A novel dual reporter embryonic stem cell line for toxicological assessment of teratogen-induced perturbation of anterior-posterior patterning of the heart

MultiCBlo: Enhancing predictions of compound-induced inhibition of cardiac ion channels with advanced multimodal learning

Predicting compound-induced inhibition of cardiac ion channels is crucial and challenging, significantly impacting cardiac drug efficacy and safety assessments. Despite the development of various computational methods for compound-induced inhibition prediction in cardiac ion channels, their performance remains limited. Most methods struggle to fuse multi-source data, relying solely on specific dataset training, leading to poor accuracy and generalization. We introduce MultiCBlo, a model that fuses multimodal information through a progressive learning approach, designed to predict compound-induced inhibition of cardiac ion channels with high accuracy. MultiCBlo employs progressive multimodal information fusion technology to integrate the compound's SMILES sequence, graph structure, and fingerprint, enhancing its representation. This is the first application of progressive multimodal learning for predicting compound-induced inhibition of cardiac ion channels, to our knowledge. The objective of this study was to predict the compound-induced inhibition of three major cardiac ion channels: hERG, Cav1.2, and Nav1.5. The results indicate that MultiCBlo significantly outperforms current models in predicting compound-induced inhibition of cardiac ion channels. We hope that MultiCBlo will facilitate cardiac drug development and reduce compound toxicity risks. Code and data are accessible at: https://github.com/taowang11/MultiCBlo. The online prediction platform is freely accessible at: https://huggingface.co/spaces/wtttt/PCICB.

TAF1 bromodomain inhibition as a candidate epigenetic driver of congenital heart disease

Heart formation requires transcriptional regulators that underlie congenital anomalies and the fetal gene program activated during heart failure. Attributing the effects of congenital heart disease (CHD) missense variants to disruption of specific protein domains allows for a mechanistic understanding of CHDs and improved diagnostics. A combined chemical and genetic approach was employed to identify novel CHD drivers, consisting of chemical screening during pluripotent stem cell (PSC) differentiation, gene expression analyses of native tissues and primary cell culture models, and the in vitro study of damaging missense variants from CHD patients. An epigenetic inhibitor of the TATA-Box Binding Protein Associated Factor 1 (TAF1) bromodomain was uncovered in an unbiased chemical screen for activators of atrial and ventricular fetal myosins in differentiating PSCs, leading to the development of a high affinity inhibitor (5.1 nM) of the TAF1 bromodomain, a component of the TFIID complex. TAF1 bromodomain inhibitors were tested for their effects on stem cell viability and cardiomyocyte differentiation, implicating a role for TAF1 in cardiogenesis. Damaging TAF1 missense variants from CHD patients were studied by mutational analysis of the TAF1 bromodomain, demonstrating a repressive role of TAF1 that can be abrogated by the introduction of damaging bromodomain variants or chemical TAF1 bromodomain inhibition. These results indicate that targeting the TAF1/TFIID complex with chemical compounds modulates cardiac transcription and identify an epigenetically-driven CHD mechanism due to damaging variants within the TAF1 bromodomain.

Pharmacological Manipulation of Wnt/β-Catenin Signaling Pathway in Human Neural Precursor Cells Alters Their Differentiation Potential and Neuronal Yield

The canonical Wnt/β-catenin pathway is a master-regulator of cell fate during embryonic and adult neurogenesis and is therefore a major pharmacological target in basic and clinical research. Chemical manipulation of Wnt signaling during in vitro neuronal differentiation of stem cells can alter both the quantity and the quality of the derived neurons. Accordingly, the use of Wnt activators and blockers has become an integral part of differentiation protocols applied to stem cells in recent years. Here, we investigated the effects of the glycogen synthase kinase-3β inhibitor CHIR99021, which upregulates β-catenin agonizing Wnt; and the tankyrase-1/2 inhibitor XAV939, which downregulates β-catenin antagonizing Wnt. Both drugs and their potential neurogenic and anti-neurogenic effects were studied using stable lines human neural precursor cells (hNPCs), derived from embryonic stem cells, which can be induced to generate mature neurons by chemically-defined conditions. We found that Wnt-agonism by CHIR99021 promotes induction of neural differentiation, while also reducing cell proliferation and survival. This effect was not synergistic with those of pro-neural growth factors during long-term neuronal differentiation. Conversely, antagonism of Wnt by XAV939 consistently prevented neuronal progression of hNPCs. We show here how these two drugs can be used to manipulate cell fate and how self-renewing hNPCs can be used as reliable human in vitro drug-screening platforms.

