Spatial transcriptomic approaches for characterising the bone marrow landscape: pitfalls and potential
Rosalin Cooper, Emily Thomas, Anna Sozanska, Carlo Pescia, Daniel Royston
Abstract
Recent years have seen the rapid emergence of spatial transcriptomic (ST) technologies that provide spatially resolved expression-based descriptions of tissue architecture. These approaches can offer a high degree of transcriptional coverage, providing novel opportunities for high-resolution characterisation of tissue microenvironments. Whilst there is now an extensive literature providing benchmarking for quality control (QC) of ST data [ 1 , 2 , 3 , 4 , 5 ], these workflows have exclusively focussed on downstream analysis of expression data without reference to other critical QC steps, namely assessment of cellular morphology, tissue integrity and architectural preservation. We recognise the need for wider discussion of these aspects to inform reliable and accurate ST analysis. Here, we outline existing approaches for spatially-resolved profiling of the bone marrow (BM) and the potential for ST analysis in this context. Drawing on our experience of ST analysis of human BM [ 6 ] we also present a workflow for the preparation of bone marrow trephine (BMT) material and integration with H&E morphology to support reliable downstream analysis, outlining potential pitfalls. Our insights have implications beyond the assessment of BMT material and provide a framework of good practice for generating and analysing ST data.