Abstract
The capability to spatially explore RNA biology in formalin-fixed paraffin-embedded (FFPE) tissues holds transformative potential for histopathology research. Here, we present pathology-compatible deterministic barcoding in tissue (Patho-DBiT) by combining in situ polyadenylation and computational innovation for spatial whole transcriptome sequencing, tailored to probe the diverse RNA species in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for 5 years. Furthermore, genome-wide single-nucleotide RNA variants can be captured to distinguish malignant subclones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis. Single-cell level Patho-DBiT dissects the spatiotemporal cellular dynamics driving tumor clonal architecture and progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to aid in clinical pathology evaluation.
Overview
- The study presents Patho-DBiT, a method for spatially exploring RNA biology in formalin-fixed paraffin-embedded (FFPE) tissues. The method combines in situ polyadenylation and computational innovation for spatial whole transcriptome sequencing, tailored to probe the diverse RNA species in clinically archived FFPE samples. The primary objective of the study is to demonstrate the feasibility and potential of Patho-DBiT for spatial whole transcriptome sequencing in FFPE tissues, and to identify key RNA biology features in these tissues. The study aims to provide a valuable platform for clinical pathology evaluation.
Comparative Analysis & Findings
- The study demonstrates the feasibility of Patho-DBiT for spatial whole transcriptome sequencing in FFPE tissues, and identifies key RNA biology features in these tissues. The method allows for spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for 5 years. The study also identifies genome-wide single-nucleotide RNA variants that can distinguish malignant subclones from non-malignant cells in human lymphomas. Furthermore, the method maps microRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis. Single-cell level Patho-DBiT dissects the spatiotemporal cellular dynamics driving tumor clonal architecture and progression.
Implications and Future Directions
- The study's findings demonstrate the potential of Patho-DBiT for clinical pathology evaluation and provide a valuable platform for unraveling rich RNA biology in FFPE tissues. The method's ability to map microRNA regulatory networks and RNA splicing dynamics, and to distinguish malignant subclones from non-malignant cells, highlights its potential for identifying key drivers of tumorigenesis and progression. Future research directions could include expanding the method's applicability to other types of tissues and diseases, and integrating it with other molecular profiling techniques to provide a more comprehensive understanding of tissue-level biology. Additionally, the method's ability to map single-cell level RNA dynamics could be leveraged for personalized cancer treatment and drug discovery.