Control Cell Fate Research Articles

Regulation of developmental gatekeeping and cell fate transition by the calpain protease DEK1 in Physcomitrium patens

Calpains are cysteine proteases that control cell fate transitions whose loss of function causes severe, pleiotropic phenotypes in eukaryotes. Although mainly considered as modulatory proteases, human calpain targets are directed to the N-end rule degradation pathway. Several such targets are transcription factors, hinting at a gene-regulatory role. Here, we analyze the gene-regulatory networks of the moss Physcomitrium patens and characterize the regulons that are misregulated in mutants of the calpain DEFECTIVE KERNEL1 (DEK1). Predicted cleavage patterns of the regulatory hierarchies in five DEK1-controlled subnetworks are consistent with a pleiotropic and regulatory role during cell fate transitions targeting multiple functions. Network structure suggests DEK1-gated sequential transitions between cell fates in 2D-to-3D development. Our method combines comprehensive phenotyping, transcriptomics and data science to dissect phenotypic traits, and our model explains the protease function as a switch gatekeeping cell fate transitions potentially also beyond plant development.

The histone methyltransferase ASH1L protects against bone loss by inhibiting osteoclastogenesis.

Absent, small, or homeotic1-like (ASH1L) is a histone lysine methyltransferase that generally functions as a transcriptional activator in controlling cell fate. So far, its physiological relevance in bone homeostasis and osteoclast differentiation remains elusive. Here, by conditional deleting Ash1l in osteoclast progenitors of mice, we found ASH1L deficiency resulted in osteoporosis and potentiation of osteoclastogenesis in vivo and in vitro. Mechanistically, ASH1L binds the promoter of the Src homology 3 and cysteine-rich domain 2 (Stac2) and increases the gene's transcription via histone 3 lysine 4 (H3K4) trimethylation modification, thus augmenting the STAC2's protection against receptor activator of nuclear factor kB ligand (RANKL)-initiated inflammation during osteoclast formation. Collectively, we demonstrate the first piece of evidence to prove ASH1L as a critical checkpoint during osteoclastogenesis. The work sheds new light on our understanding about the biological function of ASH1L in bone homeostasis, therefore providing a valuable therapeutic target for the treatment of osteoporosis or inflammatory bone diseases.

AGO1 controls protein folding in mouse embryonic stem cell fate decisions

Argonaute (AGO) proteins are evolutionarily conserved RNA-binding proteins that control gene expression through the small RNAs they interact with. Whether AGOs have regulatory roles independent of RNAs, however, is unknown. Here, we show that AGO1 controls cell fate decisions through facilitating protein folding. We found that in mouse embryonic stem cells (mESCs), while AGO2 facilitates differentiation via the microRNA (miRNA) pathway, AGO1 controls stemness independently of its binding to small RNAs. We determined that AGO1 specifically interacts with HOP, a co-chaperone for the HSP70 and HSP90 chaperones, and enhances the folding of a set of HOP client proteins with intrinsically disordered regions. This AGO1-mediated facilitation of protein folding is important for maintaining stemness in mESCs. Our results demonstrate divergent functions between AGO1 and AGO2 in controlling cellular states and identify an RNA-independent function of AGO1 in controlling gene expression and cell fate decisions.

Unveiling the Intricate Connection: Cell Volume as a Key Regulator of Mechanotransduction.

The volumes of living cells undergo dynamic changes to maintain the cells' structural and functional integrity in many physiological processes. Minor fluctuations in cell volume can serve as intrinsic signals that play a crucial role in cell fate determination during mechanotransduction. In this review, we discuss the variability of cell volume and its role in vivo, along with an overview of the mechanisms governing cell volume regulation. Additionally, we provide insights into the current approaches used to control cell volume in vitro. Furthermore, we summarize the biological implications of cell volume regulation and discuss recent advances in understanding the fundamental relationship between cell volume and mechanotransduction. Finally, we delve into the potential underlying mechanisms, including intracellular macromolecular crowding and cellular mechanics, that govern the global regulation of cell fate in response to changes in cell volume. By exploring the intricate interplay between cell volume and mechanotransduction, we underscore the importance of considering cell volume as a fundamental signaling cue to unravel the basic principles of mechanotransduction. Additionally, we propose future research directions that can extend our current understanding of cell volume in mechanotransduction. Overall, this review highlights the significance of considering cell volume as a fundamental signal in understanding the basic principles in mechanotransduction and points out the possibility of controlling cell volume to control cell fate, mitigate disease-related damage, and facilitate the healing of damaged tissues.

