An approach to analyze spatiotemporal patterns of gene expression at single-cell resolution in Candida albicans-infected mouse tongues
ABSTRACT Microbial gene expression measurements derived from infected organs are invaluable to understand pathogenesis. However, current methods are limited to “bulk” analyses that neglect microbial cell heterogeneity and the lesion's spatial architecture. Here, we report the use of hybridizati...
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American Society for Microbiology
2024-09-01
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| Online Access: | https://journals.asm.org/doi/10.1128/msphere.00282-24 |
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| author | Elena Lindemann-Perez Diana L. Rodríguez J. Christian Pérez |
| author_facet | Elena Lindemann-Perez Diana L. Rodríguez J. Christian Pérez |
| author_sort | Elena Lindemann-Perez |
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| description | ABSTRACT Microbial gene expression measurements derived from infected organs are invaluable to understand pathogenesis. However, current methods are limited to “bulk” analyses that neglect microbial cell heterogeneity and the lesion's spatial architecture. Here, we report the use of hybridization chain reaction RNA fluorescence in situ hybridization (HCR RNA-FISH) to visualize and quantify Candida albicans transcripts at single-cell resolution in tongues of infected mice. The method is compatible with fixed-frozen and formalin-fixed paraffin-embedded tissues. We document cell-to-cell variation and intriguing spatiotemporal expression patterns for C. albicans mRNAs that encode products implicated in oral candidiasis. The approach provides a spatial dimension to gene expression analyses of host-Candida interactions.IMPORTANCECandida albicans is a fungal pathobiont inhabiting multiple mucosal surfaces of the human body. Immunosuppression, antibiotic-induced microbial dysbiosis, or implanted medical devices can impair mucosal integrity enabling C. albicans to overgrow and disseminate, causing either mucosal diseases such as oropharyngeal candidiasis or life-threatening systemic infections. Profiling fungal genes that are expressed in the infected mucosa or in any other infected organ is paramount to understand pathogenesis. Ideally, these transcript profiling measurements should reveal the expression of any gene at the single-cell level. The resolution typically achieved with current approaches, however, limits most gene expression measurements to cell population averages. The approach described in this report provides a means to dissect fungal gene expression in infected tissues at single-cell resolution. |
| format | Article |
| id | doaj-art-d27dfc21702c453897e19d47b29960ca |
| institution | OA Journals |
| issn | 2379-5042 |
| language | English |
| publishDate | 2024-09-01 |
| publisher | American Society for Microbiology |
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| series | mSphere |
| spelling | doaj-art-d27dfc21702c453897e19d47b29960ca2025-08-20T01:55:12ZengAmerican Society for MicrobiologymSphere2379-50422024-09-019910.1128/msphere.00282-24An approach to analyze spatiotemporal patterns of gene expression at single-cell resolution in Candida albicans-infected mouse tonguesElena Lindemann-Perez0Diana L. Rodríguez1J. Christian Pérez2Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USADepartment of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USADepartment of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USAABSTRACT Microbial gene expression measurements derived from infected organs are invaluable to understand pathogenesis. However, current methods are limited to “bulk” analyses that neglect microbial cell heterogeneity and the lesion's spatial architecture. Here, we report the use of hybridization chain reaction RNA fluorescence in situ hybridization (HCR RNA-FISH) to visualize and quantify Candida albicans transcripts at single-cell resolution in tongues of infected mice. The method is compatible with fixed-frozen and formalin-fixed paraffin-embedded tissues. We document cell-to-cell variation and intriguing spatiotemporal expression patterns for C. albicans mRNAs that encode products implicated in oral candidiasis. The approach provides a spatial dimension to gene expression analyses of host-Candida interactions.IMPORTANCECandida albicans is a fungal pathobiont inhabiting multiple mucosal surfaces of the human body. Immunosuppression, antibiotic-induced microbial dysbiosis, or implanted medical devices can impair mucosal integrity enabling C. albicans to overgrow and disseminate, causing either mucosal diseases such as oropharyngeal candidiasis or life-threatening systemic infections. Profiling fungal genes that are expressed in the infected mucosa or in any other infected organ is paramount to understand pathogenesis. Ideally, these transcript profiling measurements should reveal the expression of any gene at the single-cell level. The resolution typically achieved with current approaches, however, limits most gene expression measurements to cell population averages. The approach described in this report provides a means to dissect fungal gene expression in infected tissues at single-cell resolution.https://journals.asm.org/doi/10.1128/msphere.00282-24Candida albicanshybridization chain reactionRNA-FISHCandida-host interactionsoropharyngeal candidiasisCandida-infected tissue |
| spellingShingle | Elena Lindemann-Perez Diana L. Rodríguez J. Christian Pérez An approach to analyze spatiotemporal patterns of gene expression at single-cell resolution in Candida albicans-infected mouse tongues mSphere Candida albicans hybridization chain reaction RNA-FISH Candida-host interactions oropharyngeal candidiasis Candida-infected tissue |
| title | An approach to analyze spatiotemporal patterns of gene expression at single-cell resolution in Candida albicans-infected mouse tongues |
| title_full | An approach to analyze spatiotemporal patterns of gene expression at single-cell resolution in Candida albicans-infected mouse tongues |
| title_fullStr | An approach to analyze spatiotemporal patterns of gene expression at single-cell resolution in Candida albicans-infected mouse tongues |
| title_full_unstemmed | An approach to analyze spatiotemporal patterns of gene expression at single-cell resolution in Candida albicans-infected mouse tongues |
| title_short | An approach to analyze spatiotemporal patterns of gene expression at single-cell resolution in Candida albicans-infected mouse tongues |
| title_sort | approach to analyze spatiotemporal patterns of gene expression at single cell resolution in candida albicans infected mouse tongues |
| topic | Candida albicans hybridization chain reaction RNA-FISH Candida-host interactions oropharyngeal candidiasis Candida-infected tissue |
| url | https://journals.asm.org/doi/10.1128/msphere.00282-24 |
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