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Jaroenlak P, McCarty KL, Xia B, Lam C, Zwack EE, Yanai I, Bhabha G, Ekiert DC. scRNA-seq reveals transcriptional dynamics of Encephalitozoon intestinalis parasites in human macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596468. [PMID: 38853846 PMCID: PMC11160751 DOI: 10.1101/2024.05.30.596468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Microsporidia are single-celled intracellular parasites that cause opportunistic diseases in humans. Encephalitozoon intestinalis is a prevalent human-infecting species that invades the small intestine. Dissemination to other organ systems is also observed, and is potentially facilitated by macrophages. The macrophage response to infection and the developmental trajectory of the parasite are not well studied. Here we use single cell RNA sequencing to investigate transcriptional changes in both the host and parasite during infection. While a small population of infected macrophages mount a response, most remain transcriptionally unchanged, suggesting that the majority of parasites may avoid host detection. The parasite transcriptome reveals large transcriptional changes throughout the life cycle, providing a blueprint for parasite development. The stealthy microsporidian lifestyle likely allows these parasites to harness macrophages for replication and dissemination. Together, our data provide insights into the host response in primary human macrophages and the E. intestinalis developmental program.
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Affiliation(s)
- Pattana Jaroenlak
- Department of Cell Biology, New York University Grossman School of Medicine, New York 10016, USA
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kacie L. McCarty
- Department of Cell Biology, New York University Grossman School of Medicine, New York 10016, USA
- Department of Microbiology, New York University Grossman School of Medicine, New York 10016, USA
| | - Bo Xia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cherry Lam
- Department of Cell Biology, New York University Grossman School of Medicine, New York 10016, USA
| | - Erin E. Zwack
- Department of Microbiology, New York University Grossman School of Medicine, New York 10016, USA
| | - Itai Yanai
- Institute for Computational Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Gira Bhabha
- Department of Cell Biology, New York University Grossman School of Medicine, New York 10016, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Damian C. Ekiert
- Department of Cell Biology, New York University Grossman School of Medicine, New York 10016, USA
- Department of Microbiology, New York University Grossman School of Medicine, New York 10016, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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2
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Tersigni J, Tamim El Jarkass H, James EB, Reinke AW. Interactions between microsporidia and other members of the microbiome. J Eukaryot Microbiol 2024:e13025. [PMID: 38561869 DOI: 10.1111/jeu.13025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
Abstract
The microbiome is the collection of microbes that are associated with a host. Microsporidia are intracellular eukaryotic parasites that can infect most types of animals. In the last decade, there has been much progress to define the relationship between microsporidia and the microbiome. In this review, we cover an increasing number of reports suggesting that microsporidia are common components of the microbiome in both invertebrates and vertebrates. These microsporidia infections can range from mutualistic to pathogenic, causing several physiological phenotypes, including death. Infection with microsporidia often causes a disruption in the normal microbiome, with both increases and decreases of bacterial, fungal, viral, and protozoan species being observed. This impact on the microbiome can occur through upregulation and downregulation of innate immunity as well as morphological changes to tissues that impact interactions with these microbes. Other microbes, particularly bacteria, can inhibit microsporidia and have been exploited to control microsporidia infections. These bacteria can function through regulating immunity, secreting anti-microsporidia compounds, and, in engineered versions, expressing double-stranded RNA targeting microsporidia genes. We end this review by discussing potential future directions to further understand the complex interactions between microsporidia and the other members of the microbiome.
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Affiliation(s)
- Jonathan Tersigni
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Edward B James
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Aaron W Reinke
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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3
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Antao NV, Lam C, Davydov A, Riggi M, Sall J, Petzold C, Liang FX, Iwasa JH, Ekiert DC, Bhabha G. 3D reconstructions of parasite development and the intracellular niche of the microsporidian pathogen Encephalitozoon intestinalis. Nat Commun 2023; 14:7662. [PMID: 37996434 PMCID: PMC10667486 DOI: 10.1038/s41467-023-43215-0] [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] [Received: 06/30/2023] [Accepted: 11/02/2023] [Indexed: 11/25/2023] Open
Abstract
Microsporidia are an early-diverging group of fungal pathogens with a wide host range. Several microsporidian species cause opportunistic infections in humans that can be fatal. As obligate intracellular parasites with highly reduced genomes, microsporidia are dependent on host metabolites for successful replication and development. Our knowledge of microsporidian intracellular development remains rudimentary, and our understanding of the intracellular niche occupied by microsporidia has relied on 2D TEM images and light microscopy. Here, we use serial block-face scanning electron microscopy (SBF-SEM) to capture 3D snapshots of the human-infecting species, Encephalitozoon intestinalis, within host cells. We track E. intestinalis development through its life cycle, which allows us to propose a model for how its infection organelle, the polar tube, is assembled de novo in developing spores. 3D reconstructions of parasite-infected cells provide insights into the physical interactions between host cell organelles and parasitophorous vacuoles, which contain the developing parasites. The host cell mitochondrial network is substantially remodeled during E. intestinalis infection, leading to mitochondrial fragmentation. SBF-SEM analysis shows changes in mitochondrial morphology in infected cells, and live-cell imaging provides insights into mitochondrial dynamics during infection. Our data provide insights into parasite development, polar tube assembly, and microsporidia-induced host mitochondria remodeling.
