JAK/STAT signaling regulates tissue outgrowth and male germline stem cell fate in Drosophila

In multicellular organisms, biological activities are regulated by cell signaling. The various signal transduction path- ways regulate cell fate, proliferation, migration, and polarity. Miscoordination of the communicative signals will lead to disasters like cancer and other fatal diseases. The JAK/STAT signal transduction pathway is one of the pathways, which was first identified in vertebrates and is highly conserved throughout evolution. Studying the JAK/STAT signal transduc- tion pathway in Drosophila provides an excellent opportunity to understand the molecular mechanism of the cell regu- lation during development and tumor formation. In this review, we discuss the general overview of JAK/STAT signaling in Drosophila with respect to its functions in the eye development and stem cell fate determination.

Metabolic-epigenetic nexus in regulation of stem cell fate

Stem cell fate determination is one of the central questions in stem cell biology,and although its regulation has been studied at genomic and proteomic levels,a variety of biological activities in cells occur at the metabolic level.Metabolomics studies have established the metabolome during stem cell differentiation and have revealed the role of metabolites in stem cell fate determination.While metabolism is considered to play a biological regulatory role as an energy source,recent studies have suggested the nexus between metabolism and epigenetics because several metabolites function as cofactors and substrates in epigenetic mechanisms,including histone modification,DNA methylation,and microRNAs.Additionally,the epigenetic modification is sensitive to the dynamic metabolites and consequently leads to changes in transcription.The nexus between metabolism and epigenetics proposes a novel stem cell-based therapeutic strategy through manipulating metabolites.In the present review,we summarize the possible nexus between metabolic and epigenetic regulation in stem cell fate determination,and discuss the potential preventive and therapeutic strategies via targeting metabolites.

Regulation of neural stem cell fate decisions by mitochondrial dynamics

Stem cells possess the ability to divide symmetrically or asymmet- rically to allow for maintenance of the stem cell pool or become committed progenitors and differentiate into various cell lineages. The unique self-renewal capabilities and pluripotency of stem cells are integral to tissue regeneration and repair （Oh et al., 2014）. Mul- tiple mechanisms including intracellular programs and extrinsic cues are reported to regulate neural stem cell （NSC） fate （Bond et al., 2015）. A recent study, published in Cell Stern Cell, identified a novel mechanism whereby mitochondrial dynamics drive NSC fate （Khacho et al., 2016）.

MicroRNAs as novel regulators of stem cell fate

Mounting evidence in stem cell biology has shown that microRNAs(miRNAs) play a crucial role in cell fate specification, including stem cell self-renewal, lineagespecific differentiation, and somatic cell reprogramming.These functions are tightly regulated by specific gene expression patterns that involve miRNAs and transcription factors. To maintain stem cell pluripotency, specific miRNAs suppress transcription factors that promote differentiation, whereas to initiate differentiation, lineagespecific miRNAs are upregulated via the inhibition of transcription factors that promote self-renewal. Small molecules can be used in a similar manner as natural miRNAs, and a number of natural and synthetic small molecules have been isolated and developed to regulate stem cell fate. Using miRNAs as novel regulators of stem cell fate will provide insight into stem cell biology and aid in understanding the molecular mechanisms and crosstalk between miRNAs and stem cells.Ultimately, advances in the regulation of stem cell fate will contribute to the development of effective medical therapies for tissue repair and regeneration. This review summarizes the current insights into stem cell fate determination by miRNAs with a focus on stem cell self-renewal, differentiation, and reprogramming. Small molecules that control stem cell fate are also highlighted.

