A Pilot Single Cell Analysis of the Zebrafish Embryo Cellular Responses to Uropathogenic Escherichia coli Infection
Background: Uropathogenic Escherichia coli (UPEC) infections are common and when they disseminate can be of high morbidity. Methods: We studied the effects of UPEC infection using single cell RNA sequencing (scRNAseq) in zebrafish. Bulk RNA sequencing has historically been used to evaluate gene e...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Case Western Reserve University
2022-02-01
|
| Series: | Pathogens and Immunity |
| Subjects: | |
| Online Access: | https://www.paijournal.com/index.php/paijournal/article/view/479 |
| _version_ | 1798039366618054656 |
|---|---|
| author | Ashley Rawson Vijay Saxena Hongyu Gao Jenaya Hooks Xiaoling Xuei Patrick McGuire Takashi Hato David Hains Ryan Anderson Andrew Schwaderer |
| author_facet | Ashley Rawson Vijay Saxena Hongyu Gao Jenaya Hooks Xiaoling Xuei Patrick McGuire Takashi Hato David Hains Ryan Anderson Andrew Schwaderer |
| author_sort | Ashley Rawson |
| collection | DOAJ |
| description |
Background: Uropathogenic Escherichia coli (UPEC) infections are common and when they disseminate can be of high morbidity.
Methods: We studied the effects of UPEC infection using single cell RNA sequencing (scRNAseq) in zebrafish. Bulk RNA sequencing has historically been used to evaluate gene expression patterns, but scRNAseq allows gene expression to be evaluated at the single cell level and is optimal for evaluating heterogeneity within cell types and rare cell types. Zebrafish cohorts were injected with either saline or UPEC,and scRNAseq and canonical pathway analyses were performed.
Results: Canonical pathway analysis of scRNAseq data provided key information regarding innate immune pathways in the cells determined to be thymus cells, ionocytes, macrophages/monocytes, and pronephros cells. Pathways activated in thymus cells included interleukin 6 (IL-6) signaling and production of reactive oxygen species. Fc receptor-mediated phagocytosis was a leading canonical pathway in the pronephros and macrophages. Genes that were downregulated in UPEC vs saline exposed embryos involved the cellular response to the Gram-negative endotoxin lipopolysaccharide (LPS) and included Forkhead Box O1a (Foxo1a), Tribbles Pseudokinase 3 (Trib3), Arginase 2 (Arg2) and Polo Like Kinase 3 (Plk3).
Conclusions: Because 4-day post fertilization zebrafish embryos only have innate immune systems, the scRNAseq provides insights into pathways and genes that cell types utilize in the bacterial response. Based on our analysis, we have identified genes and pathways that might serve as genetic targets for treatment and further investigation in UPEC infections at the single cell level.
|
| first_indexed | 2024-04-11T21:52:54Z |
| format | Article |
| id | doaj.art-199c0c4ef02e4588bc7ac0f49f83fcd5 |
| institution | Directory Open Access Journal |
| issn | 2469-2964 |
| language | English |
| last_indexed | 2024-04-11T21:52:54Z |
| publishDate | 2022-02-01 |
| publisher | Case Western Reserve University |
| record_format | Article |
| series | Pathogens and Immunity |
| spelling | doaj.art-199c0c4ef02e4588bc7ac0f49f83fcd52022-12-22T04:01:11ZengCase Western Reserve UniversityPathogens and Immunity2469-29642022-02-017110.20411/pai.v7i1.479A Pilot Single Cell Analysis of the Zebrafish Embryo Cellular Responses to Uropathogenic Escherichia coli InfectionAshley Rawson0Vijay Saxena1Hongyu Gao2Jenaya Hooks3Xiaoling Xuei4Patrick McGuire5Takashi Hato6David Hains7Ryan Anderson8Andrew Schwaderer9Indiana University School of Medicine, Department of Pediatrics, Division of NephrologyIndiana University School of Medicine, Department of Pediatrics, Division of NephrologyIndiana University School of Medicine, Department of Medical & Molecular GeneticsIndiana University School of Medicine, Department of Pediatrics, Division of NephrologyIndiana University School of Medicine, Department of Medical & Molecular GeneticsIndiana University School of Medicine, Department of Medical & Molecular GeneticsIndiana University School of Medicine, Department of Medicine, Division of NephrologyIndiana University School of Medicine, Department of Pediatrics, Division of NephrologyUniversity of Chicago, Section of Endocrinology, Diabetes and MetabolismIndiana University School of Medicine, Department of Pediatrics, Division of Nephrology Background: Uropathogenic Escherichia coli (UPEC) infections are common and when they disseminate can be of high morbidity. Methods: We