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IGTP joins new ISIDORE project for cross-research activity: PATH2XNAT

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PATH2XNAT is an integrated solution for Digital Pathomics (DP) and Spatial Transcriptomics (ST) image analysis, facilitating research into the pathogenesis of infectious diseases. Founded by ISIDORe's Joint Research Activities Programme 2023-2025, PATH2XNAT is a data management and analysis platform leveraging the open-source software tools XNAT and Galaxy, to accelerate investigations into the pathogenesis of infectious diseases.

PATH2XNAT is a groundbreaking consortium coordinated by Erasmus MC (EMC), University Medical Centre Rotterdam, which aims to:

  • Enhance the XNAT data management platform to accommodate Digital Pathomics (DP) and Spatial Transcriptomics (ST) data.
  • Establish connectivity between XNAT and the Galaxy analysis platform.
  • Demonstrate the efficacy of PATH2XNAT through a study on SARS-CoV-2 pathogenesis.

PATH2XNAT is a collaborative effort that merges the capabilities of 3 European research infrastructures: Euro-BioImaging, ELIXIR, and EATRIS through a consortium comprised by the following partners: Germans Trias i Pujol Research Institute (IGTP), EMC and Charité Universitätsmedizin Berlin.

This project therefore presents a true joint research action. The consortium partners have very complementary expertise: EMC, with the Population Imaging node, will expand XNAT's capabilities to support DP and ST images and develop Galaxy workflows for DP and ST analysis. Charité will generate ST data from SARS-CoV-2 infected tissue for testing, while the High Content Genomics and Bioinformatics team at IGTP will conduct further analysis on ST data and serve as a pilot user for the PATH2XNAT platform. 

“Through this project we want to incorporate know-how to the IGTP in spatial transcriptomic data analysis. The project allows us to hire a person full-time. Data will be generated from COVID19 patient lung samples and analysed in depth at the individual cell level while preserving the histology of the tissue. The study is focused on determining predictive markers of progression in prothrombotic lesions triggering patient death, through the study of the expression of 300 human and SARS-COV2 virus genes, incorporating novel markers for cell types and states derived from state-of-the-art single cell lung atlases” explains Lauro Sumoy, head of the High Content Genomics and Bioinformatics platform at IGTP.

ISIDORe's funding has enabled the assembly of the consortium, which will focus on the creation of PATH2XNAT, a data management and analysis platform leveraging XNAT and Galaxy, that aims to accelerate investigations into the pathogenesis of infectious diseases. This enhanced platform will integrate fast-tracking workflows and preparedness tools to advance in understanding the interactions between host-pathogen that will lead to innovative prevention and treatment approaches of infectious diseases.