Human Cell Atlas & single-cell biology of organoids

Single-cell sequencing and spatial profiling technologies uncover the molecular complexity that is inherent in human organs. We contribute to the Human Cell Atlas on its quest to map all human cell types, with a focus on human organoids as experimentally tractable models of development, disease, and therapy.

Single-cell technologies provide a fundamentally new perspective for understanding biology, with profound potential to drive therapeutic advances. They enable us to revisit human anatomy and physiology with unprecedented molecular resolution. Moreover, these assays help uncover the hidden cellular heterogeneity that is present both in primary tissues and in complex in vitro disease models, thereby contributing to robust, reproducible biomedical research and clinical translation.

We are using single-cell technologies in a range of applications, organs, and diseases. Most notably, we have initiated an Organoid Cell Atlas initiative, as a ‘Biological Network’ within the Human Cell Atlas (HCA), and we coordinate the HCA|Organoid consortium aimed at establishing comprehensive single-cell profiles of brain and colon organoids (funded by the European Union).

Organoids recapitulate important aspects of human biology in the lab, thereby allowing us to perform highly interventional studies that would otherwise be impossible in human. Using high-throughput functional assays such as CRISPR screens with single-cell sequencing readout (with our CROP-seq and scifi-RNA-seq methods) and cell-cell interaction profiling in co-cultures of organoids and immune cells, we study human biology and human diseases in an exciting new way.

Publications

The Organoid Cell Atlas

The Organoid Cell Atlas

Bock C, Boutros M, Camp JG, Clarke L, Clevers H, Knoblich JA, Liberali P, Regev A, Rios AC, Stegle O, Stunnenberg HG, Teichmann SA, Treutlein B, Vries RGJ, the Human Cell Atlas ‘Biological Network’ Organoids

Nature Biotechnology  39, 13-17 (2021). DOI: 10.1038/s41587-020-00762-x

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Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets

Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets

Marquina-Sanchez B*, Fortelny N*, Farlik M*, Vieira A, Collombat P, Bock C*, Kubicek S*

Genome Biology  21, 106 (2020). DOI: 10.1186/s13059-020-02006-2

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Ultra-high throughput single-cell RNA sequencing by combinatorial fluidic indexing

Ultra-high throughput single-cell RNA sequencing by combinatorial fluidic indexing

Datlinger P*, Rendeiro AF*, Boenke T, Krausgruber T, Barreca D, Bock C

Manuscript submitted  (2019). DOI: 10.1101/2019.12.17.879304

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Pooled CRISPR screening with single-cell transcriptome readout

Pooled CRISPR screening with single-cell transcriptome readout

Datlinger P, Schmidl C, Rendeiro A, Krausgruber T, Traxler P, Klughammer J, Schuster L, Kuchler A, Alpar D, Bock C

Nature Methods  14, 297-301 (2017). DOI: 10.1038/nmeth.4177

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Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types

Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types

Li J*, Klughammer J*, Farlik M*, Penz T*, Spittler A, Barbieux C, Berishvili E, Bock C*, Kubicek S*

EMBO Reports  17, 178-187 (2016). DOI: 10.15252/embr.201540946

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* shared first or shared senior authorship

The Organoid Cell Atlas