An iron rheostat controls hematopoietic stem cell fate

Mechanisms governing the maintenance of blood-producing hematopoietic stem and multipotent progenitor cells (HSPCs) are incompletely understood, particularly those regulating fate, ensuring long-term maintenance, and preventing aging-associated stem cell dysfunction. We uncovered a role for transitory free cytoplasmic iron as a rheostat for adult stem cell fate control. We found that HSPCs harbor comparatively small amounts of free iron and show the activation of a conserved molecular response to limited iron-particularly during mitosis. To study the functional and molecular consequences of iron restriction, we developed models allowing for transient iron bioavailability limitation and combined single-molecule RNA quantification, metabolomics, and single-cell transcriptomic analyses with functional studies. Our data reveal that the activation of the limited iron response triggers coordinated metabolic and epigenetic events, establishing stemness-conferring gene regulation. Notably, we find that aging-associated cytoplasmic iron loading reversibly attenuates iron-dependent cell fate control, explicating intervention strategies for dysfunctional aged stem cells.

Time-integrated BMP signaling determines fate in a stem cell model for early human development

How paracrine signals are interpreted to yield multiple cell fate decisions in a dynamic context during human development in vivo and in vitro remains poorly understood. Here we report an automated tracking method to follow signaling histories linked to cell fate in large numbers of human pluripotent stem cells (hPSCs). Using an unbiased statistical approach, we discover that measured BMP signaling history correlates strongly with fate in individual cells. We find that BMP response in hPSCs varies more strongly in the duration of signaling than the level. However, both the level and duration of signaling activity control cell fate choices only by changing the time integral. Therefore, signaling duration and level are interchangeable in this context. In a stem cell model for patterning of the human embryo, we show that signaling histories predict the fate pattern and that the integral model correctly predicts changes in cell fate domains when signaling is perturbed. Our data suggest that mechanistically, BMP signaling is integrated by SOX2.

DNA binding redistributes activation domain ensemble and accessibility in pioneer factor Sox2

More than 1600 human transcription factors orchestrate the transcriptional machinery to control gene expression and cell fate. Their function is conveyed through intrinsically disordered regions (IDRs) containing activation or repression domains but lacking quantitative structural ensemble models prevents their mechanistic decoding. Here we integrate single-molecule FRET and NMR spectroscopy with molecular simulations showing that DNA binding can lead to complex changes in the IDR ensemble and accessibility. The C-terminal IDR of pioneer factor Sox2 is highly disordered but its conformational dynamics are guided by weak and dynamic charge interactions with the folded DNA binding domain. Both DNA and nucleosome binding induce major rearrangements in the IDR ensemble without affecting DNA binding affinity. Remarkably, interdomain interactions are redistributed in complex with DNA leading to variable exposure of two activation domains critical for transcription. Charged intramolecular interactions allowing for dynamic redistributions may be common in transcription factors and necessary for sensitive tuning of structural ensembles.

Robust axis elongation by Nodal-dependent restriction of BMP signaling.

Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm.

A65 THE YAP-PER: CAN YAP/TAZ MEDIATE EPITHELIAL-IMMUNE CROSSTALK DURING PYLORIC METAPLASIA?

