Scoping Review: Methods and Applications of Spatial Transcriptomics in Tumor Research

Area of Science:

• Genomics and Molecular Biology
• Cancer Research
• Bioinformatics

Background:

• Spatial transcriptomics (ST) integrates gene expression data with tissue morphology.
• Advances in ST technology have significantly increased its application in cancer research.
• Understanding gene expression in spatial context is crucial for deciphering complex biological systems.

Purpose of the Study:

• To review current challenges and practical applications of spatial transcriptomics in neoplasm research.
• To summarize existing methods, trends, and data analysis techniques for ST in cancer studies.
• To identify areas for improvement in reproducibility and reliability of ST research.

Main Methods:

• Scoping review of 41 articles published by the end of 2023.
• Analysis of public data repositories.
• Synthesis of common ST platforms, data analysis methods, and integrated data types.

Main Results:

• Cancer biology is a primary focus for ST research, with a growing number of annual publications.
• Visium (10x Genomics) is the dominant ST platform; SCTransform (Seurat) is preferred for data normalization.
• Common applications include tumor microenvironment characterization and cell interaction analysis.
• Nearly half of the reviewed studies lacked comprehensive data processing protocols, impacting reproducibility.

Conclusions:

• Increased transparency in sharing analysis methods is crucial for enhancing ST study reproducibility.
• Careful adaptation of single-cell analysis techniques is recommended for ST data.
• Future ST research in cancer should prioritize robust data processing and transparent reporting to improve reliability.