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Spatial transcriptomics in bone research: navigating hype and hurdles
Dimitri Sokolowskei1, Achira Shah1, Alexander J Trostle1
1Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA.
Pathology
|December 31, 2025
Summary
Spatial transcriptomics (ST) offers insights into musculoskeletal tissues but faces challenges with bone processing and platform limitations. This review covers ST applications, bone sample preparation, and future directions for understanding tissue biology.
Area of Science:
- Biotechnology and Molecular Biology
- Musculoskeletal Research
- Genomics
Background:
- Spatial transcriptomics (ST) measures gene expression within native tissue architecture.
- ST is vital for understanding musculoskeletal tissue heterogeneity, injury mechanisms, and homeostasis.
- Bone tissue processing for omics presents unique challenges for ST applications.
Purpose of the Study:
- To review current spatial transcriptomics platforms and their limitations.
- To discuss bone sample processing for omics-based approaches.
- To summarize bioinformatics considerations and future directions for ST in musculoskeletal research.
Main Methods:
- Review of existing spatial transcriptomics technologies.
- Analysis of bone tissue decalcification and processing methods for omics.
- Summary of bioinformatics workflows for spatial transcriptomics data.
- Case examples of ST application in musculoskeletal tissues and animal models.
Main Results:
- Current ST platforms have distinct advantages and limitations for musculoskeletal research.
- Bone sample processing requires specific adaptations for successful omics integration.
- Bioinformatics pipelines are essential for analyzing complex spatial transcriptomics data.
- ST has been successfully applied to diverse musculoskeletal tissues and models.
Conclusions:
- Spatial transcriptomics holds significant promise for advancing musculoskeletal research.
- Overcoming technical challenges in bone processing and data analysis is key to wider adoption.
- Future ST applications can address critical biological questions in tissue homeostasis and disease.
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