Abstract Background Gastric cancer is one of the leading causes of cancer-related deaths and its prevalence has been associated with infection by Helicobacter pylori. H. pylori persistence leads to chronic inflammation, which results in the elimination of acid-secreting parietal cells and the appearance of abnormal mucus-producing cells at the base of the gastric glands, known as spasmolytic polypeptide/trefoil factor 2-expressing metaplasia (SPEM) cells. The processes driving these alterations in epithelial cell fate during H. pylori infection and their function in regeneration of the gastric epithelium remain unclear. Previous work done in our lab have demonstrated that Hippo signalling, more specifically the transcriptional effectors yes-associated protein 1 (YAP) and transcription coactivator with PDZ-binding motif (TAZ), plays an essential role in controlling cell fate during gastric tissue regeneration in a chemical injury model. In the same model, loss of YAP/TAZ resulted in chronic immune cell infiltration in corpus glands, suggesting an immunomodulatory role for YAP and TAZ. Aims The objectives of this project is to characterize the immunomodulatory function of YAP/TAZ in an in vivo model of acute injury as well as an in vivo model of H. pylori infection. Methods Acute injury is induced by high-dose tamoxifen treatment in conditional knock-out (cKO) mice with YAP/TAZ deleted throughout the gastric epithelium. Subsequent immunophenotyping experiments such as flow cytometry and multiplex analysis are performed to characterize the role played by YAP/TAZ in regulating the immune response. For a more biologically relevant model, cKO mice are also infected with H. pylori, and similar immunophenotyping analyses are performed. Results Preliminary results showed that the loss of YAP/TAZ resulted in differential type II response as well as chronic B cell infiltration upon tissue injury. Conclusions This project aims to provide important insights on immune-epithelial cell interactions important for tissue regeneration and tumorigenesis as well as host-pathogen interactions implicated in H. pylori persistence. Funding Agencies CIHRFRQS

OptoREACT: Optogenetic Receptor Activation on Nonengineered Human T Cells.

Optogenetics is a versatile and powerful tool for the control and analysis of cellular signaling processes. The activation of cellular receptors by light using optogenetic switches usually requires genetic manipulation of cells. However, this considerably limits the application in primary, nonengineered cells, which is crucial for the study of physiological signaling processes and for controlling cell fate and function for therapeutic purposes. To overcome this limitation, we developed a system for the light-dependent extracellular activation of cell surface receptors of nonengineered cells termed OptoREACT (Optogenetic Receptor Activation) based on the light-dependent protein interaction of A. thaliana phytochrome B (PhyB) with PIF6. In the OptoREACT system, a PIF6-coupled antibody fragment binds the T cell receptor (TCR) of Jurkat or primary human T cells, which upon illumination is bound by clustered phytochrome B to induce receptor oligomerization and activation. For clustering of PhyB, we either used tetramerization by streptavidin or immobilized PhyB on the surface of cells to emulate the interaction of a T cell with an antigen-presenting cell. We anticipate that this extracellular optogenetic approach will be applicable for the light-controlled activation of further cell surface receptors in primary, nonengineered cells for versatile applications in fundamental and applied research.

Stem cell mTOR signaling directs region-specific cell fate decisions during intestinal nutrient adaptation.

The adult intestine is a regionalized organ, whose size and cellular composition are adjusted in response to nutrient status. This involves dynamic regulation of intestinal stem cell (ISC) proliferation and differentiation. How nutrient signaling controls cell fate decisions to drive regional changes in cell-type composition remains unclear. Here, we show that intestinal nutrient adaptation involves region-specific control of cell size, cell number, and differentiation. We uncovered that activation of mTOR complex 1 (mTORC1) increases ISC size in a region-specific manner. mTORC1 activity promotes Delta expression to direct cell fate toward the absorptive enteroblast lineage while inhibiting secretory enteroendocrine cell differentiation. In aged flies, the ISC mTORC1 signaling is deregulated, being constitutively high and unresponsive to diet, which can be mitigated through lifelong intermittent fasting. In conclusion, mTORC1 signaling contributes to the ISC fate decision, enabling regional control of intestinal cell differentiation in response to nutrition.

