Bentley-Abbot, C., Heslop, R., Pirillo, C., Chandrasegaran, P., McConnell, G., Roberts, E. , Hutchinson, E. and MacLeod, A. (2024) An easy to use tool for the analysis of subcellular mRNA transcript colocalisation in smFISH data. Scientific Reports, 14, 8348. (doi: 10.1038/s41598-024-58641-3) (PMID:38594373) (PMCID:PMC11004122)
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Abstract
Single molecule fluorescence in situ hybridisation (smFISH) has become a valuable tool to investigate the mRNA expression of single cells. However, it requires a considerable amount of programming expertise to use currently available open-source analytical software packages to extract and analyse quantitative data about transcript expression. Here, we present FISHtoFigure, a new software tool developed specifically for the analysis of mRNA abundance and co-expression in QuPath-quantified, multi-labelled smFISH data. FISHtoFigure facilitates the automated spatial analysis of transcripts of interest, allowing users to analyse populations of cells positive for specific combinations of mRNA targets without the need for computational image analysis expertise. As a proof of concept and to demonstrate the capabilities of this new research tool, we have validated FISHtoFigure in multiple biological systems. We used FISHtoFigure to identify an upregulation in the expression of Cd4 by T-cells in the spleens of mice infected with influenza A virus, before analysing more complex data showing crosstalk between microglia and regulatory B-cells in the brains of mice infected with Trypanosoma brucei brucei. These analyses demonstrate the ease of analysing cell expression profiles using FISHtoFigure and the value of this new tool in the field of smFISH data analysis.
| Item Type: | Articles |
|---|---|
| Additional Information: | The work to produce this dataset was funded by a Sir Henry Wellcome postdoctoral fellowship (221640/Z/20/Z to J.F.Q.) and a Wellcome Trust ISSF Catalyst grant awarded to J.F.Q. (204820/Z/16/Z to JFQ). We also thank Colin Loney for his assistance in the acquisition of the images forming the spleen dataset used during validation. We also thank Ruaridh Wilson for providing feedback from the perspective of a computational scientist during the writing of this manuscript. |
| Status: | Published |
| Refereed: | Yes |
| Glasgow Author(s) Enlighten ID: | Roberts, Dr Ed and Heslop, Rhiannon and MacLeod, Professor Annette and Chandrasegaran, Miss Praveena and Hutchinson, Dr Edward and Bentley-Abbot, Cal |
| Authors: | Bentley-Abbot, C., Heslop, R., Pirillo, C., Chandrasegaran, P., McConnell, G., Roberts, E., Hutchinson, E., and MacLeod, A. |
| College/School: | College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine College of Medical Veterinary and Life Sciences > School of Cancer Sciences College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research |
| Journal Name: | Scientific Reports |
| Publisher: | Nature Research |
| ISSN: | 2045-2322 |
| ISSN (Online): | 2045-2322 |
| Copyright Holders: | Copyright © 2024 The Authors |
| First Published: | First published in Scientific Reports 14: 8348 |
| Publisher Policy: | Reproduced under a Creative Commons License |
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