, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Hans de Cock
- Microbiology & Institute of Biomembranes, Department of Biology, Utrecht University, Utrecht, Netherlands
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18
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Seidel C, Moreno-Velásquez SD, Ben-Ghazzi N, Gago S, Read ND, Bowyer P. Phagolysosomal Survival Enables Non-lytic Hyphal Escape and Ramification Through Lung Epithelium During Aspergillus fumigatus Infection. Front Microbiol 2020; 11:1955. [PMID: 32973709 PMCID: PMC7468521 DOI: 10.3389/fmicb.2020.01955] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/24/2020] [Indexed: 12/20/2022] Open
Abstract
Aspergillus fumigatus is the most important mould pathogen in immunosuppressed patients. Suboptimal clearance of inhaled spores results in the colonisation of the lung airways by invasive hyphae. The first point of contact between A. fumigatus and the host is the lung epithelium. In vitro and ex vivo studies have characterised critical aspects of the interaction of invasive hyphae on the surface of epithelial cells. However, the cellular interplay between internalised A. fumigatus and the lung epithelium remains largely unexplored. Here, we use high-resolution live-cell confocal microscopy, 3D rendered imaging and transmission electron microscopy to define the development of A. fumigatus after lung epithelium internalisation in vitro. Germination, morphology and growth of A. fumigatus were significantly impaired upon internalisation by alveolar (A549) and bronchial (16HBE) lung epithelial cells compared to those growing on the host surface. Internalised spores and germlings were surrounded by the host phagolysosome membrane. Sixty per cent of the phagosomes containing germlings were not acidified at 24 h post infection allowing hyphal development. During escape, the phagolysosomal membrane was not ruptured but likely fused to host plasma membrane allowing hyphal exit from the intact host cell in an non-lytic Manner. Subsequently, escaping hyphae elongated between or through adjacent epithelial lung cells without penetration of the host cytoplasm. Hyphal tips penetrating new epithelial cells were surrounded by the recipient cell plasma membrane. Altogether, our results suggest cells of lung epithelium survive fungal penetration because the phagolysosomal and plasma membranes are never breached and that conversely, fungal spores survive due to phagosome maturation failure. Consequently, fungal hyphae can grow through the epithelial cell layer without directly damaging the host. These processes likely prevent the activation of downstream immune responses alongside limiting the access of professional phagocytes to the invading fungal hypha. Further research is needed to investigate if these events also occur during penetration of fungi in endothelial cells, fibroblasts and other cell types.
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Affiliation(s)
- Constanze Seidel
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Core Technology Facility, Manchester, United Kingdom
| | - Sergio D Moreno-Velásquez
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Core Technology Facility, Manchester, United Kingdom
| | - Nagwa Ben-Ghazzi
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Core Technology Facility, Manchester, United Kingdom
| | - Sara Gago
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Core Technology Facility, Manchester, United Kingdom
| | - Nick D Read
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Core Technology Facility, Manchester, United Kingdom
| | - Paul Bowyer
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Core Technology Facility, Manchester, United Kingdom
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19
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Role of Amino Acid Metabolism in the Virulence of Human Pathogenic Fungi. CURRENT CLINICAL MICROBIOLOGY REPORTS 2019. [DOI: 10.1007/s40588-019-00124-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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Marsh JW, Hayward RJ, Shetty AC, Mahurkar A, Humphrys MS, Myers GSA. Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments. Brief Bioinform 2019; 19:1115-1129. [PMID: 28535295 DOI: 10.1093/bib/bbx043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Indexed: 12/18/2022] Open
Abstract
Bacterial pathogens subvert host cells by manipulating cellular pathways for survival and replication; in turn, host cells respond to the invading pathogen through cascading changes in gene expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial virulence factors or host response pathways is crucial for improved diagnostics and therapeutics. Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. This approach builds on the high sensitivity and resolution of RNA sequencing technology and is applicable to any bacteria that interact with eukaryotic cells, encompassing parasitic, commensal or mutualistic lifestyles. Several laboratory protocols have been presented that outline the collection, extraction and sequencing of total RNA for dRNA-Seq experiments, but there is relatively little guidance available for the detailed bioinformatic analyses required. This protocol outlines a typical dRNA-Seq experiment, based on a Chlamydia trachomatis-infected host cell, with a detailed description of the necessary bioinformatic analyses with currently available software tools.
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Affiliation(s)
- James W Marsh
- The ithree institute, University of Technology Sydney
| | | | - Amol C Shetty
- Institute for Genome Sciences at the University of Maryland, Baltimore
| | - Anup Mahurkar
- Institute for Genome Sciences at the University of Maryland, Baltimore
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21
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Interactions of an Emerging Fungal Pathogen Scedosporium aurantiacum with Human Lung Epithelial Cells. Sci Rep 2019; 9:5035. [PMID: 30903006 PMCID: PMC6430781 DOI: 10.1038/s41598-019-41435-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 02/18/2019] [Indexed: 01/25/2023] Open
Abstract
Scedosporium fungi are found in various natural and host-associated environments, including the lungs of cystic fibrosis patients. However, their role in infection development remains underexplored. Here the attachment of conidia of a virulent S. aurantiacum strain WM 06.482 onto the human lung epithelial A549 cells in vitro was visualized using microscopy to examine the initial steps of infection. We showed that 75-80% of fungal conidia were bound to the A549 cells within four hours of co-incubation, and started to produce germ tubes. The germinating conidia seemed to invade the cells through the intercellular space, no intracellular uptake of fungal conidia by the airway epithelial cells after conidial attachment. Transcriptomic analysis of the A549 cells revealed that the up-regulated genes were mainly associated with cell repair and inflammatory processes indicating a protective response against S. aurantiacum infection. Network analysis of the differentially expressed genes showed activation of the innate immune system (NF-kB pathway) leading to the release of pro-inflammatory cytokines. We believe this is the first report showing the transcriptomic response of human alveolar epithelial cells exposed to S. aurantiacum conidia paving a way for better understanding of the mechanism of the infection process.
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22
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Thakur R, Shankar J. Proteome Analysis Revealed Jak/Stat Signaling and Cytoskeleton Rearrangement Proteins in Human Lung Epithelial Cells During Interaction with Aspergillus terreus. ACTA ACUST UNITED AC 2019. [DOI: 10.2174/1574362413666180529123513] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Aspergillus terreus is an emerging etiological agent of invasive and
allergic aspergillosis in immunocompromised individuals. The main risk groups are individuals
having cancer, acute leukemia and those who undergo bone marrow transplantation. The human
lung epithelial cells constitute the first line of defense against inhaled conidia of A. terreus. The
aim of the study was to understand how human lung epithelial cells respond to A. terreus conidia
during the interaction and to decipher proteins/pathways underlying in host defense.
Methods:
Protein samples were extracted from human lung epithelial cells (A549) infected with
and without A. terreus conidia. Proteins were identified using QTOF-LC-MS/MS followed by
analysis using Protein Lynx Global Services software (2.2.5) against Homo sapiens UniProt
database.
Results:
A total of 1253 proteins in human lung epithelial cells were identified during the
interaction with Aspergillus terreus conidia, whereas 427 proteins were identified in uninfected
lung epithelial cells. We have observed 63 proteins in both the conditions. Gene ontology and
KEEG pathway analysis of proteins from infected lung epithelial cells showed proteins from
cytoskeleton rearrangement, transport, transcription and signal transduction pathways, such as
Jak/Stat, NOD like receptor signaling, Toll–like receptor signaling, NF-kβ signaling and TNF
signaling pathways. These signaling proteins suggested the strong immune response in lung
epithelial cells against A. terreus conidia. Also, cytoskeleton rearrangement proteins depicted the
internalization of A. terreus conidia by human lung epithelial cells.
Conclusion:
Our study has contributed to understand the interaction response of human lung
epithelial cells during A. terreus infection. Also, our study may facilitate the identification of
inflammatory biomarker against A. terreus.