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Affiliation(s)
- Noelle V Antao
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Cherry Lam
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Ari Davydov
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Margot Riggi
- Department of Biochemistry, University of Utah, Salt Lake City, USA
| | - Joseph Sall
- Office of Science and Research Microscopy Laboratory, New York University School of Medicine, New York, NY, USA
| | - Christopher Petzold
- Office of Science and Research Microscopy Laboratory, New York University School of Medicine, New York, NY, USA
| | - Feng-Xia Liang
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
- Office of Science and Research Microscopy Laboratory, New York University School of Medicine, New York, NY, USA
| | - Janet H Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, USA
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
- Department of Microbiology, New York University School of Medicine, New York, NY, USA.
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
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Akossi RF, Delbac F, El Alaoui H, Wawrzyniak I, Peyretaillade E. The intracellular parasite Anncaliia algerae induces a massive miRNA down-regulation in human cells. Noncoding RNA Res 2023; 8:363-375. [PMID: 37275245 PMCID: PMC10238475 DOI: 10.1016/j.ncrna.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/27/2023] [Accepted: 05/07/2023] [Indexed: 06/07/2023] Open
Abstract
Anncaliia algerae belongs to microsporidia, a group of obligate intracellular parasites related to fungi. These parasites are largely spread in water and food-webs and can infect a wide variety of hosts ranging from invertebrates to vertebrates including humans. In humans, microsporidian infections are mainly opportunistic as immunocompetent hosts can clear parasites naturally. Recent studies however have reported persistent microsporidian infections and have highlighted them as a risk factor in colon cancer. This may be a direct result of cell infection or may be an indirect effect of the infectious microenvironment and the host's response. In both cases, this raises the question of the effects of microsporidian infection at the host and host-cell levels. We aimed to address the question of human host intracellular response to microsporidian infection through a transcriptomic kinetic study of human foreskin fibroblasts (HFF) infected with A.algerae, a human infecting microsporidia with an exceptionally wide host range. We focused solely on host response studying both coding and small non-coding miRNA expression. Our study revealed a generalized down-regulation of cell miRNAs throughout infection with up to 547 different miRNAs downregulated at some timepoints and also transcriptomic dysregulations that could facilitate parasite development with immune and lipid metabolism genes modulation. We also hypothesize possible small nucleic acid expropriation explaining the miRNA downregulation. This work contributes to a better understanding of the dialogue that can occur between an intracellular parasite and its host at the cellular level, and can guide future studies on microsporidian infection biology to unravel the mode of action of these minimalist parasites at the tissue or host levels.We have also generated a kinetic and comprehensive transcriptomic data set of an infectious process that can help support comparative studies in the broader field of parasitology. Lastly, these results may warrant for caution regarding microsporidian exposure and persistent infections.
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Affiliation(s)
- Reginald Florian Akossi
- Laboratoire “Microorganismes: Génome et Environnement” (LMGE), UMR 6023, Université Clermont Auvergne and CNRS, F-63000, Clermont-Ferrand, France
| | - Fréderic Delbac
- Laboratoire “Microorganismes: Génome et Environnement” (LMGE), UMR 6023, Université Clermont Auvergne and CNRS, F-63000, Clermont-Ferrand, France
| | - Hicham El Alaoui
- Laboratoire “Microorganismes: Génome et Environnement” (LMGE), UMR 6023, Université Clermont Auvergne and CNRS, F-63000, Clermont-Ferrand, France
| | - Ivan Wawrzyniak
- Laboratoire “Microorganismes: Génome et Environnement” (LMGE), UMR 6023, Université Clermont Auvergne and CNRS, F-63000, Clermont-Ferrand, France
| | - Eric Peyretaillade
- Laboratoire “Microorganismes: Génome et Environnement” (LMGE), UMR 6023, Université Clermont Auvergne and CNRS, F-63000, Clermont-Ferrand, France
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Antao NV, Lam C, Davydov A, Riggi M, Sall J, Petzold C, Liang FX, Iwasa J, Ekiert DC, Bhabha G. 3D reconstructions of parasite development and the intracellular niche of the microsporidian pathogen E. intestinalis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.02.547383. [PMID: 37425741 PMCID: PMC10327200 DOI: 10.1101/2023.07.02.547383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Microsporidia are an early-diverging group of fungal pathogens that infect a wide range of hosts. Several microsporidian species infect humans, and infections can lead to fatal disease in immunocompromised individuals. As obligate intracellular parasites with highly reduced genomes, microsporidia are dependent on metabolites from their hosts for successful replication and development. Our knowledge of how microsporidian parasites develop inside the host remains rudimentary, and our understanding of the intracellular niche occupied by microsporidia has thus far relied largely on 2D TEM images and light microscopy. Here, we use serial block face scanning electron microscopy (SBF-SEM) to capture 3D snapshots of the human-infecting microsporidian, Encephalitozoon intestinalis , within host cells. We track the development of E. intestinalis through its life cycle, which allows us to propose a model for how its infection organelle, the polar tube, is assembled de novo in each developing spore. 3D reconstructions of parasite-infected cells provide insights into the physical interactions between host cell organelles and parasitophorous vacuoles, which contain the developing parasites. The host cell mitochondrial network is substantially remodeled during E. intestinalis infection, leading to mitochondrial fragmentation. SBF-SEM analysis shows changes in mitochondrial morphology in infected cells, and live-cell imaging provides insights into mitochondrial dynamics during infection. Together, our data provide insights into parasite development, polar tube assembly, and microsporidia-induced mitochondrial remodeling in the host cell.
