Biology subjects

Haendeler, S.

Publications and source records attributed to Haendeler, S..

3 recordsLinked to original sources

bioRxiv2026

An improved CRISPR-LICHT screen of 120 Tdark genes illuminates new biologically relevant SOX2 targets in human brain organoids

SOX2 is a transcription factor and central regulator of neural progenitor identity, yet the downstream molecular networks through which it supports human brain development remain incompletely characterized. Here, we applied CRISPR-lineage tracing at cellular resolution in heterogeneous tissue (CRISPR-LICHT) to human cerebral organoids to functionally interrogate SOX2-dependent regulatory networks. Using a SOX2-focused library targeting SOX2 together with conserved neurodevelopmental regulators expressed in neural progenitor cells, we showed that CRISPR-LICHT detects reproducible lineage- depletion phenotypes across genes already known to be involved in progenitor maintenance, fate specification, glial differentiation and neuronal maturation. This extends the application of CRISPR-LICHT beyond the severe neural progenitor phenotypes previously characterized for microcephaly-associated genes and demonstrates its ability to detect perturbation effects across a broader set of neurodevelopmental regulators, involving SOX2 targets previously defined in mouse and now open to further understanding in a human model setting. We further screened 120 evolutionarily conserved, poorly characterized SOX2-dependent genes classified as Tdark within the Illuminating the Druggable Genome framework and identified 28 candidate hits whose disruption impaired neural progenitor lineage expansion and/or survival. These candidates included proteins associated with cytoskeletal organization, membrane dynamics and intracellular architecture, suggesting that SOX2-dependent developmental programmes may engage cellular processes beyond transcriptional regulation. Individual downregulation of CDC42EP4, a poorly characterized CDC42 effector linked to cytoskeletal organization, revealed altered distribution of targeted progenitors between ventricular- and subventricular- like compartments, with changes consistent with altered progenitor-state progression. Together, these findings expand the functional landscape of SOX2-dependent regulation in human neural progenitors and identify cellular architecture as a potential component of SOX2-associated developmental programs.

developmental biology↗

bioRxiv2022

Multi-chamber cardioids unravel human heart development and cardiac defects

The number one cause of human fetal death are defects in heart development. Because the human embryonic heart is inaccessible, and the impacts of mutations, drugs, and environmental factors on the specialized functions of different heart compartments are not captured by in vitro models, determining the underlying causes is difficult. Here, we established a human cardioid platform that recapitulates the development of all major embryonic heart compartments, including right and left ventricles, atria, outflow tract, and atrioventricular canal. By leveraging both 2D and 3D differentiation, we efficiently generated progenitor subsets with distinct first, anterior, and posterior second heart field identities. This advance enabled the reproducible generation of cardioids with compartment-specific in vivo-like gene expression profiles, morphologies, and functions. We used this platform to unravel the ontogeny of signal and contraction propagation between interacting heart chambers and dissect how genetic and environmental factors cause region-specific defects in the developing human heart. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/499699v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@c9c629org.highwire.dtl.DTLVardef@f0d521org.highwire.dtl.DTLVardef@1389411org.highwire.dtl.DTLVardef@181098a_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTS- Mesoderm induction and patterning signals specify aSHF, pSHF, and FHF progenitors - Cardiac progenitors sort, co-develop and functionally connect in multi-chamber cardioids - Multi-chamber cardioids coordinate contraction propagation and share a lumen - Multi-chamber platform dissects genetic (ISL1, TBX5, FOXF1) and teratogenic defects

developmental biology↗

bioRxiv2021

Neutral competition within a long-lived population of symmetrically dividing cells shapes the clonal composition of cerebral organoids

Cerebral organoids model the development of the human brain and are an indispensable tool for studying neurodevelopment. Whole-organoid lineage tracing has revealed the number of progeny arising from each initial stem cell to be highly diverse, with lineage sizes ranging from one to more than 20,000 cells. This exceeds what can be explained by existing stochastic models of corticogenesis, indicating the existence of an additional source of stochasticity. We propose an explanation in terms of the SAN model in which this additional source of stochasticity is the survival time of a lineage within a long-lived population of symmetrically dividing cells under neutral competition. We demonstrate that this model explains the experimentally observed variability of lineage sizes and we derive a formula that captures the quantitative relationship between survival time and lineage size. Finally, we show that our model implies the existence of a regulatory mechanism to keeps the size of the symmetrically dividing cell population constant.

developmental biology↗