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Affiliation(s)
- R. Thakur
- Genomic Laboratory, Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat Solan-173234 Himachal Pradesh, India
| | - J. Shankar
- Genomic Laboratory, Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat Solan-173234 Himachal Pradesh, India
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23
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Culibrk L, Croft CA, Toor A, Yang SJ, Singhera GK, Dorscheid DR, Moore MM, Tebbutt SJ. Phagocytosis of Aspergillus fumigatus by Human Bronchial Epithelial Cells Is Mediated by the Arp2/3 Complex and WIPF2. Front Cell Infect Microbiol 2019; 9:16. [PMID: 30792969 PMCID: PMC6375057 DOI: 10.3389/fcimb.2019.00016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/17/2019] [Indexed: 12/01/2022] Open
Abstract
Aspergillus fumigatus is an opportunistic fungal pathogen capable of causing severe infection in humans. One of the limitations in our understanding of how A. fumigatus causes infection concerns the initial stages of infection, notably the initial interaction between inhaled spores or conidia and the human airway. Using publicly-available datasets, we identified the Arp2/3 complex and the WAS-Interacting Protein Family Member 2 WIPF2 as being potentially responsible for internalization of conidia by airway epithelial cells. Using a cell culture model, we demonstrate that RNAi-mediated knockdown of WIPF2 significantly reduces internalization of conidia into airway epithelial cells. Furthermore, we demonstrate that inhibition of Arp2/3 by a small molecule inhibitor causes similar effects. Using super-resolution fluorescence microscopy, we demonstrate that WIPF2 is transiently localized to the site of bound conidia. Overall, we demonstrate the active role of the Arp2/3 complex and WIPF2 in mediating the internalization of A. fumigatus conidia into human airway epithelial cells.
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Affiliation(s)
- Luka Culibrk
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital, Vancouver, BC, Canada
| | - Carys A Croft
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital, Vancouver, BC, Canada
| | - Amreen Toor
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital, Vancouver, BC, Canada.,Department of Graduate Studies, Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
| | - S Jasemine Yang
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital, Vancouver, BC, Canada.,Department of Graduate Studies, Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Gurpreet K Singhera
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital, Vancouver, BC, Canada.,Divison of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Delbert R Dorscheid
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital, Vancouver, BC, Canada.,Divison of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,Divison of Critical Care Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Margo M Moore
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Scott J Tebbutt
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital, Vancouver, BC, Canada.,Divison of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,Prevention of Organ Failure Centre of Excellence, Vancouver, BC, Canada
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24
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Toor A, Culibrk L, Singhera GK, Moon KM, Prudova A, Foster LJ, Moore MM, Dorscheid DR, Tebbutt SJ. Transcriptomic and proteomic host response to Aspergillus fumigatus conidia in an air-liquid interface model of human bronchial epithelium. PLoS One 2018; 13:e0209652. [PMID: 30589860 PMCID: PMC6307744 DOI: 10.1371/journal.pone.0209652] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 12/10/2018] [Indexed: 12/31/2022] Open
Abstract
Aspergillus fumigatus (A. fumigatus) is a wide-spread fungus that is a potent allergen in hypersensitive individuals but also an opportunistic pathogen in immunocompromised patients. It reproduces asexually by releasing airborne conidiospores (conidia). Upon inhalation, fungal conidia are capable of reaching the airway epithelial cells (AECs) in bronchial and alveolar tissues. Previous studies have predominantly used submerged monolayer cultures for studying this host-pathogen interaction; however, these cultures do not recapitulate the mucocililary differentiation phenotype of the in vivo epithelium in the respiratory tract. Thus, the aim of this study was to use well-differentiated primary human bronchial epithelial cells (HBECs) grown at the air-liquid interface (ALI) to determine their transcriptomic and proteomic responses following interaction with A. fumigatus conidia. We visualized conidial interaction with HBECs using confocal laser scanning microscopy (CLSM), and applied NanoString nCounter and shotgun proteomics to assess gene expression changes in the human cells upon interaction with A. fumigatus conidia. Western blot analysis was used to assess the expression of top three differentially expressed proteins, CALR, SET and NUCB2. CLSM showed that, unlike submerged monolayer cultures, well-differentiated ALI cultures of primary HBECs were estimated to internalize less than 1% of bound conidia. Nevertheless, transcriptomic and proteomic analyses revealed numerous differentially expressed host genes; these were enriched for pathways including apoptosis/autophagy, translation, unfolded protein response and cell cycle (up-regulated); complement and coagulation pathways, iron homeostasis, nonsense mediated decay and rRNA binding (down-regulated). CALR and SET were confirmed to be up-regulated in ALI cultures of primary HBECs upon exposure to A. fumigatus via western blot analysis. Therefore, using transcriptomics and proteomics approaches, ALI models recapitulating the bronchial epithelial barrier in the conductive zone of the respiratory tract can provide novel insights to the molecular response of bronchial epithelial cells upon exposure to A. fumigatus conidia.
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Affiliation(s)
- Amreen Toor
- Experimental Medicine, University of British Columbia, Vancouver, Canada
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, Canada
| | - Luka Culibrk
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, Canada
| | - Gurpreet K. Singhera
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, Canada
| | - Kyung-Mee Moon
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Anna Prudova
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Margo M. Moore
- Department of Biological Sciences, Simon Fraser University, Burnaby, Canada
| | - Delbert R. Dorscheid
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, Canada
| | - Scott J. Tebbutt
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, Canada
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25
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Shankar J, Cerqueira GC, Wortman JR, Clemons KV, Stevens DA. RNA-Seq Profile Reveals Th-1 and Th-17-Type of Immune Responses in Mice Infected Systemically with Aspergillus fumigatus. Mycopathologia 2018; 183:645-658. [PMID: 29500637 PMCID: PMC6067991 DOI: 10.1007/s11046-018-0254-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/19/2018] [Indexed: 01/15/2023]
Abstract
With the increasing numbers of immunocompromised hosts, Aspergillus fumigatus emerges as a lethal opportunistic fungal pathogen. Understanding innate and acquired immunity responses of the host is important for a better therapeutic strategy to deal with aspergillosis patients. To determine the transcriptome in the kidneys in aspergillosis, we employed RNA-Seq to obtain single 76-base reads of whole-genome transcripts of murine kidneys on a temporal basis (days 0; uninfected, 1, 2, 3 and 8) during invasive aspergillosis. A total of 6284 transcripts were downregulated, and 5602 were upregulated compared to baseline expression. Gene ontology enrichment analysis identified genes involved in innate and adaptive immune response, as well as iron binding and homeostasis, among others. Our results showed activation of pathogen recognition receptors, e.g., β-defensins, C-type lectins (e.g., dectin-1), Toll-like receptors (TLR-2, TLR-3, TLR-8, TLR-9 and TLR-13), as well as Ptx-3 and C-reactive protein among the soluble receptors. Upregulated transcripts encoding various differentiating cytokines and effector proinflammatory cytokines, as well as those encoding for chemokines and chemokine receptors, revealed Th-1 and Th-17-type immune responses. These studies form a basic dataset for experimental prioritization, including other target organs, to determine the global response of the host against Aspergillus infection.
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Affiliation(s)
- Jata Shankar
- Jaypee University of Information Technology, Solan, HP, India
- California Institute for Medical Research, San Jose, CA, USA
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | | | | | - Karl V Clemons
- California Institute for Medical Research, San Jose, CA, USA.
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.
