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Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Spatially Resolved Expression of Transposable Elements in Disease and Somatic Tissue with SpatialTE
Braulio Valdebenito-Maturana1, Cristina Guatimosim2, Mónica Alejandra Carrasco3
1Núcleo Científico Multidisciplinario, School of Medicine, Universidad de Talca, Campus Talca, Talca 3460000, Chile.
International Journal of Molecular Sciences
|December 24, 2021
Summary
Transposable elements (TEs) are now analyzable in spatial transcriptomics (ST) data using the new SpatialTE tool. This reveals TEs have spatial expression patterns and are altered in ALS disease, suggesting regulatory roles.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Spatial transcriptomics (ST) offers position-specific gene expression analysis within tissues.
- Transposable elements (TEs) are typically excluded from bulk RNA-Seq due to repetitive sequences.
- TEs are increasingly recognized as crucial regulators of gene expression.
Purpose of the Study:
- To develop a computational tool, SpatialTE, for analyzing transposable element (TE) expression in spatial transcriptomics (ST) datasets.
- To investigate the spatial expression patterns of TEs in different tissue types.
- To explore alterations in TE expression profiles in disease contexts, specifically Amyotrophic Lateral Sclerosis (ALS).
Main Methods:
- Development of the SpatialTE software tool for TE expression analysis from ST data.
- Application of SpatialTE to analyze TE expression in both healthy (somatic) and diseased tissues.
- Comparative analysis of TE expression profiles in normal versus ALS-affected tissues.
Main Results:
- TEs exhibit distinct, spatially regulated expression patterns within tissues.
- Spatial expression profiles of TEs are significantly altered in Amyotrophic Lateral Sclerosis (ALS) diseased tissues.
- The findings suggest TEs play differential regulatory roles in tissue organization and function.
Conclusions:
- SpatialTE enables the study of TE expression in a spatially resolved manner, opening new avenues in gene regulation research.
- Altered TE expression in ALS indicates their potential involvement in disease pathogenesis.
- TEs may possess significant, spatially defined regulatory functions within organs that are disrupted in disease states.
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