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

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Deterministic Barcoding in Tissue sequencing plus (DBiTplus) integrates spatial transcriptomics and protein profiling. This approach enables single-cell resolution spatial atlasing and pathway exploration cell-by-cell.

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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.