| | - David A Stevens
- California Institute for Medical Research, San Jose, CA, USA
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
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26
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Escobar N, Valdes ID, Keizer EM, Ordonez SR, Ohm RA, Wösten HAB, de Cock H. Expression profile analysis reveals that Aspergillus fumigatus but not Aspergillus niger makes type II epithelial lung cells less immunological alert. BMC Genomics 2018; 19:534. [PMID: 30005605 PMCID: PMC6044037 DOI: 10.1186/s12864-018-4895-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/25/2018] [Indexed: 12/17/2022] Open
Abstract
Background Aspergillus fumigatus is the main causative agent of aspergillosis. Infections rarely occur in immunocompetent individuals, indicating efficient clearance of conidia by pulmonary defense mechanisms. Other aspergilli like Aspergillus niger also cause infections but to a much lesser extent. Our previous studies showed that A. fumigatus and A. niger have different behavior in the presence of type II alveolar A549 epithelial cells. A. fumigatus conidia are more efficiently internalized by these cells and germination is delayed when compared to A. niger. In addition, hyphae that have escaped the epithelial cells grow parallel to the epithelium, while A. niger grows away from this cell layer. Results Here it is shown that global gene expression of A. fumigatus and A. niger is markedly different upon contact with A549 cells. A total of 545 and 473 genes of A. fumigatus and A. niger, respectively, were differentially expressed when compared to growth in the absence of A549 cells. Notably, only 53 genes (approximately 10%) were shared in these gene sets. The different response was also illustrated by the fact that only 4 out of 75 GO terms were shared that were enriched in the differentially expressed gene sets. The orthologues of A. fumigatus genes involved in hypoxia regulation and heat shock were also up-regulated in A. niger, whereas thioredoxin reductase and allergen genes were found up-regulated in A. fumigatus but down-regulated in A. niger. Infection with A. fumigatus resulted in only 62 up and 47 down-regulated genes in A549. These numbers were 17 and 34 in the case of A. niger. GO terms related with immune response were down-regulated upon exposure to A. fumigatus but not in the case of A. niger. This indicates that A. fumigatus reprograms A549 to be less immunologically alert. Conclusions Our dual transcriptomic analysis supports earlier observations of a marked difference in life style between A. fumigatus and A. niger when grown in the presence of type II epithelial cells. The results indicate important differences in gene expression, amongst others down regulation of immune response genes in lung epithelial cells by A. fumigatus but not by A niger. Electronic supplementary material The online version of this article (10.1186/s12864-018-4895-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Natalia Escobar
- Microbiology & Institute of Biomembranes, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Ivan D Valdes
- Microbiology & Institute of Biomembranes, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Esther M Keizer
- Microbiology & Institute of Biomembranes, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Soledad R Ordonez
- Department of Infectious Diseases and Immunology, Division Molecular Host Defence, Utrecht University, Yalelaan 1, 3584CL, Utrecht, The Netherlands
| | - Robin A Ohm
- Microbiology & Institute of Biomembranes, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Han A B Wösten
- Microbiology & Institute of Biomembranes, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Hans de Cock
- Microbiology & Institute of Biomembranes, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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27
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Fernandes J, Hamidi F, Leborgne R, Beau R, Castier Y, Mordant P, Boukkerou A, Latgé JP, Pretolani M. Penetration of the Human Pulmonary Epithelium by Aspergillus fumigatus Hyphae. J Infect Dis 2018; 218:1306-1313. [DOI: 10.1093/infdis/jiy298] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 05/23/2018] [Indexed: 12/12/2022] Open
Affiliation(s)
- Julien Fernandes
- INSERM UMR1152, Physiopathologie et Epidémiologie des Maladies Respiratoires, Paris, France
- Université Paris Diderot, Sorbonne Paris-Cité, Faculté de Médecine, site Bichat, France
- Laboratory of Excellence INFLAMEX, Université Sorbonne Paris-Cité, France
- Département Hospitalo-Universitaire FIRE, Paris, France
| | - Fatima Hamidi
- INSERM UMR1152, Physiopathologie et Epidémiologie des Maladies Respiratoires, Paris, France
- Université Paris Diderot, Sorbonne Paris-Cité, Faculté de Médecine, site Bichat, France
- Laboratory of Excellence INFLAMEX, Université Sorbonne Paris-Cité, France
- Département Hospitalo-Universitaire FIRE, Paris, France
| | - Remi Leborgne
- ImagoSeine Electron Microscopy Facility, Institut Jacques Monod, Centre National de la Recherche Scientifique UMR 7592, Université Paris Diderot, Sorbonne Paris-Cité, France
| | - Remi Beau
- Unité des Aspergillus, Institut Pasteur, Paris, France
| | - Yves Castier
- INSERM UMR1152, Physiopathologie et Epidémiologie des Maladies Respiratoires, Paris, France
- Université Paris Diderot, Sorbonne Paris-Cité, Faculté de Médecine, site Bichat, France
- Laboratory of Excellence INFLAMEX, Université Sorbonne Paris-Cité, France
- Département Hospitalo-Universitaire FIRE, Paris, France
- Service de Chirurgie Thoracique, Groupement Hospitalier Universitaire Nord Bichat-Claude Bernard, Assistance Publique des Hopitaux de Paris, France
| | - Pierre Mordant
- INSERM UMR1152, Physiopathologie et Epidémiologie des Maladies Respiratoires, Paris, France
- Université Paris Diderot, Sorbonne Paris-Cité, Faculté de Médecine, site Bichat, France
- Laboratory of Excellence INFLAMEX, Université Sorbonne Paris-Cité, France
- Département Hospitalo-Universitaire FIRE, Paris, France
- Service de Chirurgie Thoracique, Groupement Hospitalier Universitaire Nord Bichat-Claude Bernard, Assistance Publique des Hopitaux de Paris, France
| | - Amira Boukkerou
- INSERM UMR1152, Physiopathologie et Epidémiologie des Maladies Respiratoires, Paris, France
- Université Paris Diderot, Sorbonne Paris-Cité, Faculté de Médecine, site Bichat, France
- Laboratory of Excellence INFLAMEX, Université Sorbonne Paris-Cité, France
- Département Hospitalo-Universitaire FIRE, Paris, France
| | | | - Marina Pretolani
- INSERM UMR1152, Physiopathologie et Epidémiologie des Maladies Respiratoires, Paris, France
- Université Paris Diderot, Sorbonne Paris-Cité, Faculté de Médecine, site Bichat, France
- Laboratory of Excellence INFLAMEX, Université Sorbonne Paris-Cité, France
- Département Hospitalo-Universitaire FIRE, Paris, France
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28
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Schneider A, Blatzer M, Posch W, Schubert R, Lass-Flörl C, Schmidt S, Lehrnbecher T. Aspergillus fumigatus responds to natural killer (NK) cells with upregulation of stress related genes and inhibits the immunoregulatory function of NK cells. Oncotarget 2018; 7:71062-71071. [PMID: 27738337 PMCID: PMC5342063 DOI: 10.18632/oncotarget.12616] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 09/17/2016] [Indexed: 11/25/2022] Open
Abstract
Natural Killer (NK) cells are active against Aspergillus fumigatus, which in turn is able to impair the host defense. Unfortunately, little is known on the mutual interaction of NK cells and A. fumigatus. We coincubated human NK cells with A. fumigatus hyphae and assessed the gene expression and protein concentration of selected molecules. We found that A. fumigatus up-regulates the gene expression of pro-inflammatory molecules in NK cells, but inhibited the release of these molecules resulting in intracellular accumulation and limited extracellular availability. A. fumigatus down-regulatedmRNA levels of perforin in NK cells, but increased its intra- and extracellular protein concentration. The gene expression of stress related molecules of A. fumigatus such as heat shock protein hsp90 was up-regulated by human NK cells. Our data characterize for the first time the immunosuppressive effect of A. fumigatus on NK cells and may help to develop new therapeutic antifungal strategies.
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Affiliation(s)
- Andreas Schneider
- Division of Pediatric Hematology and Oncology, Hospital for Children and Adolescents, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Michael Blatzer
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Wilfried Posch
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ralf Schubert
- Division of Pediatric Pulmonology, Allergology and Cystic Fibrosis, Hospital for Children and Adolescents, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Stanislaw Schmidt
- Division of Pediatric Hematology and Oncology, Hospital for Children and Adolescents, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Thomas Lehrnbecher
- Division of Pediatric Hematology and Oncology, Hospital for Children and Adolescents, Johann Wolfgang Goethe-University, Frankfurt, Germany
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29
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Watkins TN, Liu H, Chung M, Hazen TH, Dunning Hotopp JC, Filler SG, Bruno VM. Comparative transcriptomics of Aspergillus fumigatus strains upon exposure to human airway epithelial cells. Microb Genom 2018; 4. [PMID: 29345613 PMCID: PMC5857381 DOI: 10.1099/mgen.0.000154] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aspergillus fumigatus is an opportunistic, ubiquitous, saprophytic mould that can cause severe allergic responses in atopic individuals as well as life-threatening infections in immunocompromised patients. A critical step in the establishment of infection is the invasion of airway epithelial cells by the inhaled fungi. Understanding how A. fumigatus senses and responds to airway cells is important to understand the pathogenesis of invasive pulmonary aspergillosis. Here, we analysed the transcriptomes of two commonly used clinical isolates, Af293 and CEA10, during infection of the A549 type II pneumocyte cell line in vitro. We focused our RNA-seq analysis on the core set of genes that are present in the genomes of the two strains. Our results suggest that: (a) A. fumigatus does not mount a conserved transcriptional response to airway epithelial cells in our in vitro model and (b) strain background and time spent in the tissue culture media have a greater impact on the transcriptome than the presence of host cells. Our analyses reveal both common and strain-specific transcriptional programmes that allow for the generation of hypotheses about gene function as it pertains to pathogenesis and the significant phenotypic heterogeneity that is observed among A. fumigatus isolates.