Small molecules for mesenchymal stem cell fate determination

Mesenchymal stem cells(MSCs)are adult stem cells harboring self-renewal and multilineage differentiation potential that are capable of differentiating into osteoblasts,adipocytes,or chondrocytes in vitro,and regulating the bone marrow microenvironment and adipose tissue remodeling in vivo.The process of fate determination is initiated by signaling molecules that drive MSCs into a specific lineage.Impairment of MSC fate determination leads to different bone and adipose tissue-related diseases,including aging,osteoporosis,and insulin resistance.Much progress has been made in recent years in discovering small molecules and their underlying mechanisms control the cell fate of MSCs both in vitro and in vivo.In this review,we summarize recent findings in applying small molecules to the trilineage commitment of MSCs,for instance,genistein,medicarpin,and icariin for the osteogenic cell fate commitment;isorhamnetin,risedronate,and arctigenin for pro-adipogenesis;and atractylenolides and dihydroartemisinin for chondrogenic fate determination.We highlight the underlying mechanisms,including direct regulation,epigenetic modification,and post-translational modification of signaling molecules in the AMPK,MAPK,Notch,PI3K/AKT,Hedgehog signaling pathways etc.and discuss the small molecules that are currently being studied in clinical trials.The target-based manipulation of lineage-specific commitment by small molecules offers substantial insights into bone marrow microenvironment regulation,adipose tissue homeostasis,and therapeutic strategies for MSC-related diseases.

Orchestrating stem cell fate: Novel tools for regenerative medicine

Mesenchymal stem cells are undifferentiated cells able to acquire different phenotypes under specific stimuli. In vitro manipulation of these cells is focused on understanding stem cell behavior, proliferation and pluripotency. Latest advances in the field of stem cells concern epigenetics and its role in maintaining self-renewal and differentiation capabilities. Chemical and physical stimuli can modulate cell commitment, acting on gene expression of Oct-4, Sox-2 and Nanog, the main stemness markers, and tissue-lineage specific genes. This activation or repression is related to the activity of chromatin-remodeling factors and epigenetic regulators, new targets of many cell therapies. The aim of this review is to afford a view of the current state of in vitro and in vivo stem cell applications, highlighting the strategies used to influence stem cell commitment for current and future cell therapies. Identifying the molecular mechanisms controlling stem cell fate could open up novel strategies for tissue repairing processes and other clinical applications.

A single-cell transcriptome atlas reveals the trajectory of early cell fate transition during callus induction in Arabidopsis

The acquisition of pluripotent callus from somatic cells plays an important role in plant development studies and crop genetic improvement.This developmental process incorporates a series of cell fate transitions and reprogramming.However,our understanding of cell heterogeneity and mechanisms of cell fate transition during callus induction remains quite limited.Here,we report a time-series single-cell transcriptome experiment on Arabidopsis root explants that were induced in callus induction medium for 0,1,and 4 days,and the construction of a detailed single-cell transcriptional atlas of the callus induction process.We identify the cell types responsible for initiating the early callus:lateral root primordium-initiating(LRPI)-like cells and quiescent center(QC)-like cells.LRPI-like cells are derived from xylem pole pericycle cells and are similar to lateral root primordia.We delineate the developmental trajectory of the dedifferentiation of LRPI-like cells into QC-like cells.QC-like cells are undifferentiated pluripotent acquired cells that appear in the early stages of callus formation and play a critical role in later callus development and organ regeneration.We also identify the transcription factors that regulate QC-like cells and the gene expression signatures that are related to cell fate decisions.Overall,our cell-lineage transcriptome atlas for callus induction provides a distinct perspective on cell fate transitions during callus formation,significantly improving our understanding of callus formation.

Omics Views of Mechanisms for Cell Fate Determination in Early Mammalian Development

During mammalian preimplantation development,a totipotent zygote undergoes several cell cleavages and two rounds of cell fate determination,ultimately forming a mature blastocyst.Along with compaction,the establishment of apicobasal cell polarity breaks the symmetry of an embryo and guides subsequent cell fate choice.Although the lineage segregation of the inner cell mass(ICM)and trophectoderm(TE)is the first symbol of cell differentiation,several molecules have been shown to bias the early cell fate through their inter-cellular variations at much earlier stages,including the 2-and 4-cell stages.The underlying mechanisms of early cell fate determination have long been an important research topic.In this review,we summarize the molecular events that occur during early embryogenesis,as well as the current understanding of their regulatory roles in cell fate decisions.Moreover,as powerful tools for early embryogenesis research,single-cell omics techniques have been applied to both mouse and human preimplantation embryos and have contributed to the discovery of cell fate regulators.Here,we summarize their applications in the research of preimplantation embryos,and provide new insights and perspectives on cell fate regulation.

