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Home / Equine Research Bank / PLoS One / Exploring a pico-well based scRNA-seq method (HIVE) for simp...
PloS one2025; 20(1); e0317343; doi: 10.1371/journal.pone.0317343

Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells.

Abstract: Single-cell RNA sequencing (scRNA-seq) is a valuable tool for investigating cellular heterogeneity in diseases such as equine asthma (EA). This study evaluates the HIVE™ scRNA-seq method, a pico-well-based technology, for processing bronchoalveolar lavage (BAL) cells from horses with EA. The HIVE method offers practical advantages, including compatibility with both field and clinical settings, as well as a gentle workflow suited for handling sensitive cells. Our results show that the major cell types in equine BAL were successfully identified; however, the proportions of T cells and macrophages deviated from cytological expectations, with macrophages being overrepresented and T cells underrepresented. Despite these limitations, the HIVE method confirmed previously identified T cell and macrophage subpopulations and defined other BAL cell subsets. However, compared to previous studies T helper subsets were less clearly defined. Additionally, consistent with previous scRNA-seq studies, the HIVE method detected fewer granulocytes and mast cells than anticipated in the total BAL samples. Nevertheless, applying the method to purified mast cells recovered an expected number of cells. A small set of eosinophils were also detected which have not been characterized in earlier studies. In summary these findings suggest that while the HIVE method shows promise for certain applications, further optimization is needed to improve the accuracy of cell type representation, particularly for granulocytes and mast cells, in BAL samples.
Copyright: © 2025 Fegraeus et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Publication Date: 2025-01-24 PubMed ID: 39854349PubMed Central: PMC11760581DOI: 10.1371/journal.pone.0317343Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research evaluates a single-cell RNA sequencing method known as HIVE that is used for processing lung fluid cells from horses suffering from asthma. The method is found to identify most major cell types but with inaccuracies in the proportion representation of certain cell types.

Overview of the Research

  • This research is centered around the study of equine asthma (EA), and focuses on an evaluation of the HIVE™ single-cell RNA sequencing (scRNA-seq) method. The scRNA-seq is employed to study the cellular heterogeneity, or differences, in the disease. The scientists used this method to process bronchoalveolar lavage (BAL) cells, a type of cells gathered from lung fluids of horses suffering from EA.
  • The HIVE method was chosen because of its many practical advantages – it’s applicable in both field and clinical settings and has a gentle workflow ideal for dealing with sensitive cells. However, the study’s results revealed that while some cell types were accurately identified, the proportions of certain cell types deviated from expectations.

Findings of the Research

  • The study noted that the HIVE method managed successfully to identify the major cell types in equine BAL. However, there were discrepancies noted in the proportions of T cells and macrophages, where macrophages were overrepresented and T cells underrepresented.
  • Despite these limitations, the HIVE method was able to support findings from previous research on T cell and macrophage subpopulations while also defining other BAL cell subsets. Nevertheless, compared to prior studies, T helper subsets were less clearly defined with this method.
  • The study also found that fewer granulocytes and mast cells were identified than expected in the total BAL samples, a finding that aligns with previous scRNA-seq studies. However, when the HIVE method was applied to purified mast cells, it recovered an expected number of cells.
  • Additionally, the HIVE method was able to detect a small set of eosinophils, a type of white blood cell, which had not been characterized in previous studies.

Conclusion of the Research

  • The study concluded by noting the potential of the HIVE method for certain applications, but highlighted that further optimization is needed. The researchers are specifically concerned with improving the accuracy of cell type representation in the bronchoalveolar lavage samples, particularly for granulocytes and mast cells.

Cite This Article

APA
Fegraeus K, Riihimäki M, Nordlund J, Akula S, Wernersson S, Raine A. (2025). Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells. PLoS One, 20(1), e0317343. https://doi.org/10.1371/journal.pone.0317343

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 20
Issue: 1
Pages: e0317343
PII: e0317343

Researcher Affiliations

Fegraeus, Kim
  • Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
  • Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
Riihimäki, Miia
  • Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Nordlund, Jessica
  • Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
  • Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
Akula, Srinivas
  • Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Wernersson, Sara
  • Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Raine, Amanda
  • Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
  • Science for Life Laboratory, Uppsala University, Uppsala, Sweden.

MeSH Terms

  • Animals
  • Horses
  • Bronchoalveolar Lavage Fluid / cytology
  • Single-Cell Analysis / methods
  • Asthma / genetics
  • Asthma / veterinary
  • Sequence Analysis, RNA / methods
  • Sequence Analysis, RNA / veterinary
  • Macrophages / metabolism
  • Macrophages / cytology
  • RNA-Seq / methods
  • Mast Cells / cytology
  • Horse Diseases / genetics
  • Eosinophils / cytology
  • Bronchoalveolar Lavage / methods
  • T-Lymphocytes / metabolism
  • T-Lymphocytes / cytology
  • Single-Cell Gene Expression Analysis

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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