GATA-targeted compounds modulate cardiac subtype cell differentiation in dual reporter stem cell line

Background

Pharmacological modulation of cell fate decisions and developmental gene regulatory networks holds promise for the treatment of heart failure. Compounds that target tissue-specific transcription factors could overcome non-specific effects of small molecules and lead to the regeneration of heart muscle following myocardial infarction. Due to cellular heterogeneity in the heart, the activation of gene programs representing specific atrial and ventricular cardiomyocyte subtypes would be highly desirable. Chemical compounds that modulate atrial and ventricular cell fate could be used to improve subtype-specific differentiation of endogenous or exogenously delivered progenitor cells in order to promote cardiac regeneration.

Methods

Transcription factor GATA4-targeted compounds that have previously shown in vivo efficacy in cardiac injury models were tested for stage-specific activation of atrial and ventricular reporter genes in differentiating pluripotent stem cells using a dual reporter assay. Chemically induced gene expression changes were characterized by qRT-PCR, global run-on sequencing (GRO-seq) and immunoblotting, and the network of cooperative proteins of GATA4 and NKX2-5 were further explored by the examination of the GATA4 and NKX2-5 interactome by BioID. Reporter gene assays were conducted to examine combinatorial effects of GATA-targeted compounds and bromodomain and extraterminal domain (BET) inhibition on chamber-specific gene expression.

Results

GATA4-targeted compounds 3i-1000 and 3i-1103 were identified as differential modulators of atrial and ventricular gene expression. More detailed structure-function analysis revealed a distinct subclass of GATA4/NKX2-5 inhibitory compounds with an acetyl lysine-like domain that contributed to ventricular cells (%Myl2-eGFP+). Additionally, BioID analysis indicated broad interaction between GATA4 and BET family of proteins, such as BRD4. This indicated the involvement of epigenetic modulators in the regulation of GATA-dependent transcription. In this line, reporter gene assays with combinatorial treatment of 3i-1000 and the BET bromodomain inhibitor (+)-JQ1 demonstrated the cooperative role of GATA4 and BRD4 in the modulation of chamber-specific cardiac gene expression.

Conclusions

Collectively, these results indicate the potential for therapeutic alteration of cell fate decisions and pathological gene regulatory networks by GATA4-targeted compounds modulating chamber-specific transcriptional programs in multipotent cardiac progenitor cells and cardiomyocytes. The compound scaffolds described within this study could be used to develop regenerative strategies for myocardial regeneration.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13287-021-02259-z.

Cholecystokinin peptide signaling is regulated by a TBX5-MEF2 axis in the heart

The procholecystokinin (proCCK) gene encodes a secreted peptide known to regulate the digestive, endocrine, and nervous systems. Though recently proposed as a biomarker for heart dysfunction, its physiological role in both the embryonic and adult heart is poorly understood, and there are no reports of tissue-specific regulators of cholecystokinin signaling in the heart or other tissues. In the present study, mRNA of proCCK was observed in cardiac tissues during mouse embryonic development, establishing proCCK as an early marker of differentiated cardiomyocytes which is later restricted to anatomical subdomains of the neonatal heart. Three-dimensional analysis of the expression of proCCK and CCKAR/CCKBR receptors was performed using in situ hybridization and optical projection tomography, illustrating chamber-specific expression patterns in the postnatal heart. Transcription factor motif analyses indicated developmental cardiac transcription factors TBX5 and MEF2C as upstream regulators of proCCK, and this regulatory activity was confirmed in reporter gene assays. proCCK mRNA levels were also measured in the infarcted heart and in response to cyclic mechanical stretch and endothelin-1, indicating dynamic transcriptional regulation which might be leveraged for improved biomarker development. Functional analyses of exogenous cholecystokinin octapeptide (CCK-8) administration were performed in differentiating mouse embryonic stem cells (mESCs), and the results suggest that CCK-8 does not act as a differentiation modulator of cardiomyocyte subtypes. Collectively, these findings indicate that proCCK is regulated at the transcriptional level by TBX5-MEF2 and neurohormonal signaling, informing use of proCCK as a biomarker and future strategies for upstream manipulation of cholecystokinin signaling in the heart and other tissues.