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Affiliation(s)
- Tonya N Watkins
- 1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hong Liu
- 2Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Matthew Chung
- 1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tracy H Hazen
- 1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Julie C Dunning Hotopp
- 1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Scott G Filler
- 2Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA.,3David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Vincent M Bruno
- 1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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30
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Bertuzzi M, Hayes GE, Icheoku UJ, van Rhijn N, Denning DW, Osherov N, Bignell EM. Anti-Aspergillus Activities of the Respiratory Epithelium in Health and Disease. J Fungi (Basel) 2018; 4:E8. [PMID: 29371501 PMCID: PMC5872311 DOI: 10.3390/jof4010008] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/03/2018] [Accepted: 01/05/2018] [Indexed: 02/06/2023] Open
Abstract
Respiratory epithelia fulfil multiple roles beyond that of gaseous exchange, also acting as primary custodians of lung sterility and inflammatory homeostasis. Inhaled fungal spores pose a continual antigenic, and potentially pathogenic, challenge to lung integrity against which the human respiratory mucosa has developed various tolerance and defence strategies. However, respiratory disease and immune dysfunction frequently render the human lung susceptible to fungal diseases, the most common of which are the aspergilloses, a group of syndromes caused by inhaled spores of Aspergillus fumigatus. Inhaled Aspergillus spores enter into a multiplicity of interactions with respiratory epithelia, the mechanistic bases of which are only just becoming recognized as important drivers of disease, as well as possible therapeutic targets. In this mini-review we examine current understanding of Aspergillus-epithelial interactions and, based upon the very latest developments in the field, we explore two apparently opposing schools of thought which view epithelial uptake of Aspergillus spores as either a curative or disease-exacerbating event.
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Affiliation(s)
- Margherita Bertuzzi
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, UK.
| | - Gemma E Hayes
- Northern Devon Healthcare NHS Trust, North Devon District Hospital, Raleigh Park, Barnstaple EX31 4JB, UK.
| | - Uju J Icheoku
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, UK.
| | - Norman van Rhijn
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, UK.
| | - David W Denning
- The National Aspergillosis Centre, Education and Research Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester M23 9LT, UK.
| | - Nir Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Elaine M Bignell
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, UK.
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31
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Fungi in Bronchiectasis: A Concise Review. Int J Mol Sci 2018; 19:ijms19010142. [PMID: 29300314 PMCID: PMC5796091 DOI: 10.3390/ijms19010142] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 12/29/2017] [Accepted: 12/31/2017] [Indexed: 12/13/2022] Open
Abstract
Although the spectrum of fungal pathology has been studied extensively in immunosuppressed patients, little is known about the epidemiology, risk factors, and management of fungal infections in chronic pulmonary diseases like bronchiectasis. In bronchiectasis patients, deteriorated mucociliary clearance—generally due to prior colonization by bacterial pathogens—and thick mucosity propitiate, the persistence of fungal spores in the respiratory tract. The most prevalent fungi in these patients are Candida albicans and Aspergillus fumigatus; these are almost always isolated with bacterial pathogens like Haemophillus influenzae and Pseudomonas aeruginosa, making very difficult to define their clinical significance. Analysis of the mycobiome enables us to detect a greater diversity of microorganisms than with conventional cultures. The results have shown a reduced fungal diversity in most chronic respiratory diseases, and that this finding correlates with poorer lung function. Increased knowledge of both the mycobiome and the complex interactions between the fungal, viral, and bacterial microbiota, including mycobacteria, will further our understanding of the mycobiome’s relationship with the pathogeny of bronchiectasis and the development of innovative therapies to combat it.
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32
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Vermeulen E, Carpentier S, Kniemeyer O, Sillen M, Maertens J, Lagrou K. Proteomic Differences between Azole-Susceptible and -Resistant <i>Aspergillus fumigatus</i> Strains. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/aim.2018.81007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Guruceaga X, Ezpeleta G, Mayayo E, Sueiro-Olivares M, Abad-Diaz-De-Cerio A, Aguirre Urízar JM, Liu HG, Wiemann P, Bok JW, Filler SG, Keller NP, Hernando FL, Ramirez-Garcia A, Rementeria A. A possible role for fumagillin in cellular damage during host infection by Aspergillus fumigatus. Virulence 2018; 9:1548-1561. [PMID: 30251593 PMCID: PMC6177242 DOI: 10.1080/21505594.2018.1526528] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 09/10/2018] [Indexed: 01/31/2023] Open
Abstract
Virulence mechanisms of the pathogenic fungus Aspergillus fumigatus are multifactorial and depend on the immune state of the host, but little is known about the fungal mechanism that develops during the process of lung invasion. In this study, microarray technology was combined with a histopathology evaluation of infected lungs so that the invasion strategy followed by the fungus could be described. To achieve this, an intranasal mice infection was performed to extract daily fungal samples from the infected lungs over four days post-infection. The pathological study revealed a heavy fungal progression throughout the lung, reaching the blood vessels on the third day after exposure and causing tissue necrosis. One percent of the fungal genome followed a differential expression pattern during this process. Strikingly, most of the genes of the intertwined fumagillin/pseurotin biosynthetic gene cluster were upregulated as were genes encoding lytic enzymes such as lipases, proteases (DppIV, DppV, Asp f 1 or Asp f 5) and chitinase (chiB1) as well as three genes related with pyomelanin biosynthesis process. Furthermore, we demonstrate that fumagillin is produced in an in vitro pneumocyte cell line infection model and that loss of fumagillin synthesis reduces epithelial cell damage. These results suggest that fumagillin contributes to tissue damage during invasive aspergillosis. Therefore, it is probable that A. fumigatus progresses through the lungs via the production of the mycotoxin fumagillin combined with the secretion of lytic enzymes that allow fungal growth, angioinvasion and the disruption of the lung parenchymal structure.
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Affiliation(s)
- Xabier Guruceaga
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Guillermo Ezpeleta
- Preventive Medicine and Hospital Hygiene Service, Complejo Hospitalario de Navarra, Pamplona, Spain
- Department of Preventive Medicine and Public Health, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Emilio Mayayo
- Pathology Unit, Medicine and Health Science Faculty, University of Rovira i Virgili, Reus, Tarragona, Spain
| | - Monica Sueiro-Olivares
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Ana Abad-Diaz-De-Cerio
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - José Manuel Aguirre Urízar
- Department of Stomatology II, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Hong G. Liu
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Scott G. Filler
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Fernando L. Hernando
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Andoni Ramirez-Garcia
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Aitor Rementeria
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
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Ries LNA, Beattie S, Cramer RA, Goldman GH. Overview of carbon and nitrogen catabolite metabolism in the virulence of human pathogenic fungi. Mol Microbiol 2017; 107:277-297. [PMID: 29197127 DOI: 10.1111/mmi.13887] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/20/2017] [Accepted: 11/23/2017] [Indexed: 12/12/2022]
Abstract
It is estimated that fungal infections, caused most commonly by Candida albicans, Aspergillus fumigatus and Cryptococcus neoformans, result in more deaths annually than malaria or tuberculosis. It has long been hypothesized the fungal metabolism plays a critical role in virulence though specific nutrient sources utilized by human pathogenic fungi in vivo has remained enigmatic. However, the metabolic utilisation of preferred carbon and nitrogen sources, encountered in a host niche-dependent manner, is known as carbon catabolite and nitrogen catabolite repression (CCR, NCR), and has been shown to be important for virulence. Several sensory and uptake systems exist, including carbon and nitrogen source-specific sensors and transporters, that allow scavenging of preferred nutrient sources. Subsequent metabolic utilisation is governed by transcription factors, whose functions and essentiality differ between fungal species. Furthermore, additional factors exist that contribute to the implementation of CCR and NCR. The role of the CCR and NCR-related factors in virulence varies greatly between fungal species and a substantial gap in knowledge exists regarding specific pathways. Further elucidation of carbon and nitrogen metabolism mechanisms is therefore required in a fungal species- and animal model-specific manner in order to screen for targets that are potential candidates for anti-fungal drug development.
