Vision & Objectives

Single-cell technologies enable a fundamentally new perspective for understanding biology, with great potential to drive therapeutic advances in precision and regenerative medicine. In order to streamline research endeavours worldwide, the Human Cell Atlas (HCA) initiative provides global coordination and serves as a comprehensive reference map of the types and properties of all human cells aiming to advance our understanding of human physiology and pathology.

As European contribution to this global endeavour, HCA|Organoid sets out to create the first “Organoid Cell Atlas” as a key component of the HCA that complements profiling of primary tissue samples with comprehensive maps of a tractable model for functional studies. By pre-publication data sharing via the HCA infrastructure and by establishing an Organoid Cell Atlas Portal for user-friendly analysis, the project will firmly root organoids within the HCA.

The HCA|Organoid project brings together specialists in organoid technology, single-cell epigenome/transcriptome profiling, advanced imaging technology, bioinformatics and systems genetics from Austria, Germany, the Netherlands and Switzerland. The core focus of the interdisciplinary research team is the establishment of single-cell maps for organoids from healthy donors, including induced brain organoids derived from pluripotent stem cells and colon organoids derived from primary patient samples.

The HCA|Organoid pursues following visions and objectives:

  • Foster synergies between single-cell profiling and organoid technologies

    The comprehensive analysis of cell types using single-cell technologies allows comparative molecular profiling of organoids and matched primary tissue which empowers the development of improved organoid protocols, while simultaneously providing a scalable readout for functional experiments.

    HCA|Organoid will set up an “Organoid Data Portal” providing user‐friendly access to organoid single‐cell data and connecting organoid profiles with single‐cell profiles of primary human organs.

  • Characterize and validate organoids as faithful models of human biology

    The Organoid Cell Atlas seeks to establish organoids as in vitro models within the HCA to deliver on the HCA’s goal of deeply impacting biology and medicine, since organoids enable detailed functional dissection and perturbation studies in a human context.

    Single-cell technologies are valuable tools for better characterization of organoids and will help to define quality standards and reference catalogs. Ultimately, this will guide the development of new organoid models that recapitulate the heterogeneous complexity of primary tissues, and it will leverage the power of organoids for large-scale perturbations and functional studies.

  • Building a network for organoid research

    HCA|Organoid establishes the first version of the Organoid Cell Atlas, which may act as a nucleus for a broader, collaborative, global initiative. In that sense, HCA|Organoid seeks to:

    • Encourage and standardize single-cell profiling of human organoids
    • Facilitate access to single-cell organoid data (and informative metadata) via HCA data infrastructure
    • Establish computational methods and tools for connecting organoid profiles with primary tissue data
    • Put organoids into their biological context using HCA profiles of the in vivo counterparts
  • Maximize the utility and impact for the broader scientific community

    HCA|Organoid is committed to pursue following strategy:

    • Newly established organoids will be made available as a “living biobank” (colon) or as a set of precise protocols for derivation from biobanked iPS cell lines (brain).
    • Single-cell profiles will be made public as rapidly as possible, in concordance with the HCA’s strong commitment to data sharing, local ethical regulations, and the European data protection law (GDPR).
    • The practical utility of the Organoid Cell Atlas will be explored in a series of disease-centric pilot studies, pursuing CRISPR single-cell profiling and disease modeling.
    • The Organoid Cell Atlas Portal will be developed into a public, sustainable, and widely used infrastructure for finding, accessing, analyzing, and interpreting single-cell data of human organoids.