Biology subjects

Gruen, D.

Publications and source records attributed to Gruen, D..

6 recordsLinked to original sources

bioRxiv2026

Notch-independent Her6 contributes to control of neural stem cell maintenance by shifting Notch signaling from lateral inhibition towards lateral induction mode

The growing brain faces the challenge to establish neural stem cell (NSC) populations that accomplish both stable NSC maintenance and dynamic generation of progenitors. Lineage-specific scRNA-seq and time series transcriptome analyses upon overexpression of Notch signaling components in the larval zebrafish brain reveal differential contributions of Notch signaling and Notch-independent Her6, a HES1 homolog, to NSC regulation. Notch signaling and Her6 distinctly regulate cell cycle genes to control G0/G1 or G2 exit and promote quiescence. Her6 and Notch activity combined differentially control delta, jagged, lfng and notch3 expression to potentially shift Notch signaling from Delta-driven lateral inhibition to Jagged-Notch3-mediated lateral induction. We propose that Her6 integrates cell-autonomous lineage-based information and lateral induction-mediated non-autonomous self-organization of neural proliferation zones. Her6-dependent lateral induction maintains persistent NSC patches in ventricular compartments with ongoing neurogenesis, and establishes coherent populations of long-term NSCs in active proliferation zones.

developmental biology↗

bioRxiv2023

Piezo1 stretch-activated channel activity differs between bone marrow-derived and cardiac tissue-resident macrophages

Macrophages (M{Phi}) play pivotal roles in tissue homeostasis and repair. Their mechanical environment recently emerged as a key modulator of various cell functions, and M{Phi} mechanosensitivity is likely to be critical for cellular activity in particular in a rhythmically contracting organ such as the heart. M{Phi}, in-vitro-differentiated from bone marrow (M{Phi}BM), form a popular cell model for research. This study explores the activity of stretch-activated ion channels (SAC) in murine M{Phi}BM and compares it to SAC activity in cardiac tissue-resident M{Phi} (M{Phi}TR). Our main findings are: i) M{Phi}BM and M{Phi}TR have stretch-induced currents, indicating expression of functional SAC at their plasma membrane; ii) the current profiles in M{Phi}BM and in M{Phi}TR show characteristics of cation non-selective SAC; iii) unlike in M{Phi}BM, Piezo1 ion channel activity at the plasma membrane of M{Phi}TR is not detectable, neither by assessing electrophysiological activity using the patch clamp technique, nor by measuring cytosolic calcium concentration upon perfusion with Yoda1, a Piezo1 channel agonist. In mature scars after ventricular cryoablation, stretch-induced current characteristics of M{Phi}TR are not significantly different compared to non-injured control tissue, even though scars are expected to contain a mix of pre-existing and circulation-recruited M{Phi}. This suggests that M{Phi} invading injured cardiac tissue either phenoconvert their mechanosensitivity from M{Phi}BM to M{Phi}TR, or that the in vitro differentiation protocols used to obtain M{Phi}BM generate cells that differ from M{Phi} recruited from the circulation during tissue repair in vivo. Further investigations will explore SAC identity in lineage-traced M{Phi} in scar tissue, and compare mechanosensitivity of circulating monocytes with that of M{Phi}BM. Key pointsO_LIM{Phi}BM and M{Phi}TR have stretch-induced currents, indicating expression of functional SAC at their plasma membrane; C_LIO_LIThe current profiles in M{Phi}BM and in M{Phi}TR show characteristics of cation non-selective SAC; C_LIO_LIUnlike in M{Phi}BM, Piezo1 ion channel activity at the plasma membrane of M{Phi}TR is not detectable C_LI