Regulation of Cell Adhesion on Physically Crosslinked Hydrogels Composed of Amino Acid‐Based Polymers by Changing Elastic Modulus Using Shape Fix/Memory Properties

AbstractThe elastic modulus of hydrogels is one of the most important factors for controlling cell fate. In this study, hydrogels composed of poly(N‐acryloylglycinamide) (PNAGAm) grafted with arginine (R)–glycine (G)–aspartic acid (D)–serine (S) peptide is designed without a chemical crosslinker. The hydrogels are prepared by the conventional radical copolymerization of N‐acryloylglycinamide with a polymerizable RGDS peptide. The peptide grafting ratio is easily controlled by adjusting the feed composition for polymerization. The hydrogels exhibit thermo‐responsiveness of the upper critical solution temperature type based on the PNAGAm moiety. This characteristic reflects the shape fix/memory properties of hydrogels because of the reversible formation of multiple hydrogen bonds. The cell adhesiveness of the hydrogels drastically improves in the presence of a small amount of the peptide graft. The hydrogels exhibit good biocompatibility; the adhered cells proliferate on the hydrogels, and macrophages do not show activation or inflammation. Surfaces with different elastic modulus regions are successfully constructed on the same hydrogel by using shape fix/memory properties, allowing the regulation of cell adhesion. This hydrogel system offers promising opportunities for the design and application of functional cell scaffolds.

Evaluating the daily modulation of FADD and related molecular markers in different brain regions in male rats.

Fas-Associated protein with Death Domain (FADD), a key molecule controlling cell fate by balancing apoptotic versus non-apoptotic functions, is dysregulated in post-mortem brains of subjects with psychopathologies, in animal models capturing certain aspects of these disorders, and by several pharmacological agents. Since persistent disruptions in normal functioning of daily rhythms are linked with these conditions, oscillations over time of key biomarkers, such as FADD, could play a crucial role in balancing the clinical outcome. Therefore, we characterized the 24-h regulation of FADD (and linked molecular partners: p-ERK/t-ERK ratio, Cdk-5, p35/p25, cell proliferation) in key brain regions for FADD regulation (prefrontal cortex, striatum, hippocampus). Samples were collected during Zeitgeber time (ZT) 2, ZT5, ZT8, ZT11, ZT14, ZT17, ZT20, and ZT23 (ZT0, lights-on or inactive period; ZT12, lights-off or active period). FADD showed similar daily fluctuations in all regions analyzed, with higher values during lights off, and opposite to p-ERK/t-ERK ratios regulation. Both Cdk-5 and p35 remained stable and did not change across ZT. However, p25 increased during lights off, but exclusively in striatum. Finally, no 24-h modulation was observed for hippocampal cell proliferation, although higher values were present during lights off. These results demonstrated a clear daily modulation of FADD in several key brain regions, with a more prominent regulation during the active time of rats, and suggested a key role for FADD, and molecular partners, in the normal physiological functioning of the brain's daily rhythmicity, which if disrupted might participate in the development of certain pathologies.

PROTEIN ARGININE METHYLTRANSFERASE 1 REGULATES ADULT INTESTINAL CELL PROLIFERATION AND ENTEROENDOCRINE CELLS DIFFERENTIATION