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Affiliation(s)
- Laure Nicolas Annick Ries
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, Ribeirão Preto, São Paulo, 3900, CEP 14049-900, Brazil
| | - Sarah Beattie
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, 74 College Street Remsen 213, Hanover, NH 03755, USA
| | - Robert A Cramer
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, 74 College Street Remsen 213, Hanover, NH 03755, USA
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n°, Ribeirão Preto, São Paulo, CEP 14040903, Brazil
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Takahashi-Nakaguchi A, Sakai K, Takahashi H, Hagiwara D, Toyotome T, Chibana H, Watanabe A, Yaguchi T, Yamaguchi M, Kamei K, Gonoi T. Aspergillus fumigatus adhesion factors in dormant conidia revealed through comparative phenotypic and transcriptomic analyses. Cell Microbiol 2017; 20. [PMID: 29113011 PMCID: PMC5838799 DOI: 10.1111/cmi.12802] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/11/2017] [Accepted: 10/30/2017] [Indexed: 01/29/2023]
Abstract
Aspergillus fumigatus is an important fungal pathogen of humans. Inhaled conidia of A. fumigatus adhere to pulmonary epithelial cells, causing opportunistic infection. However, little is known about the molecular mechanism of the adherence of resting conidia. Fungal molecules adhesive to host cells are presumed to be displayed on the conidial surface during conidial formation as a result of changes in gene expression. Therefore, we exhaustively searched for adhesion molecules by comparing the phenotypes and the gene expression profiles of A. fumigatus strains that have conidia showing either high or low adherence to human pulmonary A549 cells. Morphological observation suggested that strains that produce conidia of reduced size, hydrophobicity, or number show decreased adherence to A549 cells. K-means cluster analyses of gene expression revealed 31 genes that were differentially expressed in the high-adherence strains during conidial formation. We knocked out three of these genes and showed that the conidia of AFUA_4G01030 (encoding a hypothetical protein) and AFUA_4G08805 (encoding a haemolysin-like protein) knockout strains had significantly reduced adherence to host cells. Furthermore, the conidia of these knockout strains had lower hydrophobicity and fewer surface spikes compared to the control strain. We suggest that the selectively expressed gene products, including those we identified experimentally, have composite synergistic roles in the adhesion of conidia to pulmonary epithelial cells.
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Affiliation(s)
| | - Kanae Sakai
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Daisuke Hagiwara
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | | | - Hiroji Chibana
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Akira Watanabe
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Takashi Yaguchi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | | | - Katsuhiko Kamei
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Tohru Gonoi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
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Kale SD, Ayubi T, Chung D, Tubau-Juni N, Leber A, Dang HX, Karyala S, Hontecillas R, Lawrence CB, Cramer RA, Bassaganya-Riera J. Modulation of Immune Signaling and Metabolism Highlights Host and Fungal Transcriptional Responses in Mouse Models of Invasive Pulmonary Aspergillosis. Sci Rep 2017; 7:17096. [PMID: 29213115 PMCID: PMC5719083 DOI: 10.1038/s41598-017-17000-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/20/2017] [Indexed: 02/04/2023] Open
Abstract
Incidences of invasive pulmonary aspergillosis, an infection caused predominantly by Aspergillus fumigatus, have increased due to the growing number of immunocompromised individuals. While A. fumigatus is reliant upon deficiencies in the host to facilitate invasive disease, the distinct mechanisms that govern the host-pathogen interaction remain enigmatic, particularly in the context of distinct immune modulating therapies. To gain insights into these mechanisms, RNA-Seq technology was utilized to sequence RNA derived from lungs of 2 clinically relevant, but immunologically distinct murine models of IPA on days 2 and 3 post inoculation when infection is established and active disease present. Our findings identify notable differences in host gene expression between the chemotherapeutic and steroid models at the interface of immunity and metabolism. RT-qPCR verified model specific and nonspecific expression of 23 immune-associated genes. Deep sequencing facilitated identification of highly expressed fungal genes. We utilized sequence similarity and gene expression to categorize the A. fumigatus putative in vivo secretome. RT-qPCR suggests model specific gene expression for nine putative fungal secreted proteins. Our analysis identifies contrasting responses by the host and fungus from day 2 to 3 between the two models. These differences may help tailor the identification, development, and deployment of host- and/or fungal-targeted therapeutics.
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Affiliation(s)
- Shiv D Kale
- Nutrional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute of Virginia Tech., Blacksburg, VA, 24061, USA.
| | - Tariq Ayubi
- Nutrional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute of Virginia Tech., Blacksburg, VA, 24061, USA
| | - Dawoon Chung
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
- National Marine Biodiversity Institute of Korea, Seochun-gun, 33662, Republic of Korea
| | - Nuria Tubau-Juni
- Nutrional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute of Virginia Tech., Blacksburg, VA, 24061, USA
| | - Andrew Leber
- Nutrional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute of Virginia Tech., Blacksburg, VA, 24061, USA
| | - Ha X Dang
- Nutrional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute of Virginia Tech., Blacksburg, VA, 24061, USA
- McDonnell Genome Institute at Washington University, St. Louis, MO, 63108, USA
| | - Saikumar Karyala
- Nutrional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute of Virginia Tech., Blacksburg, VA, 24061, USA
| | - Raquel Hontecillas
- Nutrional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute of Virginia Tech., Blacksburg, VA, 24061, USA
| | | | - Robert A Cramer
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Josep Bassaganya-Riera
- Nutrional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute of Virginia Tech., Blacksburg, VA, 24061, USA
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Takahashi H, Kusuya Y, Hagiwara D, Takahashi-Nakaguchi A, Sakai K, Gonoi T. Global gene expression reveals stress-responsive genes in Aspergillus fumigatus mycelia. BMC Genomics 2017; 18:942. [PMID: 29202712 PMCID: PMC5715996 DOI: 10.1186/s12864-017-4316-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/17/2017] [Indexed: 11/10/2022] Open
Abstract
Background Aspergillus fumigatus is a human fungal pathogen that causes aspergillosis in immunocompromised hosts. A. fumigatus is believed to be exposed to diverse environmental stresses in the host cells. The adaptation mechanisms are critical for infections in human bodies. Transcriptional networks in response to diverse environmental challenges remain to be elucidated. To gain insights into the adaptation to environmental stresses in A. fumigatus mycelia, we conducted time series transcriptome analyses. Results With the aid of RNA-seq, we explored the global gene expression profiles of mycelia in A. fumigatus upon exposure to diverse environmental changes, including heat, superoxide, and osmotic stresses. From the perspective of global transcriptomes, transient responses to superoxide and osmotic stresses were observed while responses to heat stresses were gradual. We identified the stress-responsive genes for particular stresses, and the 266 genes whose expression levels drastically fluctuated upon exposure to all tested stresses. Among these, the 77 environmental stress response genes are conserved in S. cerevisiae, suggesting that these genes might be more general prerequisites for adaptation to environmental stresses. Finally, we revealed the strong correlations among expression profiles of genes related to ‘rRNA processing’. Conclusions The time series transcriptome analysis revealed the stress-responsive genes underlying the adaptation mechanisms in A. fumigatus mycelia. These results will shed light on the regulatory networks underpinning the adaptation of the filamentous fungi. Electronic supplementary material The online version of this article (10.1186/s12864-017-4316-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan. .,Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan.
| | - Yoko Kusuya
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
| | - Daisuke Hagiwara
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
| | | | - Kanae Sakai
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
| | - Tohru Gonoi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
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Marsh JW, Humphrys MS, Myers GSA. A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro. Front Microbiol 2017; 8:1830. [PMID: 28983295 PMCID: PMC5613115 DOI: 10.3389/fmicb.2017.01830] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/06/2017] [Indexed: 12/15/2022] Open
Abstract
Dual RNA-Sequencing leverages established next-generation sequencing (NGS)-enabled RNA-Seq approaches to measure genome-wide transcriptional changes of both an infecting bacteria and host cells. By simultaneously investigating both organisms from the same biological sample, dual RNA-Seq can provide unique insight into bacterial infection processes and reciprocal host responses at once. However, the difficulties involved in handling both prokaryotic and eukaryotic material require distinct, optimized procedures. We previously developed and applied dual RNA-Seq to measure prokaryotic and eukaryotic expression profiles of human cells infected with bacteria, using in vitro Chlamydia-infected epithelial cells as proof of principle. Here we provide a detailed laboratory protocol for in vitro dual RNA-Seq that is readily adaptable to any host-bacteria system of interest.