Anticonvulsants and Chromatin-Genes Expression: A Systems Biology Investigation

Embryofetal development is a critical process that needs a strict epigenetic control, however, perturbations in this balance might lead to the occurrence of congenital anomalies. It is known that anticonvulsants potentially affect epigenetics-related genes, however, it is not comprehended whether this unbalance could explain the anticonvulsants-induced fetal syndromes. In the present study, we aimed to evaluate the expression of epigenetics-related genes in valproic acid, carbamazepine, or phenytoin exposure. We selected these three anticonvulsants exposure assays, which used murine or human embryonic stem-cells and were publicly available in genomic databases. We performed a differential gene expression (DGE) and weighted gene co-expression network analysis (WGCNA), focusing on epigenetics-related genes. Few epigenetics genes were differentially expressed in the anticonvulsants' exposure, however, the WGCNA strategy demonstrated a high enrichment of chromatin remodeling genes for the three drugs. We also identified an association of 46 genes related to Fetal Valproate Syndrome, containing SMARCA2 and SMARCA4, and nine genes to Fetal Hydantoin Syndrome, including PAX6, NEUROD1, and TSHZ1. The evaluation of stem-cells under drug exposure can bring many insights to understand the drug-induced damage to the embryofetal development. The candidate genes here presented are potential biomarkers that could help in future strategies for the prevention of congenital anomalies.

Vitamin A as a Transcriptional Regulator of Cardiovascular Disease

Vitamin A is a micronutrient and signaling molecule that regulates transcription, cellular differentiation, and organ homeostasis. Additionally, metabolites of Vitamin A are utilized as differentiation agents in the treatment of hematological cancers and skin disorders, necessitating further study into the effects of both nutrient deficiency and the exogenous delivery of Vitamin A and its metabolites on cardiovascular phenotypes. Though vitamin A/retinoids are well-known regulators of cardiac formation, recent evidence has emerged that supports their role as regulators of cardiac regeneration, postnatal cardiac function, and cardiovascular disease progression. We here review findings from genetic and pharmacological studies describing the regulation of both myocyte- and vascular-driven cardiac phenotypes by vitamin A signaling. We identify the relationship between retinoids and maladaptive processes during the pathological hypertrophy of the heart, with a focus on the activation of neurohormonal signaling and fetal transcription factors (Gata4, Tbx5). Finally, we assess how this information might be leveraged to develop novel therapeutic avenues.

Comparative assessment of toxic responses in 3D embryoid body differentiation model and mouse early embryos treated with 5-hydroxytryptophan

Pluripotent stem cells recapitulate in vitro the early developmental stages and are considered promising cell models for predictive developmental toxicity studies. To investigate the consistency between adverse drug effects on early development and the early stages of embryonic stem cell differentiation in three-dimensional (3D) in vitro culture, the toxic responses to 5-hydroxytryptophan (5-HTP; 0.5-2 mM) were evaluated in early mouse embryos and the embryoid body (EB) differentiation model. 3D architectures, developmental and differentiation dynamics and the cell death rates were analyzed in early mouse embryos (E2.5-E5.5) and EBs at 1 and 6 days of differentiation using a combination of confocal immunofluorescence microscopy with high content imaging analysis and quantitative gene expression analysis. Comparative analysis of toxic responses in early embryos and EBs revealed a similar dose- and stage-dependent decrease in the 5-HTP toxic effects during development and differentiation. The integral toxic responses in the early embryos and EBs were significantly dependent on their 3D architecture and cellular composition. Treatment with 5-HTP (1 mM and above) induced developmental arrest, growth inhibition, and increased cell death in the early embryos without the trophoblasts (E2.5) and those with impaired trophoblasts and in early EBs, whereas later embryos and EBs were more resistant due to the protection of the extraembryonic tissues. This study demonstrates that the EB differentiation model is a relevant 3D-model of early mammalian development and can be useful for the predictive evaluation of toxic and teratogenic effects in embryos at the preimplantation and early post-implantation developmental stages.