biophysics↗

bioRxiv2023

A common gene signature of the right ventricle in failing rat and human hearts

The molecular mechanisms of progressive right heart failure are incompletely understood. We systematically compared rat models of pulmonary artery or aortic banding to identify the transcriptomic changes that occur over months in the failing right versus left ventricle. Detailed bioinformatics analyses of 181 RNAseq datasets from cardiomyocytes or whole heart samples from these models, led to the identification of gene signatures, protein, and transcription factor networks specific to ventricles, compensated or decompensated disease states and type of heart failure. RNA-FISH approaches confirmed PAB-mediated regulation of key genes and revealed striking, spatially heterogeneous mRNA expression in the heart. Intersection of rat PAB-specific gene sets with 95 transcriptome data sets from human patients with chronic thromboembolic pulmonary hypertension led to the identification of more than 50 genes whose expression levels strongly correlated with the severity of right heart disease. Together, these data define a conserved, differentially regulated genetic network that coordinates progressive right heart failure in rats and humans. HighlightsO_LISide-by-side comparisons of RV or LV transcriptomes in the slowly failing rat heart C_LIO_LIIdentification of RV-specific gene sets in heart hypertrophy versus heart failure C_LIO_LIIdentification of RV gene sets correlating with severity of human CTEPH C_LIO_LIDevelopment of a core gene signature characteristic for RV failure C_LI

genomics↗

bioRxiv2022

DOT1L activity affects cell lineage progression in the developing brain by controlling metabolic programs

Cortical neurogenesis depends on the tight balance between self-renewal and differentiation of apical progenitors (APs), the key progenitor type generating all other neural cells including neocortical neurons. We here report the activity of the histone methyltransferase DOT1L as a gatekeeper for AP cell identity. Combining lineage tracing with single-cell RNA sequencing of clonally related cells, we explore consequences of DOT1L inhibition on AP lineage progression during neurogenesis in the embryonic mouse neocortex. At the cellular level, DOT1L inhibition led to increased neurogenesis driven by a shift from asymmetric self-renewing to symmetric neurogenic divisions of APs. At the molecular level, we show that DOT1L activity preserved AP identity by promoting transcription of a gene set involved in AP metabolism. On a mechanistic level, DOT1L inhibition increased expression of metabolic genes, including microcephaly-associated Asparagine synthetase (Asns) and overexpression of ASNS in APs resulted in increased neuronal differentiation. Asns expression was predicted to be controlled through EZH2 and we show that DOT1L activity allows PRC2-mediated repression of Asns expression. Importantly, inhibition of ASNS activity rescued increased AP differentiation upon DOT1L inhibition. Our data show that DOT1L activity/PRC2 crosstalk controls AP lineage progression by regulating AP metabolism, and they provide a mechanistic view on how DOT1L activity might affect neocortical neurogenesis.

developmental biology↗

bioRxiv2020

Spatiotemporal sequence of mesoderm and endoderm lineage segregation during mouse gastrulation

Anterior mesoderm (AM) and definitive endoderm (DE) progenitors represent the earliest embryonic cell types that are specified during germ layer formation at the primitive streak (PS) of the mouse embryo. Genetic experiments indicate that both lineages segregate from Eomes expressing progenitors in response to different NODAL signaling levels. However, the precise spatiotemporal pattern of the emergence of these cell types and molecular details of lineage segregation remain unexplored. We combined genetic fate labeling and imaging approaches with scRNA-seq to follow the transcriptional identities and define lineage trajectories of Eomes dependent cell types. All cells moving through the PS during the first day of gastrulation express Eomes. AM and DE specification occurs before cells leave the PS from discrete progenitor populations that are generated in distinct spatiotemporal patterns. Importantly, we dont find evidence for the existence of progenitors that co-express markers of both cell lineages suggesting an immediate and complete separation of AM and DE lineages. Summary statementCells lineages are specified in the mouse embryo already within the primitive streak where Mesp1+ mesoderm and Foxa2+ endoderm are generated in a spatial and temporal sequence from unbiased progenitors.

developmental biology↗

bioRxiv2018

Tdrd6a regulates the aggregation of Buc into functional subcellular compartments that drive germ cell specification

In recent years, it has become clear that phase separation represents an important class of subcellular compartmentalization. However, relatively little is known about how the formation or disassembly of such compartments is regulated. In zebrafish, the Balbiani body (Bb) and the germ plasm (Gp) are phase-separated structures essential for germ cell specification and home to many germ cell-specific mRNAs and proteins. Throughout development, these structures range from a single large aggregate (Bb), to a dispersed state and back to relatively large assemblies (Gp). Formation of the Bb requires Bucky ball (Buc), a protein with prion-like properties. We found that the multi-tudor domain-containing protein Tdrd6a interacts directly with Buc, affecting its mobility and aggregation properties. Importantly, lack of this regulatory interaction leads to significant defects in germ cell development. Our work presents a new mechanism for how prion-like protein-aggregations can be regulated and highlights the biological relevance of such regulatory events.

molecular biology↗