Single-cell spatial transcriptomics of fixed, paraffin-embedded biopsies reveals colitis-associated cell networks

Area of Science:

• Biotechnology
• Genomics
• Immunology

Background:

• Archived formalin-fixed, paraffin-embedded (FFPE) tissues offer vast potential for translational research.
• Developing robust imaging-based, single-cell spatial transcriptomics (iSCST) for FFPE samples is crucial for analyzing clinical specimens.

Purpose of the Study:

• To establish a reliable iSCST framework for analyzing archived FFPE mucosal biopsies from inflammatory bowel disease (IBD) patients.
• To benchmark different iSCST platforms for FFPE tissue analysis.

Main Methods:

• Benchmarking three iSCST platforms using 57 FFPE mucosal biopsies (9 healthy controls, 11 ulcerative colitis patients).
• Applying a uniform data processing pipeline including cell segmentation, transcript detection, annotation, differential gene expression, and neighborhood enrichment.
• Validating iSCST findings with external bulk transcriptomic datasets.

Main Results:

• A custom 290-plex Xenium gene panel demonstrated high sensitivity and specificity for transcript detection in FFPE tissues.
• Identified inflammation-associated fibroblasts (IAFs) and monocytes as a colitis-associated cellular neighborhood.
• Discovered distinct transcriptomic signatures associated with Vedolizumab (VDZ) responsiveness, differentiating responders from non-responders.

Conclusions:

• The optimized iSCST framework enables the study of colitis-associated cellular networks in routine clinical FFPE samples.
• FFPE-based biomarkers derived from iSCST can be integrated into clinical workflows for potential patient risk stratification.