Safeguarding Cell Fate by Terminal Repression during Development and Disease

Project Information

SafeFate

Grant agreement ID: 804710

DOI

10.3030/804710

Project closed

EC signature date 14 January 2019

Start date 1 February 2019

End date 31 January 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 761 489,00

EU contribution

€ 1 761 489,00

Coordinated by

DEUTSCHES KREBSFORSCHUNGSZENTRUM HEIDELBERG
Germany

Periodic Reporting for period 4 - SafeFate (Safeguarding Cell Fate by Terminal Repression during Development and Disease)

Reporting period: 2023-08-01 to 2025-01-31

Summary of the context and overall objectives of the project

Molecular master regulators and transcription factors that activate gene networks during development are well characterized, whereas the mechanisms that terminally repress alternative cell fates to determine cell identity and function remain only partially understood. This project aimed to demonstrate that active cell type-specfic gene silencing, so-called safeguard repression, is a universal mechanism essential to induce and maintain stable cell identity. Our previous work showed that the neuron-specific transcriptional repressor MYT1L is crucial for neuronal cell identity, as it represses non-neuronal gene programs in neurons. This project further investigated whether there are additional safeguard repressors that prevent alternative lineages from developing, and whether failure to repress unwanted cell fate programs due to mutations in these factors could result in disease. Our research aimed to deliver new insights into how to prevent or treat diseases associated with cell identity loss, such as neurological disorders or cancer, and to develop new strategies to reprogram cells for regenerative medicine. Our overarching concept can be extended to various other cell types, providing the basis for improved disease modelling and cell-based therapies.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We have successfully completed our research goals across all three aims:

For Aim 1, which investigates whether MYT1L depletion leads to loss of neuronal identity and mental disorders, we have generated and studied new Myt1l knockout mouse models and CRISPR-engineered human induced neurons. MYT1L-deficient mice displayed striking neurological and behavioural phenotypes resembling MYT1L syndrome in patients, including impaired social behaviour and altered neuronal gene expression. Importantly, we showed that MYT1L-deficient human neurons exhibit similar molecular and electrophysiological defects. An unexpected key finding was that these neuronal dysfunctions can be reversed by acutely applying an FDA-approved anti-epileptic drug (Weigel et al., Molecular Psychiatry 2023). Our data now demonstrate for the first time that MYT1L haploinsufficiency can cause neurodevelopmental disorders, but also reveal that treatment options for these conditions exist.

For Aim 2, which focuses on the mechanistic link between safeguard repressors and the epigenetic machinery, we identified interaction partners of MYT1L directly in human neurons (Weigel et al., Molecular Psychiatry 2023). We found that MYT1L associates with chromatin regulators implicated in autism spectrum disorders, suggesting that they function together to maintain proper neuronal development. Using genetic rescue experiments, we further demonstrated that overexpression of MYT1L in mature neurons can restore neuronal function, suggesting its lifelong role in safeguarding neuronal identity.

For Aim 3, which seeks to identify safeguard repressors in non-neuronal cell types, we predicted safeguard repressors across 18 cell types. Our experimental validation identified PROX1 as a liver-specific safeguard repressor that stabilizes hepatocyte identity by directly suppressing alternative gene programs. We showed that PROX1 is required for liver regeneration and prevents tumour formation in vivo. Conversely, Prox1 loss destabilizes liver identity and promotes tumour progression, consistent with clinical observations (Lim et al., Nature Genetics 2025). These results were published and resulted in a priority patent filing for potential liver cancer therapies. Moreover, this work initiated new research directions exploring the role of safeguard repressors in brain cancer, specifically glioblastoma.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Within this project, we have identified unexpected, yet highly promising, phenotypes resulting from MYT1L deficiency in both mouse models and human neurons. Notably, the observed neuronal dysfunction is amenable to acute pharmacological intervention even after brain development is complete, which contradicts prior assumptions that MYT1L-associated disorders are irreversible developmental defects. Our research shows that existing FDA-approved drugs can restore neuronal function and even normalise behavioural deficits in MYT1L-deficient mice. These results have already led to off-label treatment of patients with MYT1L syndrome, demonstrating immediate clinical relevance.

In parallel, our identification of PROX1 as a safeguard repressor in the liver represents a potential breakthrough, demonstrating that safeguard repression is not limited to the nervous system but extends to other organs as well. Manipulating PROX1 nearly doubled survival in liver cancer mouse models, potentially providing a new therapeutic strategy to stabilize cell identity and combat tumor plasticity, which holds promise for future cancer therapies.

Beyond scientific advancements, our project has generated significant societal impact. We organised the first MYT1L Syndrome Family Meeting in Germany, bringing together over 60 participants, and our research has been featured in national and international media, raising public awareness for rare diseases, cancer research, and the importance of cell identity safeguarding.

Overall, our work introduces a new biological concept—safeguard repression as a universal mechanism to protect cell identity—and provides concrete translational approaches for treating brain disorders and cancer. This opens exciting new possibilities for personalised therapies and reinforces the potential of safeguard repressors as targets for regenerative medicine and disease prevention.

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