Recent advances in optical techniques for dynamically probing cellular mechanobiology

Cellular mechanotransduction characterized by the transformation of mechanical stimuli into biochemical signals,represents a pivotal and complex process underpinning a multitude of cellular functionalities.This process is integral to diverse biological phenomena,including embryonic development,cell migration,tissue regeneration,and disease pathology,particularly in the context of cancer metastasis and cardiovascular diseases.Despite the profound biological and clinical significance of mechanotransduction,our understanding of this complex process remains incomplete.The recent development of advanced optical techniques enables in-situ force measurement and subcellular manipulation from the outer cell membrane to the organelles inside a cell.In this review,we delved into the current state-of-the-art techniques utilized to probe cellular mechanobiology,their principles,applications,and limitations.We mainly examined optical methodologies to quantitatively measure the mechanical properties of cells during intracellular transport,cell adhesion,and migration.We provided an introductory overview of various conventional and optical-based techniques for probing cellular mechanics.These techniques have provided into the dynamics of mechanobiology,their potential to unravel mechanistic intricacies and implications for therapeutic intervention.

Novel insights into cell cycle regulation of cell fate determination

The stem/progenitor cell has long been regarded as a central cell type in development,homeostasis,and regeneration,largely owing to its robust self-renewal and multilineage differentiation abilities.The balance between self-renewal and stem/progenitor cell differentiation requires the coordinated regulation of cell cycle progression and cell fate determination.Extensive studies have demonstrated that cell cycle states determine cell fates,because cells in different cell cycle states are characterized by distinct molecular features and functional outputs.Recent advances in high-resolution epigenome profiling,single-cell transcriptomics,and cell cycle reporter systems have provided novel insights into the cell cycle regulation of cell fate determination.Here,we review recent advances in cell cycle-dependent cell fate determination and functional heterogeneity,and the application of cell cycle manipulation for cell fate conversion.These findings will provide insight into our understanding of cell cycle regulation of cell fate determination in this field,and may facilitate its potential application in translational medicine.

Reprogramming cell fates by small molecules

Reprogramming cell fates towards pluripotent stem cells and other cell types has revolutionized our under- standing of cellular plasticity. During the last decade, transcription factors and microRNAs have become powerful reprogramming factors for modulating cell fates. Recently, many efforts are focused on repro- gramming cell fates by non-viral and non-integrating chemical approaches. Small molecules not only are useful in generating desired cell types in vitro for vari- ous applications, such as disease modeling and cell- based transplantation, but also hold great promise to be further developed as drugs to stimulate patients＇ endogenous cells to repair and regenerate in vivo. Here we will focus on chemical approaches for generating induced pluripotent stem cells, neurons, cardiomy- ocytes, hepatocytes and pancreatic is cells. Significantly, the rapid and exciting advances in cellular reprogramming by small molecules will help us to achieve the long-term goal of curing devastating diseases, injuries, cancers and aging.

Cell Fate Switch during In Vitro Plant Organogenesis

Plant mature cells have the capability to reverse their state of differentiation and produce new organs under cultured conditions. Two phases, dedifferenUation and redifferentiation, are commonly characterized during in vitro organogenesis. In these processes, cells undergo fate switch several times regulated by both extrinsic and intrinsic factors, which are associated with reentry to the cell cycle, the balance between euchromatin and heterochromatin, reprogramming of gene expression, and so forth. This short article reviews the advances in the mechanism of organ regeneration from plant somatic cells in molecular, genomic and epigenetic aspects, aiming to provide important information on the mechanism underlying cell fate switch during in vitro plant organogenesis.

Putting things in place for fertilization： discovering roles for importin proteins in cell fate and spermatogenesis

Importin proteins were originally characterized for their central role in protein transport through the nuclear pores, the only intracellular entry to the nucleus. This vital function must be tightly regulated to control access by transcription factors and other nuclear proteins to genomic DNA, to achieve appropriate modulation of cellular behaviors affecting cell fate. Importin-mediated nucleocytoplasmic transport relies on their specific recognition of cargoes, with each importin binding to distinct and overlapping protein subsets. Knowledge of importin function has expanded substantially in regard to three key developmental systems： embryonic stem cells, muscle cells and the germ line. In the decade since the potential for regulated nucleocytoplasmic transport to contribute to spermatogenesis was proposed, we and others have shown that the importins that ferry transcription factors into the nucleus perform additional roles, which control cell fate. This review presents key findings from studies of mammalian spermatogenesis that reveal potential new pathways by which male fertility and infertility arise. These studies of germline genesis illuminate new ways in which importin proteins govern cellular differentiation, includ ng v a d rect ng proteins to d st nct ntrace ular compartments and by determining cellular stress responses.

