Spatial transcriptomics and the anatomical pathologist: Molecular meets morphology

Abstract

In recent years anatomical pathology has been revolutionised by the incorporation of molecular findings into routine diagnostic practice, and in some diseases the presence of specific molecular alterations are now essential for diagnosis. Spatial transcriptomics describes a group of technologies that provide up to transcriptome‐wide expression profiling while preserving the spatial origin of the data, with many of these technologies able to provide these data using a single tissue section. Spatial transcriptomics allows expression profiling of highly specific areas within a tissue section potentially to subcellular resolution, and allows correlation of expression data with morphology, tissue type and location relative to other structures. While largely still research laboratory‐based, several spatial transcriptomics methods have now achieved compatibility with formalin‐fixed paraffin‐embedded tissue (FFPE), allowing their use in diagnostic tissue samples, and with further development potentially leading to their incorporation in routine anatomical pathology practice. This mini review provides an overview of spatial transcriptomics methods, with an emphasis on platforms compatible with FFPE tissue, approaches to assess the data and potential applications in anatomical pathology practice.

Molecular stratification of human fetal vaginal epithelium by spatial transcriptome analysis

“…The advent of spatial transcriptomics has ushered in a new era of expression profiling, enabling the interrogation of highly specific regions within tissue sections, even down to subcellular levels. This technology facilitates the correlation of expression data with morphological features, tissue type, and spatial relationships to other structures, thereby offering a more nuanced understanding of multiple tissues and organs [22]. Since there are no spatial transcriptomic data for the vagina, and to construct an unbiased spatial transcriptomic atlas of human vaginal epithelium, our study focused on collecting tissue samples from two human fetuses, aborted at 22 +5 and 22 +6 post-conceptual weeks (PCW).…”