Project description
How gene regulatory networks enable precise cell engineering
Engineered human cells grown in the laboratory have greatly improved our ability to model human biology and disease. However, single-cell transcriptomic reveals that these cells often differ from natural cells found in the human body. Achieving precise cell engineering remains difficult without understanding the gene regulatory networks (GRNs) that define cell identity. The ERC-funded DECIPHER project aims to address this challenge by decoding GRNs using advanced single-cell technologies. The project will convert human induced pluripotent stem cells into specific neuronal and glial subtypes and study how these cells interact within a multicellular environment. By revealing how GRNs control cell identity and drive maturation, DECIPHER seeks to enable more precise engineering of human cells for disease modelling, cell therapy and regenerative medicine.
Objective
Human cells engineered in vitro have revolutionized our ability to model human biology and diseases, offering exciting opportunities for therapeutic screening and intervention. However, single-cell transcriptomics (scRNA-seq) reveals that engineered cells often remain heterogeneous, immature, and dissimilar to primary counterparts. Precise cell engineering remains challenging without systematic interrogation of gene regulatory networks (GRNs) that establish cell identity. Here, we propose to engineer precise cell fates and states by coupling GRN decoding, perturbation screening, and single-cell technologies. Our vision is to decode GRNs that shape cell identities in fate specification, multicellular communication, and maturation, and use this insight to 1) engineer precise cell subtypes, 2) reconstruct niche-specific signatures, and 3) accelerate maturation. Using human induced pluripotent stem cell (iPSC)-derived neural cells, we will first couple combinatorial transcription factor screening with scRNA-seq to directly induce iPSCs into specific neuron subtypes guided by primary neuron GRNs. Second, we will program glial cell subtypes and reconstruct multi-cellular niche with neurons, analyze how niche cross-talk impacts cell fates and states, and use emerged GRNs to engineer niche-specific signatures. Finally, we will decode dynamic GRNs during neural maturation and screen for determinants to accelerate maturation. DECIPHER aims to dissect the causal links between GRNs and cell identities, offering mechanistic insights into drivers of cell identity changes with the ambitious goals to engineer precise and mature cell subtypes for disease modeling, cell therapy, and regenerative medicine. Our approach holds great potential to study diverse cell fate and state transition events, such as development, reprogramming, regeneration, and cancer. The perturbation atlas generated here will empower AI-driven predictive modelling to guide future cell engineering.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
This project's classification has been human-validated.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
This project's classification has been human-validated.
Keywords
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Programme(s)
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
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HORIZON.1.1 - European Research Council (ERC)
MAIN PROGRAMME
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Topic(s)
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Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Funding Scheme
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Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
HORIZON-ERC - HORIZON ERC Grants
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Call for proposal
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Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
(opens in new window) ERC-2025-STG
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08003 Barcelona
Spain
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