A Helm model for microRNA regulation in cell fate decision and conversion

microRNAs （miRNAs） constitute a unique class of endogenous small non-coding RNAs that regulate gene expression post-transcriptionally. Studies over the past decade have uncovered a r^curring paradigm in which miRNAs are key regulators of cellular behavior under various physiological and pathological conditions. Most surprising is the recent observation that miRNAs have emerged as competent players in somatic cell reprogramming, suggesting an especially significant role for these small RNAs in cell fate settings. Here, we discuss the possible mechanisms underlying miRNA-mediated cell programming （i.e., the development and differentiation of embryonic stem cells） and reprogramming （i.e., turning somatic cells into pluripo- tent stem cells or other lineages）, and provide a ＂Helm＂ model of miRNAs in cell fate decision and conversion.

3D-printed bioactive ceramic scaffolds with biomimetic micro/nano-HAp surfaces mediated cell fate and promoted bone augmentation of the bone-implant interface in vivo

Calcium phosphate bio-ceramics are osteo-conductive,but it remains a challenge to promote the induction of bone augmentation and capillary formation.The surface micro/nano-topography of materials can be recognized by cells and then the cell fate are mediated.Traditional regulation methods of carving surface structures on bio-ceramics employ mineral reagents and organic additives,which might introduce impurity phases and affect the biological results.In a previous study,a facile and novel method was utilized with ultrapure water as the unique reagent for hydrothermal treatment,and a uniform hydroxyapatite(HAp)surface layer was constructed on composite ceramics(β-TCP/CaSiO_(3))in situ.Further combined with 3D printing technology,biomimetic hierarchical structure scaffolds were fabricated with interconnected porous composite ceramic scaffolds as the architecture and micro/nano-rod hybrid HAp as the surface layer.The obtained HAp surface layer favoured cell adhesion,alleviated the cytotoxicity of precursor scaffolds,and upregulated the cellular differentiation of mBMSCs and gene expression of HUVECs in vitro.In vivo studies showed that capillary formation,bone augmentation and new bone matrix formation were upregulated after the HAp surface layer was obtained,and the results confirmed that the fabricated biomimetic hierarchical structure scaffold could be an effective candidate for bone regeneration.

Involvement of C2H2 zinc finger proteins in the regulation of epidermal cell fate determination in Arabidopsis

Cell fate determination is a basic developmental process during the growth of multicellular organisms.Trichomes and root hairs of Arabidopsis are both readily accessible structures originating from the epidermal cells of the aerial tissues and roots respectively, and they serve as excellent models for understanding the molecular mechanisms controlling cell fate determination and cell morphogenesis. The regulation of trichome and root hair formationis a complex program that consists of the integration of hormonal signals with a large number of transcriptional factors, including MYB and b HLH transcriptional factors.Studies during recent years have uncovered an important role of C2H2 type zinc finger proteins in the regulation of epidermal cell fate determination. Here in this minireview we briefly summarize the involvement of C2H2 zinc finger proteins in the control of trichome and root hair formation in Arabidopsis.

scGET:Predicting Cell Fate Transition During Early Embryonic Development by Single-cell Graph Entropy

During early embryonic development,cell fate commitment represents a critical transition or“tipping point”of embryonic differentiation,at which there is a drastic and qualitative shift of the cell populations.In this study,we presented a computational approach,scGET,to explore the gene–gene associations based on single-cell RNA sequencing(scRNAseq)data for critical transition prediction.Specifically,by transforming the gene expression data to the local network entropy,the single-cell graph entropy(SGE)value quantitatively characterizes the stability and criticality of gene regulatory networks among cell populations and thus can be employed to detect the critical signal of cell fate or lineage commitment at the single-cell level.Being applied to five scRNA-seq datasets of embryonic differentiation,scGET accurately predicts all the impending cell fate transitions.After identifying the“dark genes”that are non-differentially expressed genes but sensitive to the SGE value,the underlying signaling mechanisms were revealed,suggesting that the synergy of dark genes and their downstream targets may play a key role in various cell development processes.The application in all five datasets demonstrates the effectiveness of scGET in analyzing scRNA-seq data from a network perspective and its potential to track the dynamics of cell differentiation.The source code of scGET is accessible at https://github.com/zhongjiayuna/scGET_Project.