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Wan YC, Troemel ER, Reinke AW. Conservation of Nematocida microsporidia gene expression and host response in Caenorhabditis nematodes. PLoS One 2022; 17:e0279103. [PMID: 36534656 PMCID: PMC9762603 DOI: 10.1371/journal.pone.0279103] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Microsporidia are obligate intracellular parasites that are known to infect most types of animals. Many species of microsporidia can infect multiple related hosts, but it is not known if microsporidia express different genes depending upon which host species is infected or if the host response to infection is specific to each microsporidia species. To address these questions, we took advantage of two species of Nematocida microsporidia, N. parisii and N. ausubeli, that infect two species of Caenorhabditis nematodes, C. elegans and C. briggsae. We performed RNA-seq at several time points for each host infected with either microsporidia species. We observed that Nematocida transcription was largely independent of its host. We also observed that the host transcriptional response was similar when infected with either microsporidia species. Finally, we analyzed if the host response to microsporidia infection was conserved across host species. We observed that although many of the genes upregulated in response to infection are not direct orthologs, the same expanded gene families are upregulated in both Caenorhabditis hosts. Together our results describe the transcriptional interactions of Nematocida infection in Caenorhabditis hosts and demonstrate that these responses are evolutionarily conserved.
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Affiliation(s)
- Yin Chen Wan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Emily R. Troemel
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Aaron W. Reinke
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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Seatamanoch N, Kongdachalert S, Sunantaraporn S, Siriyasatien P, Brownell N. Microsporidia, a Highly Adaptive Organism and Its Host Expansion to Humans. Front Cell Infect Microbiol 2022; 12:924007. [PMID: 35782144 PMCID: PMC9245026 DOI: 10.3389/fcimb.2022.924007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/23/2022] [Indexed: 12/05/2022] Open
Abstract
Emerging infectious disease has become the center of attention since the outbreak of COVID-19. For the coronavirus, bats are suspected to be the origin of the pandemic. Consequently, the spotlight has fallen on zoonotic diseases, and the focus now expands to organisms other than viruses. Microsporidia is a single-cell organism that can infect a wide range of hosts such as insects, mammals, and humans. Its pathogenicity differs among species, and host immunological status plays an important role in infectivity and disease severity. Disseminated disease from microsporidiosis can be fatal, especially among patients with a defective immune system. Recently, there were two Trachipleistophora hominis, a microsporidia species which can survive in insects, case reports in Thailand, one patient had disseminated microsporidiosis. This review gathered data of disseminated microsporidiosis and T. hominis infections in humans covering the biological and clinical aspects. There was a total of 22 cases of disseminated microsporidiosis reports worldwide. Ten microsporidia species were identified. Maximum likelihood tree results showed some possible correlations with zoonotic transmissions. For T. hominis, there are currently eight case reports in humans, seven of which had Human Immunodeficiency Virus (HIV) infection. It is observed that risks are higher for the immunocompromised to acquire such infections, however, future studies should look into the entire life cycle, to identify the route of transmission and establish preventive measures, especially among the high-risk groups.
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Affiliation(s)
- Nirin Seatamanoch
- Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Vector Biology and Vector Borne Disease Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Switt Kongdachalert
- Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Vector Biology and Vector Borne Disease Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sakone Sunantaraporn
- Vector Biology and Vector Borne Disease Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Padet Siriyasatien
- Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Vector Biology and Vector Borne Disease Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Narisa Brownell
- Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Vector Biology and Vector Borne Disease Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- *Correspondence: Narisa Brownell,
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First person – Juan Flores and Peter M. Takvorian. J Cell Sci 2021. [DOI: 10.1242/jcs.258531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Juan Flores and Peter M. Takvorian are co-first authors on ‘Human microsporidian pathogen Encephalitozoon intestinalis impinges on enterocyte membrane trafficking and signaling’, published in JCS. Juan is a PhD student in the lab of Nan Gao, at Newark, New Jersey, USA, investigating the role of the underappreciated intestinal microbiome and pathogens by profiling their metabolic and transcriptional impacts on host cells. Peter is a Visiting Research Associate Professor (Rutgers) and Visiting Assistant Professor of Pathology (Albert Einstein College of Medicine) in the lab of Ann Cali (Rutgers, Newark, USA) and Louis M. Weiss (Albert Einstein College of Medicine, New York, USA) investigating ultrastructural studies of the host cell interaction and pathological effects of intracellular parasites and viruses.
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