Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples

We designed a Nextflow DSL2-based pipeline, Spatial Transcriptomics Quantification (STQ), for simultaneous processing of 10x Genomics Visium spatial transcriptomics data and a matched hematoxylin and eosin (H&E)-stained whole slide image (WSI), optimized for Patient-Derived Xenograft (PDX) cancer specimens. Our pipeline enables the classification of sequenced transcripts for deconvolving the mouse and human species and mapping the transcripts to reference transcriptomes. We align the H&E WSI with the spatial layout of the Visium slide and generate imaging and quantitative morphology features for each Visium spot. The pipeline design enables multiple analysis workflows, including single or dual reference genomes input and stand-alone image analysis. We show the utility of our pipeline on a dataset from Visium profiling of four melanoma PDX samples. The clustering of Visium spots and clustering of H&E imaging features reveal similar patterns arising from the two data modalities. The PDX model WISTAR WM4237-1 is a BRAF V600E mutant metastatic melanoma of a subcutaneously implanted solid tumor on NSG mouse #1337, passage 0. The tumor was grown untreated by any therapy. The four samples are near adjacent tissue sections from the tumor tissue block. The samples were analyzed with 10x Visium Spatial Gene Expression.