Intracellular Spatial Transcriptomic Analysis Toolkit (InSTAnT).

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• Imaging-based spatial transcriptomics, like MERFISH, provides detailed cellular process insights.
• Advanced analytical tools are crucial to fully leverage spatial transcriptomics data.
• Understanding intra-cellular molecular organization is key to deciphering cell function.

Approach:

• Developed InSTAnT, a computational toolkit for analyzing spatial transcriptomics data at intra-cellular resolution.
• Utilized specialized statistical tests and graph mining to detect gene co-localization patterns.
• Applied InSTAnT to human cancer cell line and mouse brain datasets.

Key Points:

• InSTAnT identifies gene pairs and modules with significant co-localization within and across cells.
• Discovered novel cell type-specific gene co-localizations in the mouse brain.
• Validated findings using external databases and RNA interaction data, identifying subcellular domains linked to RNA co-localization.

Conclusions:

• InSTAnT effectively extracts intra-cellular molecular relationships from spatial transcriptomics data.
• The identified spatial patterns correlate with RNA interactions, subcellular localization, and function.
• The toolkit generates valuable, testable hypotheses for molecular functions and cellular organization.