Abstract The adult intestinal epithelium is a complex, self-renewing tissue composed of specialized cell types with diverse functions. Intestinal stem cells (ISCs) at the base of crypts divide and differentiate into absorptive and secretory cells. Enteroendocrine cells (EEC), one type of secretory cells, are the most abundant hormone-producing cells in mammals and involved in the control of energy homeostasis. Many studies investigated the mechanisms that control cell fate determination; however, regulation of EEC development and function are still unclear or controversial. Here, we found that Protein arginine methyltransferase 1(PRMT1), a major arginine methyltransferase, is highly expressed in the proliferating transit-amplifying (TA) cells and ISCs of adult mouse intestinal crypts. By using tamoxifen-induced intestinal epithelial cell-specific deletion of PRMT1 in adult mice, we observed the number of EEC dramatically increased. Transcription analyses showed the expression levels of Enteroendocrine-specific hormone and transcription factors are upregulated in PRMT1-deficient small intestine. In addition, the top enriched upregulated pathways were all associated with EEC functions. Concomitantly, Neurogenin 3-expressing progenitor cells accumulate in the mutant small intestine, and its target genes such as Neuod1, pax4, insm1 are upregulated of mutant crypts by RT-PCR. Furthermore, intestinal epithelium of the mutant mice showed elongated crypts in the small intestine, while increased cell proliferation in TA cells. Additionally, inducible PRMT1 deletion led to increased cell death, which compensated for increased cell proliferation in the crypts to maintain overall intestinal morphology and intestinal homeostasis. Together, our results revealed that the loss of PRMT1 in the adult intestinal epithelium altered TA cell proliferation and EEC differentiation, which was probably via Neurogenin 3-mediated pathway. Thus, our results may provide potential roles of PRMT1 as an essential transcriptional regulator of EECs specification and strategy for metabolic disorder.

Assessment of the Enzymatic Dephosphorylation Kinetics in the Assemblies of a Phosphopentapeptide that Forms Intranuclear Nanoribbons.

Although the formation of peptide assemblies catalyzed by alkaline phosphatase (ALP) has received increasing attention in inhibiting cancer cells, the detailed enzyme kinetics of the dephosphorylation of the corresponding phosphopeptide assemblies have yet to be determined. We recently discovered that assemblies from a phosphopentapeptide can form intracellular nanoribbons that kill induced pluripotent stem cells or osteosarcoma cells, but the kinetics of enzymatic dephosphorylation remain unknown. Thus, we chose to examine the enzyme kinetics of the dephosphorylation of the phosphopentapeptide [NBD-LLLLpY (1)] from concentrations below to above its critical micelle concentration (CMC). Our results show that the phosphopeptide exhibits a CMC of 75 μM in phosphate saline buffer, and the apparent Vmax and Km values of alkaline phosphatase catalyzed dephosphorylation are approximately 0.24 μM/s and 5.67 mM, respectively. Despite dephosphorylation remaining incomplete at 60 min in all the concentrations tested, dephosphorylation of the phosphopeptide at concentrations of 200 μM or above mainly results in nanoribbons, dephosphorylation at concentrations of CMC largely produces nanofibers, and dephosphorylation below the CMC largely generates nanoparticles. Moreover, the formation of nanoribbons correlates with the intranuclear accumulation of the pentapeptide. By providing the first examination of the enzymatic kinetics of phosphopeptide assemblies, this work further supports the notion that the assemblies of phosphopentapeptides can act as a new functional entity for controlling cell fates.

N-acetyltransferase NAT10 controls cell fates via connecting mRNA cytidine acetylation to chromatin signaling.

Cell fate transition involves dynamic changes of gene regulatory network and chromatin landscape, requiring multiple levels of regulation, yet the cross-talk between epitranscriptomic modification and chromatin signaling remains largely unknown. Here, we uncover that suppression of N-acetyltransferase 10 (NAT10), the writer for mRNA N4-acetylcytidine (ac4C) modification, can notably affect human embryonic stem cell (hESC) lineage differentiation and pluripotent reprogramming. With integrative analysis, we identify that NAT10-mediated ac4C modification regulates the protein levels of a subset of its targets, which are strongly enriched for fate-instructive chromatin regulators, and among them, histone chaperone ANP32B is experimentally verified and functionally relevant. Furthermore, NAT10-ac4C-ANP32B axis can modulate the chromatin landscape of their downstream genes (e.g., key regulators of Wnt and TGFβ pathways). Collectively, we show that NAT10 is an essential regulator of cellular plasticity, and its catalyzed mRNA cytidine acetylation represents a critical layer of epitranscriptomic modulation and uncover a previously unrecognized, direct cross-talk between epitranscriptomic modification and chromatin signaling during cell fate transitions.