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Affiliation(s)
- James W Marsh
- School of Life Sciences, The ithree institute, University of Technology SydneyUltimo, NSW, Australia
| | - Michael S Humphrys
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimore, MD, United States
| | - Garry S A Myers
- School of Life Sciences, The ithree institute, University of Technology SydneyUltimo, NSW, Australia
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Macheleidt J, Mattern DJ, Fischer J, Netzker T, Weber J, Schroeckh V, Valiante V, Brakhage AA. Regulation and Role of Fungal Secondary Metabolites. Annu Rev Genet 2016; 50:371-392. [DOI: 10.1146/annurev-genet-120215-035203] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Juliane Macheleidt
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
| | - Derek J. Mattern
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
- Institute for Microbiology, Friedrich Schiller University Jena, 07737 Jena, Germany
| | - Juliane Fischer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
- Institute for Microbiology, Friedrich Schiller University Jena, 07737 Jena, Germany
| | - Tina Netzker
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
- Institute for Microbiology, Friedrich Schiller University Jena, 07737 Jena, Germany
| | - Jakob Weber
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
- Institute for Microbiology, Friedrich Schiller University Jena, 07737 Jena, Germany
| | - Volker Schroeckh
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
| | - Vito Valiante
- Research Group Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology (HKI), 07745 Jena, Germany;
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
- Institute for Microbiology, Friedrich Schiller University Jena, 07737 Jena, Germany
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de Castro PA, Chiaratto J, Morais ER, Dos Reis TF, Mitchell TK, Brown NA, Goldman GH. The putative flavin carrier family FlcA-C is important for Aspergillus fumigatus virulence. Virulence 2016; 8:797-809. [PMID: 27652896 DOI: 10.1080/21505594.2016.1239010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Aspergillus fumigatus is an opportunistic fungal pathogen and the most important species causing pulmonary fungal infections. The signaling by calcium is very important for A. fumigatus pathogenicity and it is regulated by the transcription factor CrzA. We have previously used used ChIP-seq (Chromatin Immunoprecipitation DNA sequencing) aiming to identify gene targets regulated by CrzA. We have identified among several genes regulated by calcium stress, the putative flavin transporter, flcA. This transporter belongs to a small protein family composed of FlcA, B, and C. The ΔflcA null mutant showed several phenotypes, such as morphological defects, increased sensitivity to calcium chelating-agent ethylene glycol tetraacetic acid (EGTA), cell wall or oxidative damaging agents and metals, repre-sentative of deficiencies in calcium signaling and iron homeostasis. Increasing calcium concentrations improved significantly the ΔflcA growth and conidiation, indicating that ΔflcA mutant has calcium insufficiency. Finally, ΔflcA-C mutants showed reduced flavin adenine dinucleotide (FAD) and were avirulent in a low dose murine infection model.
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Affiliation(s)
- Patrícia A de Castro
- a Faculdade de Ciências Farmacêuticas de Ribeirão Preto and Faculdade de Medicina de Ribeirão Preto , Universidade de São Paulo , Ribeirão Preto , Brazil
| | - Jéssica Chiaratto
- a Faculdade de Ciências Farmacêuticas de Ribeirão Preto and Faculdade de Medicina de Ribeirão Preto , Universidade de São Paulo , Ribeirão Preto , Brazil
| | - Enyara Rezende Morais
- a Faculdade de Ciências Farmacêuticas de Ribeirão Preto and Faculdade de Medicina de Ribeirão Preto , Universidade de São Paulo , Ribeirão Preto , Brazil
| | - Thaila Fernanda Dos Reis
- a Faculdade de Ciências Farmacêuticas de Ribeirão Preto and Faculdade de Medicina de Ribeirão Preto , Universidade de São Paulo , Ribeirão Preto , Brazil
| | - Thomas K Mitchell
- b Department of Plant Pathology , The Ohio State University , Columbus , OH , USA
| | - Neil A Brown
- c Plant Biology and Crop Science, Rothamsted Research , Harpenden, Herts , UK
| | - Gustavo H Goldman
- a Faculdade de Ciências Farmacêuticas de Ribeirão Preto and Faculdade de Medicina de Ribeirão Preto , Universidade de São Paulo , Ribeirão Preto , Brazil
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Croft CA, Culibrk L, Moore MM, Tebbutt SJ. Interactions of Aspergillus fumigatus Conidia with Airway Epithelial Cells: A Critical Review. Front Microbiol 2016; 7:472. [PMID: 27092126 PMCID: PMC4823921 DOI: 10.3389/fmicb.2016.00472] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/21/2016] [Indexed: 02/05/2023] Open
Abstract
Aspergillus fumigatus is an environmental filamentous fungus that also acts as an opportunistic pathogen able to cause a variety of symptoms, from an allergic response to a life-threatening disseminated fungal infection. The infectious agents are inhaled conidia whose first point of contact is most likely to be an airway epithelial cell (AEC). The interaction between epithelial cells and conidia is multifaceted and complex, and has implications for later steps in pathogenesis. Increasing evidence has demonstrated a key role for the airway epithelium in the response to respiratory pathogens, particularly at early stages of infection; therefore, elucidating the early stages of interaction of conidia with AECs is essential to understand the establishment of infection in cohorts of at-risk patients. Here, we present a comprehensive review of the early interactions between A. fumigatus and AECs, including bronchial and alveolar epithelial cells. We describe mechanisms of adhesion, internalization of conidia by AECs, the immune response of AECs, as well as the role of fungal virulence factors, and patterns of fungal gene expression characteristic of early infection. A clear understanding of the mechanisms involved in the early establishment of infection by A. fumigatus could point to novel targets for therapy and prophylaxis.
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Affiliation(s)
- Carys A Croft
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver BC, Canada
| | - Luka Culibrk
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver BC, Canada
| | - Margo M Moore
- Department of Biological Sciences, Simon Fraser University, Burnaby BC, Canada
| | - Scott J Tebbutt
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, VancouverBC, Canada; Prevention of Organ Failure Centre of Excellence, VancouverBC, Canada; Department of Medicine, Division of Respiratory Medicine, University of British Columbia, VancouverBC, Canada
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Schulze S, Schleicher J, Guthke R, Linde J. How to Predict Molecular Interactions between Species? Front Microbiol 2016; 7:442. [PMID: 27065992 PMCID: PMC4814556 DOI: 10.3389/fmicb.2016.00442] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/18/2016] [Indexed: 12/21/2022] Open
Abstract
Organisms constantly interact with other species through physical contact which leads to changes on the molecular level, for example the transcriptome. These changes can be monitored for all genes, with the help of high-throughput experiments such as RNA-seq or microarrays. The adaptation of the gene expression to environmental changes within cells is mediated through complex gene regulatory networks. Often, our knowledge of these networks is incomplete. Network inference predicts gene regulatory interactions based on transcriptome data. An emerging application of high-throughput transcriptome studies are dual transcriptomics experiments. Here, the transcriptome of two or more interacting species is measured simultaneously. Based on a dual RNA-seq data set of murine dendritic cells infected with the fungal pathogen Candida albicans, the software tool NetGenerator was applied to predict an inter-species gene regulatory network. To promote further investigations of molecular inter-species interactions, we recently discussed dual RNA-seq experiments for host-pathogen interactions and extended the applied tool NetGenerator (Schulze et al., 2015). The updated version of NetGenerator makes use of measurement variances in the algorithmic procedure and accepts gene expression time series data with missing values. Additionally, we tested multiple modeling scenarios regarding the stimuli functions of the gene regulatory network. Here, we summarize the work by Schulze et al. (2015) and put it into a broader context. We review various studies making use of the dual transcriptomics approach to investigate the molecular basis of interacting species. Besides the application to host-pathogen interactions, dual transcriptomics data are also utilized to study mutualistic and commensalistic interactions. Furthermore, we give a short introduction into additional approaches for the prediction of gene regulatory networks and discuss their application to dual transcriptomics data. We conclude that the application of network inference on dual-transcriptomics data is a promising approach to predict molecular inter-species interactions.
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Affiliation(s)
- Sylvie Schulze
- Research Group Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
| | - Jana Schleicher
- Research Group Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
| | - Reinhard Guthke
- Research Group Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
| | - Jörg Linde
- Research Group Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
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Culibrk L, Croft CA, Tebbutt SJ. Systems Biology Approaches for Host-Fungal Interactions: An Expanding Multi-Omics Frontier. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:127-38. [PMID: 26885725 PMCID: PMC4799697 DOI: 10.1089/omi.2015.0185] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Opportunistic fungal infections are an increasing threat for global health, and for immunocompromised patients in particular. These infections are characterized by interaction between fungal pathogen and host cells. The exact mechanisms and the attendant variability in host and fungal pathogen interaction remain to be fully elucidated. The field of systems biology aims to characterize a biological system, and utilize this knowledge to predict the system's response to stimuli such as fungal exposures. A multi-omics approach, for example, combining data from genomics, proteomics, metabolomics, would allow a more comprehensive and pan-optic "two systems" biology of both the host and the fungal pathogen. In this review and literature analysis, we present highly specialized and nascent methods for analysis of multiple -omes of biological systems, in addition to emerging single-molecule visualization techniques that may assist in determining biological relevance of multi-omics data. We provide an overview of computational methods for modeling of gene regulatory networks, including some that have been applied towards the study of an interacting host and pathogen. In sum, comprehensive characterizations of host-fungal pathogen systems are now possible, and utilization of these cutting-edge multi-omics strategies may yield advances in better understanding of both host biology and fungal pathogens at a systems scale.
