Biology subjects

Emmenegger, L.

Publications and source records attributed to Emmenegger, L..

3 recordsLinked to original sources

bioRxiv2026

MicroRNAs are required within a critical time window to define neural patterning during early human brain development

MicroRNAs (miRNAs) are key post-transcriptional regulators of cell state transitions, yet their function in early human brain development is largely unknown. Here, we present a longitudinal analysis of miRNA function in developing human forebrain organoids. We show that mRNAs and miRNAs expression mirrors known developmental gene programs and that miRNA biogenesis peaks at neural commitment. To test the function of miRNAs in regulating commitment, we impaired their biogenesis at defined stages. miRNA disruption during pre-neuronal commitment caused severe patterning defects, whereas post-commitment perturbation had minimal impact on forebrain identity. We show that miRNA loss during pre-commitment increased WNT and BMP signaling, thus shifting cell fates towards non-forebrain identity such as midbrain/hindbrain. These effects could be partially rescued by expressing five miRNAs. Our findings uncover a critical time window where miRNAs regulate morphogen signaling in early human neurodevelopment, establishing them as essential temporal determinants of cell fate and brain regional identity.

molecular biology↗

bioRxiv2021

Optogenetic perturbations of RNA expression in tissue space

Organoids derived from stem cells become increasingly important to study human development and to model disease. However, methods are needed to control and study spatio-temporal patterns of gene expression in organoids. To this aim, we combined optogenetics and gene perturbation technologies to activate or knock-down RNA of target genes, at single-cell resolution and in programmable spatio-temporal patterns. To illustrate the usefulness of our approach, we locally activated Sonic Hedgehog (SHH) signaling in an organoid model for human neurodevelopment. High-resolution spatial transcriptomic and single-cell analyses showed that this local induction was sufficient to generate stereotypically patterned organoids in three dimensions and revealed new insights into SHHs contribution to gene regulation in neurodevelopment. With this study, we propose optogenetic perturbations in combination with spatial transcriptomics as a powerful technology to reprogram and study cell fates and tissue patterning in organoids.

bioengineering↗

bioRxiv2019

Differential efficacies of Cas nucleases on microsatellites involved in human disorders and associated off-target mutations

Microsatellite expansions are the cause of more than 20 neurological or developmental human disorders. Shortening expanded repeats using specific DNA endonucleases may be envisioned as a gene editing approach. Here, a new assay was developed to test several CRISPR-Cas nucleases on microsatellites involved in human diseases, by measuring at the same time double-strand break rates, DNA end resection and homologous recombination efficacy. Broad variations in nuclease performances were detected on all repeat tracts. Streptococcus pyogenes Cas9 was the most efficient of all. All repeat tracts did inhibit double-strand break resection. We demonstrate that secondary structure formation on the guide RNA was a major determinant of nuclease efficacy. Using deep sequencing, off-target mutations were assessed genomewide. Out of 221 CAG/CTG or GAA/TTC trinucleotide repeats of the yeast genome, three were identified as carrying statistically significant low frequency mutations, corresponding to off-target effects.

genetics↗