Yukiko Gotoh: I am fascinated by the beauty of science.

Yukiko Gotoh is a professor in the Department of Pharmaceutical Sciences at the University of Tokyo. Her lab studies the mechanisms that underlie the regulation of neural stem/progenitor cell fate during brain development and homeostasis. They are particularly interested in the underlying genetic and epigenetic mechanisms that control cell fate and neuronal maturation, as well as the relevance of neural stem/progenitor cell dysregulation in neurodevelopmental disorders. We recently spoke to Yukiko about her current work, the joys of teamwork, and her passion for helping other scientists in Japan.

Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate

Pioneer transcription factors (TFs) regulate cell fate by establishing transcriptionally primed and active states. However, cell fate control requires the coordination of both lineage-specific gene activation and repression of alternative-lineage programs, a process that is poorly understood. Here, we demonstrate that the pioneer TF FOXA coordinates with PRDM1 TF to recruit nucleosome remodeling and deacetylation (NuRD) complexes and Polycomb repressive complexes (PRCs), which establish highly occupied, accessible nucleosome conformation with bivalent epigenetic states, thereby preventing precocious and alternative-lineage gene expression during human endoderm differentiation. Similarly, the pioneer TF OCT4 coordinates with PRDM14 to form bivalent enhancers and repress cell differentiation programs in human pluripotent stem cells, suggesting that this may be a common and critical function of pioneer TFs. We propose that pioneer and PRDM TFs coordinate to safeguard cell fate through epigenetic repression mechanisms.

Translational enhancement of target endogenous mRNA in mammalian cells using programmable RNA-binding pentatricopeptide repeat proteins

Programmable protein scaffolds are invaluable in the development of genome engineering tools. The pentatricopeptide repeat (PPR) protein is an attractive platform for RNA manipulation because of its programmable RNA-binding selectivity, which is determined by the combination of amino acid species at three specific sites in the PPR motif. Translation is a key RNA regulatory step that determines the final gene expression level and is involved in various human diseases. In this study, designer PPR protein was used to develop a translational enhancement technique by fusion with the translation initiation factor eIF4G. The results showed that the PPR-eIF4G fusion protein could activate the translation of endogenous c-Myc and p53 mRNAs and control cell fate, indicating that PPR-based translational enhancement is a versatile technique applicable to various endogenous mRNAs in mammalian cells. In addition, the translational enhancement was dependent on both the target position and presence of eIF4G, suggesting the presence of an unknown translation activation mechanism.

Altered cell fates of limbal stem cells in aniridia associated with PAX6 mutations

Proper biological function of stem cells in tissues and organs relies on their correct cell fates, and transcription factors (TFs) play key roles in controlling cell fate. Altered cell fates of stem cells due to genetic mutations or other factors can lead to developmental and homeostatic abnormalities. Aniridia is caused by mutations that affect the transcription factor PAX6, and patients with aniridia suffer from congenital and progressive corneal opacification. This is at least partly due to deficient function of limbal stem cells (LSCs) located in the periphery of the cornea. To test the hypothesis that corneal opacity is associated with altered cell fates in LSCs of aniridia patients, we performed transcriptome analyses using two different types of stem cells derived from aniridia patients: induced pluripotent stem cells (iPSCs) and primary limbal stem cells (pLSCs). First, we differentiated iPSCs to obtain induced LSCs. Our transcriptome data showed that induced LSCs derived from aniridia patients do not have the same epithelial identity as normal cells, but instead have an enhanced neural or pluripotent identity. In parallel, we investigated whether patient‐derived pLSCs could adopt the cell fate of a similar epithelial cell type, specifically skin keratinocytes, which give rise to the non‐transparent epidermis. By comparing the transcriptomes of these two cell types, we observed a clear loss of the normal LSC fate in the aniridia pLSCs as compared to normal pLSCs. However, the gain of keratinocyte cell fate was not evident. These findings demonstrate the essential role of PAX6 function in determining the correct cell fate of LSCs.