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Affiliation(s)
- Luka Culibrk
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carys A. Croft
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott J. Tebbutt
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Enguita FJ, Costa MC, Fusco-Almeida AM, Mendes-Giannini MJ, Leitão AL. Transcriptomic Crosstalk between Fungal Invasive Pathogens and Their Host Cells: Opportunities and Challenges for Next-Generation Sequencing Methods. J Fungi (Basel) 2016; 2:jof2010007. [PMID: 29376924 PMCID: PMC5753088 DOI: 10.3390/jof2010007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/12/2015] [Accepted: 12/12/2015] [Indexed: 12/22/2022] Open
Abstract
Fungal invasive infections are an increasing health problem. The intrinsic complexity of pathogenic fungi and the unmet clinical need for new and more effective treatments requires a detailed knowledge of the infection process. During infection, fungal pathogens are able to trigger a specific transcriptional program in their host cells. The detailed knowledge of this transcriptional program will allow for a better understanding of the infection process and consequently will help in the future design of more efficient therapeutic strategies. Simultaneous transcriptomic studies of pathogen and host by high-throughput sequencing (dual RNA-seq) is an unbiased protocol to understand the intricate regulatory networks underlying the infectious process. This protocol is starting to be applied to the study of the interactions between fungal pathogens and their hosts. To date, our knowledge of the molecular basis of infection for fungal pathogens is still very limited, and the putative role of regulatory players such as non-coding RNAs or epigenetic factors remains elusive. The wider application of high-throughput transcriptomics in the near future will help to understand the fungal mechanisms for colonization and survival, as well as to characterize the molecular responses of the host cell against a fungal infection.
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Affiliation(s)
- Francisco J Enguita
- Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, Lisboa 1649-028, Portugal.
| | - Marina C Costa
- Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, Lisboa 1649-028, Portugal.
| | - Ana Marisa Fusco-Almeida
- Núcleo de Proteômica, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista-UNESP, Rodovia Araraquara-Jaú Km 1, Araraquara 14801-902, São Paulo, Brazil.
| | - Maria José Mendes-Giannini
- Núcleo de Proteômica, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista-UNESP, Rodovia Araraquara-Jaú Km 1, Araraquara 14801-902, São Paulo, Brazil.
| | - Ana Lúcia Leitão
- MEtRICs, Departamento de Ciências e Tecnologia da Biomassa, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, Caparica 2829-516, Portugal.
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Challenges and Strategies for Proteome Analysis of the Interaction of Human Pathogenic Fungi with Host Immune Cells. Proteomes 2015; 3:467-495. [PMID: 28248281 PMCID: PMC5217390 DOI: 10.3390/proteomes3040467] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/23/2015] [Accepted: 12/08/2015] [Indexed: 12/17/2022] Open
Abstract
Opportunistic human pathogenic fungi including the saprotrophic mold Aspergillus fumigatus and the human commensal Candida albicans can cause severe fungal infections in immunocompromised or critically ill patients. The first line of defense against opportunistic fungal pathogens is the innate immune system. Phagocytes such as macrophages, neutrophils and dendritic cells are an important pillar of the innate immune response and have evolved versatile defense strategies against microbial pathogens. On the other hand, human-pathogenic fungi have sophisticated virulence strategies to counteract the innate immune defense. In this context, proteomic approaches can provide deeper insights into the molecular mechanisms of the interaction of host immune cells with fungal pathogens. This is crucial for the identification of both diagnostic biomarkers for fungal infections and therapeutic targets. Studying host-fungal interactions at the protein level is a challenging endeavor, yet there are few studies that have been undertaken. This review draws attention to proteomic techniques and their application to fungal pathogens and to challenges, difficulties, and limitations that may arise in the course of simultaneous dual proteome analysis of host immune cells interacting with diverse morphotypes of fungal pathogens. On this basis, we discuss strategies to overcome these multifaceted experimental and analytical challenges including the viability of immune cells during co-cultivation, the increased and heterogeneous protein complexity of the host proteome dynamically interacting with the fungal proteome, and the demands on normalization strategies in terms of relative quantitative proteome analysis.
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Tyrrell J, Callaghan M. Iron acquisition in the cystic fibrosis lung and potential for novel therapeutic strategies. MICROBIOLOGY-SGM 2015; 162:191-205. [PMID: 26643057 DOI: 10.1099/mic.0.000220] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Iron acquisition is vital to microbial survival and is implicated in the virulence of many of the pathogens that reside in the cystic fibrosis (CF) lung. The multifaceted nature of iron acquisition by both bacterial and fungal pathogens encompasses a range of conserved and species-specific mechanisms, including secretion of iron-binding siderophores, utilization of siderophores from other species, release of iron from host iron-binding proteins and haemoproteins, and ferrous iron uptake. Pathogens adapt and deploy specific systems depending on iron availability, bioavailability of the iron pool, stage of infection and presence of competing pathogens. Understanding the dynamics of pathogen iron acquisition has the potential to unveil new avenues for therapeutic intervention to treat both acute and chronic CF infections. Here, we examine the range of strategies utilized by the primary CF pathogens to acquire iron and discuss the different approaches to targeting iron acquisition systems as an antimicrobial strategy.
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Affiliation(s)
- Jean Tyrrell
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Dublin D24KT9, Ireland
| | - Máire Callaghan
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Dublin D24KT9, Ireland
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Chen F, Zhang C, Jia X, Wang S, Wang J, Chen Y, Zhao J, Tian S, Han X, Han L. Transcriptome Profiles of Human Lung Epithelial Cells A549 Interacting with Aspergillus fumigatus by RNA-Seq. PLoS One 2015; 10:e0135720. [PMID: 26273834 PMCID: PMC4537115 DOI: 10.1371/journal.pone.0135720] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 07/24/2015] [Indexed: 11/19/2022] Open
Abstract
Lung epithelial cells constitute the first defense line of host against the inhaled Aspergillus fumigatus; however, the transcriptional response of human alveolar type II epithelial cells was still unclear. Here we used RNA-Seq technology to assess the transcriptome profiles of A549 cells following direct interaction with conidia of A. fumigatus. The total number of identified genes was 19118. Compared with uninfected A549 cells, 459 genes were differentially expressed in cells co-incubated with conidia for 8 h, including 302 up-regulated genes and 157 down-regulated genes. GO and KEGG pathway enrichment analysis showed that most of the up-regulated genes were related to immune response, chemotaxis and inflammatory response and enriched in cytokine-cytokine receptor interaction, JAK-STAT and MAPK signaling pathways. The down-regulated genes were mainly enriched for terms associated with development, hemopoiesis and ion transport. Among them, EGR4 and HIST1H4J gene had the maximum of fold change in up-regulated and down-regulated genes, respectively. Fourteen up-regulated genes and three down-regulated genes were further validated and significant increase on expression of IL-6, IL-8 and TNF-α in A549 cells were confirmed by qRT-PCR during the interaction of A549 cells with A. fumigatus. Besides, western blot showed that expression of two proteins (ARC, EGR1) significantly increased in A549 cells during interaction with A. fumigatus conidia for 8h. Interference of endogenous expression of ARC or EGR1 protein in A549 cells reduced the internalization of A. fumigatus. These results provided important insights into dynamic changes of gene expression in lung epithelial cells, especially its strong immunological response against A. fumigatus infection.
