Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus

Area of Science:

• Genomics
• Proteomics
• Systems Biology
• Bioinformatics

Background:

• Understanding cellular heterogeneity and function requires simultaneous mapping of gene and protein expression within tissues.
• Current spatial omics technologies often lack the resolution or multi-modal integration needed for comprehensive cell-type identification and pathway analysis.

Purpose of the Study:

• To introduce Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multi-modal spatial omics approach.
• To enable single-cell resolution cell typing and genome-scale interrogation of biological pathways by combining spatial transcriptomics and spatial protein profiling on the same tissue section.

Main Methods:

• DBiTplus employs in situ reverse transcription for cDNA synthesis, microfluidic delivery of DNA oligos for spatial barcoding, and RNaseH-mediated retrieval of barcoded cDNA.
• The intact tissue section is preserved for high-plex protein imaging using CODEX (CO-Detection by INdexing), a cyclic immunofluorescence technique.
• Computational pipelines were developed to register and integrate data from both spatial transcriptomics (DBiT-seq) and spatial proteomics (CODEX) modalities.

Main Results:

• DBiTplus successfully integrated spatial transcriptomics and protein profiling data on the same tissue section.
• Accurate cell typing was achieved within spatial transcriptome spots, enabling image-guided decomposition for single-cell resolved spatial transcriptome atlases.
• The approach was validated on mouse embryos, human lymph nodes, and human lymphoma FFPE tissues, demonstrating its utility across different biological contexts and sample types.

Conclusions:

• DBiTplusCODEX provides a unified workflow for integrative experimental procedures and computational innovation.
• This method facilitates spatially resolved single-cell atlasing and cell-by-cell exploration of biological pathways at a genome-wide scale.
• DBiTplus significantly advances the ability to connect cellular identity with function in complex tissue architectures.