studied the effects of UPEC infection using single cell RNA sequencing (scRNAseq) in zebrafish. Bulk RNA sequencing has historically been used to evaluate gene expression patterns, but scRNAseq allows gene expression to be evaluated at the single cell level and is optimal for evaluating heterogeneity within cell types and rare cell types. Zebrafish cohorts were injected with either saline or UPEC,and scRNAseq and canonical pathway analyses were performed. Results: Canonical pathway analysis of scRNAseq data provided key information regarding innate immune pathways in the cells determined to be thymus cells, ionocytes, macrophages/monocytes, and pronephros cells. Pathways activated in thymus cells included interleukin 6 (IL-6) signaling and production of reactive oxygen species. Fc receptor-mediated phagocytosis was a leading canonical pathway in the pronephros and macrophages. Genes that were downregulated in UPEC vs saline exposed embryos involved the cellular response to the Gram-negative endotoxin lipopolysaccharide (LPS) and included Forkhead Box O1a (Foxo1a), Tribbles Pseudokinase 3 (Trib3), Arginase 2 (Arg2) and Polo Like Kinase 3 (Plk3). Conclusions: Because 4-day post fertilization zebrafish embryos only have innate immune systems, the scRNAseq provides insights into pathways and genes that cell types utilize in the bacterial response. Based on our analysis, we have identified genes and pathways that might serve as genetic targets for treatment and further investigation in UPEC infections at the single cell level. https://www.paijournal.com/index.php/paijournal/article/view/479Urinary tract infection;Urosepsis;Innate immunity;Zebrafish;Single cell RNAseq |
| spellingShingle | Ashley Rawson Vijay Saxena Hongyu Gao Jenaya Hooks Xiaoling Xuei Patrick McGuire Takashi Hato David Hains Ryan Anderson Andrew Schwaderer A Pilot Single Cell Analysis of the Zebrafish Embryo Cellular Responses to Uropathogenic Escherichia coli Infection Pathogens and Immunity Urinary tract infection; Urosepsis; Innate immunity; Zebrafish; Single cell RNAseq |
| title | A Pilot Single Cell Analysis of the Zebrafish Embryo Cellular Responses to Uropathogenic Escherichia coli Infection |
| title_full | A Pilot Single Cell Analysis of the Zebrafish Embryo Cellular Responses to Uropathogenic Escherichia coli Infection |
| title_fullStr | A Pilot Single Cell Analysis of the Zebrafish Embryo Cellular Responses to Uropathogenic Escherichia coli Infection |
| title_full_unstemmed | A Pilot Single Cell Analysis of the Zebrafish Embryo Cellular Responses to Uropathogenic Escherichia coli Infection |
| title_short | A Pilot Single Cell Analysis of the Zebrafish Embryo Cellular Responses to Uropathogenic Escherichia coli Infection |
| title_sort | pilot single cell analysis of the zebrafish embryo cellular responses to uropathogenic escherichia coli infection |
| topic | Urinary tract infection; Urosepsis; Innate immunity; Zebrafish; Single cell RNAseq |
| url | https://www.paijournal.com/index.php/paijournal/article/view/479 |
| work_keys_str_mv | AT ashleyrawson apilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT vijaysaxena apilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT hongyugao apilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT jenayahooks apilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT xiaolingxuei apilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT patrickmcguire apilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT takashihato apilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT davidhains apilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT ryananderson apilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT andrewschwaderer apilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT ashleyrawson pilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT vijaysaxena pilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT hongyugao pilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT jenayahooks pilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT xiaolingxuei pilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT patrickmcguire pilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT takashihato pilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT davidhains pilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT ryananderson pilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection AT andrewschwaderer pilotsinglecellanalysisofthezebrafishembryocellularresponsestouropathogenicescherichiacoliinfection |