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Affiliation(s)
- Fangyan Chen
- Department for Hospital Infection Control & Research, Institute of Disease Control & Prevention of PLA, Academy of Military Medical Sciences, Beijing, China
| | - Changjian Zhang
- Department for Hospital Infection Control & Research, Institute of Disease Control & Prevention of PLA, Academy of Military Medical Sciences, Beijing, China
| | - Xiaodong Jia
- Department for Hospital Infection Control & Research, Institute of Disease Control & Prevention of PLA, Academy of Military Medical Sciences, Beijing, China
| | - Shuo Wang
- Department for Hospital Infection Control & Research, Institute of Disease Control & Prevention of PLA, Academy of Military Medical Sciences, Beijing, China
| | - Jing Wang
- Department for Hospital Infection Control & Research, Institute of Disease Control & Prevention of PLA, Academy of Military Medical Sciences, Beijing, China
| | - Yong Chen
- Department for Hospital Infection Control & Research, Institute of Disease Control & Prevention of PLA, Academy of Military Medical Sciences, Beijing, China
| | - Jingya Zhao
- Department for Hospital Infection Control & Research, Institute of Disease Control & Prevention of PLA, Academy of Military Medical Sciences, Beijing, China
| | - Shuguang Tian
- Department for Hospital Infection Control & Research, Institute of Disease Control & Prevention of PLA, Academy of Military Medical Sciences, Beijing, China
| | - Xuelin Han
- Department for Hospital Infection Control & Research, Institute of Disease Control & Prevention of PLA, Academy of Military Medical Sciences, Beijing, China
- * E-mail: (LH); (XH)
| | - Li Han
- Department for Hospital Infection Control & Research, Institute of Disease Control & Prevention of PLA, Academy of Military Medical Sciences, Beijing, China
- * E-mail: (LH); (XH)
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Brogaard L, Klitgaard K, Heegaard PMH, Hansen MS, Jensen TK, Skovgaard K. Concurrent host-pathogen gene expression in the lungs of pigs challenged with Actinobacillus pleuropneumoniae. BMC Genomics 2015; 16:417. [PMID: 26018580 PMCID: PMC4446954 DOI: 10.1186/s12864-015-1557-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/20/2015] [Indexed: 12/22/2022] Open
Abstract
Background Actinobacillus pleuropneumoniae causes pleuropneumonia in pigs, a disease which is associated with high morbidity and mortality, as well as impaired animal welfare. To obtain in-depth understanding of this infection, the interplay between virulence factors of the pathogen and defense mechanisms of the porcine host needs to be elucidated. However, research has traditionally focused on either bacteriology or immunology; an unbiased picture of the transcriptional responses can be obtained by investigating both organisms in the same biological sample. Results Host and pathogen responses in pigs experimentally infected with A. pleuropneumoniae were analyzed by high-throughput RT-qPCR. This approach allowed concurrent analysis of selected genes encoding proteins known or hypothesized to be important in the acute phase of this infection. The expression of 17 bacterial and 31 porcine genes was quantified in lung samples obtained within the first 48 hours of infection. This provided novel insight into the early time course of bacterial genes involved in synthesis of pathogen-associated molecular patterns (lipopolysaccharide, peptidoglycan, lipoprotein) and genes involved in pattern recognition (TLR4, CD14, MD2, LBP, MYD88) in response to A. pleuropneumoniae. Significant up-regulation of proinflammatory cytokines such as IL1B, IL6, and IL8 was observed, correlating with protein levels, infection status and histopathological findings. Host genes encoding proteins involved in iron metabolism, as well as bacterial genes encoding exotoxins, proteins involved in adhesion, and iron acquisition were found to be differentially expressed according to disease progression. By applying laser capture microdissection, porcine expression of selected genes could be confirmed in the immediate surroundings of the invading pathogen. Conclusions Microbial pathogenesis is the product of interactions between host and pathogen. Our results demonstrate the applicability of high-throughput RT-qPCR for the elucidation of dual-organism gene expression analysis during infection. We showed differential expression of 12 bacterial and 24 porcine genes during infection and significant correlation of porcine and bacterial gene expression. This is the first study investigating the concurrent transcriptional response of both bacteria and host at the site of infection during porcine respiratory infection. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1557-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Louise Brogaard
- Innate Immunology Group, Section of Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark.
| | - Kirstine Klitgaard
- Section of Bacteriology, Pathology and Parasitology, National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark.
| | - Peter M H Heegaard
- Innate Immunology Group, Section of Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark.
| | - Mette Sif Hansen
- Section of Bacteriology, Pathology and Parasitology, National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark.
| | - Tim Kåre Jensen
- Section of Bacteriology, Pathology and Parasitology, National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark.
| | - Kerstin Skovgaard
- Innate Immunology Group, Section of Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark.
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Schulze S, Henkel SG, Driesch D, Guthke R, Linde J. Computational prediction of molecular pathogen-host interactions based on dual transcriptome data. Front Microbiol 2015; 6:65. [PMID: 25705211 PMCID: PMC4319478 DOI: 10.3389/fmicb.2015.00065] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 01/19/2015] [Indexed: 11/13/2022] Open
Abstract
Inference of inter-species gene regulatory networks based on gene expression data is an important computational method to predict pathogen-host interactions (PHIs). Both the experimental setup and the nature of PHIs exhibit certain characteristics. First, besides an environmental change, the battle between pathogen and host leads to a constantly changing environment and thus complex gene expression patterns. Second, there might be a delay until one of the organisms reacts. Third, toward later time points only one organism may survive leading to missing gene expression data of the other organism. Here, we account for PHI characteristics by extending NetGenerator, a network inference tool that predicts gene regulatory networks from gene expression time series data. We tested multiple modeling scenarios regarding the stimuli functions of the interaction network based on a benchmark example. We show that modeling perturbation of a PHI network by multiple stimuli better represents the underlying biological phenomena. Furthermore, we utilized the benchmark example to test the influence of missing data points on the inference performance. Our results suggest that PHI network inference with missing data is possible, but we recommend to provide complete time series data. Finally, we extended the NetGenerator tool to incorporate gene- and time point specific variances, because complex PHIs may lead to high variance in expression data. Sample variances are directly considered in the objective function of NetGenerator and indirectly by testing the robustness of interactions based on variance dependent disturbance of gene expression values. We evaluated the method of variance incorporation on dual RNA sequencing (RNA-Seq) data of Mus musculus dendritic cells incubated with Candida albicans and proofed our method by predicting previously verified PHIs as robust interactions.
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Affiliation(s)
- Sylvie Schulze
- Department of Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knoell-Institute Jena, Germany
| | | | | | - Reinhard Guthke
- Department of Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knoell-Institute Jena, Germany
| | - Jörg Linde
- Department of Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knoell-Institute Jena, Germany
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Perkhofer S, Zenzmaier C, Frealle E, Blatzer M, Hackl H, Sartori B, Lass-Flörl C. Differential gene expression in Aspergillus fumigatus induced by human platelets in vitro. Int J Med Microbiol 2015; 305:327-38. [PMID: 25661519 PMCID: PMC4415150 DOI: 10.1016/j.ijmm.2015.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 12/10/2014] [Accepted: 01/11/2015] [Indexed: 12/19/2022] Open
Abstract
Invasive aspergillosis is characterized by vascular invasion and thrombosis. In order to determine the antifungal activity of human platelets, hyphal elongation and metabolic activity of a clinical A. fumigatus isolate were measured. Genome-wide identification of differentially expressed genes in A. fumigatus was performed after exposure to platelets for 15, 30, 60 and 180 min. Data were analyzed by gene ontology annotation as well as functional categories (FunCat) and KEGG enrichment analyses. Platelets attenuated hyphal elongation and viability of A. fumigatus and in total 584 differentially expressed genes were identified, many of which were associated with regulation of biological processes, stress response, transport and metabolism. FunCat and KEGG enrichment analyses showed stress response and metabolic adaptation to be increased in response to platelets. Our findings demonstrate that A. fumigatus displayed a specific transcriptional response when exposed to platelets, thus reflecting their antifungal activities.
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Affiliation(s)
- Susanne Perkhofer
- University of Applied Sciences Tyrol, 6020 Innsbruck, Austria; Division of Hygiene and Medical Microbiology, Innsbruck Medical University, 6020 Innsbruck, Austria.
| | | | - Emilie Frealle
- Center for Infection and Immunity of Lille (CIIL), Institut Pasteur de Lille, Biology and Diversity of Emerging Eukaryotic Pathogens (BDEEP), INSERM U1019, CNRS UMR 8204, Univ. Lille Nord de France, Lille, France
| | - Michael Blatzer
- Division of Hygiene and Medical Microbiology, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Hubert Hackl
- Division of Bioinformatics, Biocenter, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Bettina Sartori
- Division of Hygiene and Medical Microbiology, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Innsbruck Medical University, 6020 Innsbruck, Austria
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