Mathematical modeling reveals the mechanisms of feedforward regulation in cell fate decisions in budding yeast

The determination of cell fate is one of the key questions of developmental biology. Recent experiments showed that feedforward regulation is a novel feature of regulatory networks that controls reversible cellular transitions. However, the underlying mechanism of feedforward regulation-mediated cell fate decision is still unclear. Therefore, using experimental data, we develop a full mathematical model of the molecular network responsible for cell fate selection in budding yeast. To validate our theoretical model, we first investigate the dynamical behaviors of key proteins at the Start transition point and the G1/S transition point; a crucial three-node motif consisting of cyclin （Clnl/2）, Substrate/Subunit Inhibitor of cyclin-dependent protein kinase （Sic1） and cyclin B （C165/6） is considered at these points. The rapid switches of these important components between high and low levels at two transition check points are demonstrated reasonably by our model. Many experimental observations about cell fate decision and cell size control are also theoretically reproduced. Interestingly, the feedforward regulation provides a reliable separation between different cell fates. Next, our model reveals that the threshold for the amount of WHiskey OVhi5） removed from the nucleus is higher at the Reentry point in pheromone-arrested cells compared with that at the Start point in cycling cells. Furthermore, we analyze the hysteresis in the cell cycle kinetics in response to changes in pheromone concentration, showing that Cln3 is the primary driver of reentry and Clnl/2 is the secondary driver of reentry. In particular, we demonstrate that the inhibition of C1nl/2 due to the accumulation of Factor ARrest （Far1） directly reinforces arrest. Finally, theoretical work verifies that the three-node coherent feedforward motif created by cell FUSion （Fus3）, Farl and STErile （Stel2） ensures the rapid arrest and reversibility of a cellular state. The combination of our theoretical model and the previous experimental data contributes to the understanding of the molecular mechanisms of the cell fate decision at the G1 phase in budding yeast and will stimulate further biological experiments in future.

The dynamics of three-dimensional chromatin organization and phase separation in cell fate transitions and diseases

Cell fate transition is a fascinating process involving complex dynamics of three-dimensional(3D)chromatin organization and phase separation,which play an essential role in cell fate decision by regulating gene expression.Phase separation is increasingly being considered a driving force of chromatin folding.In this review,we have summarized the dynamic features of 3D chromatin and phase separation during physiological and pathological cell fate transitions and systematically analyzed recent evidence of phase separation facilitating the chromatin structure.In addition,we discuss current advances in understanding how phase separation contributes to physical and functional enhancerpromoter contacts.We highlight the functional roles of 3D chromatin organization and phase separation in cell fate transitions,and more explorations are required to study the regulatory relationship between 3D chromatin organization and phase separation.

Human cytomegalovirus infection dysregulates neural progenitor cell fate by disrupting Hes1 rhythm and down-regulating its expression

Human cytomegalovirus(HCMV) infection is a leading cause of birth defects, primarily affecting the central nervous system and causing its maldevelopment. As the essential downstream effector of Notch signaling pathway, Hes1, and its dynamic expression, plays an essential role on maintaining neural progenitor/stem cells(NPCs) cell fate and fetal brain development. In the present study, we reported the first observation of Hes1 oscillatory expression in human NPCs, with an approximately1.5 hour periodicity and a Hes1 protein half-life of about 17(17.6 ± 0.2) minutes. HCMV infection disrupts the Hes1 rhythm and down-regulates its expression. Furthermore, we discovered that depleting Hes1 protein disturbed NPCs cell fate by suppressing NPCs proliferation and neurosphere formation, and driving NPCs abnormal differentiation. These results suggested a novel mechanism linking disruption of Hes1 rhythm and down-regulation of Hes1 expression to neurodevelopmental disorders caused by congenital HCMV infection.