---
title: "Single-cell RNA-seq reveals host and parasite transcriptional dynamics during Encephalitozoon inte"
id: "biorxiv-18-single-cell-transcriptomics-of-encephalitozoon-intestinalis-infection-in-caco-2"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-18-single-cell-transcriptomics-of-encephalitozoon-intestinalis-infection-in-caco-2"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.09.18.752679v1?rss=1"
published_at: "2026-09-20T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Single-cell RNA-seq reveals host and parasite transcriptional dynamics during Encephalitozoon inte
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-18-single-cell-transcriptomics-of-encephalitozoon-intestinalis-infection-in-caco-2
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.09.18.752679v1?rss=1)
- **Published At:** 2026-09-20T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- This preprint reports single-cell RNA sequencing (scRNA-seq) of infections by the microsporidian **Encephalitozoon intestinalis** in two common epithelial cell culture models: **Caco-2** and **Vero** cells. - Microsporidia are obligate intracellular, single-celled parasites related to fungi; E. intestinalis is an enteric species that invades small intestinal epithelium. - Most individual host cells showed no direct transcriptional response to parasite invasion or intracellular replication, indicating many infected cells either do not detect or do not mount a transcriptional response to direct infection. - A small subset of host cells detected intracellular parasites late in the parasite life cycle and signaled to neighboring cells, producing a broader activation of a **TNF-ɑ** response across the culture. - Analysis of parasite-derived transcripts uncovered a developmental transcriptional program that correlates with morphological stages of the parasite life cycle. - Findings are consistent with previous single-cell transcriptomics of E. intestinalis–infected macrophages, suggesting a shared pattern of limited direct host detection with secondary signaling-mediated inflammation. - The authors present the datasets as a community resource for future mechanistic studies of host response and parasite development in vitro. - The work is a preprint (not peer-reviewed) from Johns Hopkins University and was funded by a Johns Hopkins Catalyst Award and an NSF award (OAC1920103). - The authors declared no competing interests. - Specific experimental details, numerical results, and full dataset descriptions are available in the preprint and supplementary material; precise methods and quantitative metrics were not reproduced in the supplied source excerpt.
## Clinical Analysis & Structured Key Points
Single-cell transcriptomics of Encephalitozoon intestinalis infection in Caco-2 and Vero cells | bioRxiv Skip to main content New Results Single-cell transcriptomics of Encephalitozoon intestinalis infection in Caco-2 and Vero cells View ORCID Profile Noelle Victoria Antao , View ORCID Profile Gira Bhabha , View ORCID Profile Damian C Ekiert doi: https://doi.org/10.64898/2026.09.18.752679 Noelle Victoria Antao Johns Hopkins University Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Noelle Victoria Antao Gira Bhabha Johns Hopkins University Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Gira Bhabha Damian C Ekiert Johns Hopkins University Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Damian C Ekiert For correspondence: dekiert1{at}jh.edu Abstract Info/History Metrics Supplementary material Preview PDF Abstract Microsporidia are single-celled, obligate intracellular parasites closely related to fungi. One of the most common human-infecting microsporidian species, Encephalitozoon intestinalis , is an enteric parasite that invades and replicates within the epithelial lining of the small intestine. Two epithelial cell lines, Caco-2 and Vero cells, are routinely used as in vitro models of E. intestinalis infection. Here, we use scRNA-seq to investigate the host response to E. intestinalis infection and the transcriptional dynamics of parasite development in both Caco-2 and Vero cell lines. We observe that most host cells have no direct transcriptional response to parasite invasion or intracellular replication, suggesting that cells fail to detect and/or fail to respond to direct E. intestinalis infection, consistent with previous single-cell transcriptomics of E. intestinalis -infected macrophages. Our data suggest that a small subset of host cells detect intracellular parasites late in the life cycle, and signal to neighboring cells, leading to broad activation of a TNF-ɑ response. Analysis of parasite transcripts reveals a developmental program that correlates with the morphological stages of the parasite life cycle. Together our data provide insights into a shared host transcriptional response to E. intestinalis infection and the datasets presented are a valuable resource for future studies. Competing Interest Statement The authors have declared no competing interest. Funder Information Declared Johns Hopkins Catalyst Award , Gira Bhabha National Science Foundation (NSF) , OAC1920103 Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Back to top Previous Next Posted September 20, 2026. Download PDF Supplementary Material Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. You are going to email the following Single-cell transcriptomics of Encephalitozoon intestinalis infection in Caco-2 and Vero cells Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website. Your Personal Message CAPTCHA This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Share Single-cell transcriptomics of Encephalitozoon intestinalis infection in Caco-2 and Vero cells Noelle Victoria Antao , Gira Bhabha , Damian C Ekiert bioRxiv 2026.09.18.752679; doi: https://doi.org/10.64898/2026.09.18.752679 Share This Article: Copy Citation Tools Single-cell transcriptomics of Encephalitozoon intestinalis infection in Caco-2 and Vero cells Noelle Victoria Antao , Gira Bhabha , Damian C Ekiert bioRxiv 2026.09.18.752679; doi: https://doi.org/10.64898/2026.09.18.752679 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Areas All Articles Animal Behavior and Cognition (8013) Biochemistry (18739) Bioengineering (14888) Bioinformatics (44418) Biophysics (22599) Cancer Biology (19723) Cell Biology (26899) Clinical Trials (138) Developmental Biology (13965) Ecology (21005) Epidemiology (2067) Evolutionary Biology (25455) Genetics (16166) Genomics (23507) Immunology (18705) Microbiology (42503) Molecular Biology (18059) Neuroscience (93451) Paleontology (700) Pathology (2977) Pharmacology and Toxicology (5095) Physiology (8114) Plant Biology (15999) Scientific Communication and Education (2095) Synthetic Biology (4560) Systems Biology (10235) Zoology (2391)
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