3,070 results on '"CELL FATE"'
Search Results
2. Fate erasure logic of gene networks underlying direct neuronal conversion of somatic cells by microRNAs
- Author
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Cates, Kitra, Yuan, Luorongxin, Yang, Yan, and Yoo, Andrew S.
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- 2025
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3. Activation-derepression synergy enables a bHLH network to coordinate a signal-specific fate response
- Author
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Nandagopal, Sandy, Terrio, Alexsandra, Vicente, Fernando Z., Megason, Sean G., Jambhekar, Ashwini, and Lahav, Galit
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- 2024
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- View/download PDF
4. Netrin1 patterns the dorsal spinal cord through modulation of Bmp signaling
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Alvarez, Sandy, Gupta, Sandeep, Mercado-Ayon, Yesica, Honeychurch, Kaitlyn, Rodriguez, Cristian, Kawaguchi, Riki, and Butler, Samantha J.
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- 2024
- Full Text
- View/download PDF
5. Deep conservation complemented by novelty and innovation in the insect eye ground plan.
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Gao, Ke, Donati, Antoine, Ainsworth, Julia, Wu, Di, Terner, Eleanor, and Perry, Michael
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cell fate ,development ,evolution ,photoreceptor ,visual system ,Animals ,Photoreceptor Cells ,Invertebrate ,Insecta ,Insect Proteins ,Compound Eye ,Arthropod ,Signal Transduction ,Biological Evolution ,Retina - Abstract
A spectacular diversity of forms and features allow species to thrive in different environments, yet some structures remain relatively unchanged. Insect compound eyes are easily recognizable despite dramatic differences in visual abilities across species. It is unknown whether distant insect species use similar or different mechanisms to pattern their eyes or what types of genetic changes produce diversity of form and function. We find that flies, mosquitos, butterflies, moths, beetles, wasps, honeybees, and crickets use homologous developmental programs to pattern their retinas. Transcription factor expression can be used to establish homology of different photoreceptor (PR) types across the insects: Prospero (Pros) for R7, Spalt (Sal) for R7+R8, and Defective proventriculus (Dve) for R1-6. Using gene knockout (CRISPR/Cas9) in houseflies, butterflies, and crickets and gene knockdown (RNAi) in beetles, we found that like Drosophila, EGFR and Sevenless (Sev) signaling pathways are required to recruit motion and color vision PRs, though Drosophila have a decreased reliance on Sev signaling relative to other insects. Despite morphological and physiological variation across species, retina development passes through a highly conserved phylotypic stage when the unit eyes (ommatidia) are first patterned. This patterning process likely represents an insect eye ground plan that is established by an ancient developmental program. We identify three types of developmental patterning modifications (ground plan modification, nonstochastic patterns, and specialized regions) that allow for the diversification of insect eyes. We suggest that developmental divergence after the ground plan is established is responsible for the exceptional diversity observed across insect visual systems.
- Published
- 2025
6. Time-resolved transcriptomes reveal diverse B cell fate trajectories in the early response to Epstein-Barr virus infection
- Author
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SoRelle, Elliott D., Dai, Joanne, Reinoso-Vizcaino, Nicolás M., Barry, Ashley P., Chan, Cliburn, and Luftig, Micah A.
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- 2022
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7. Mechanisms of Regulation of Cell Fate in Breast Development and Cancer
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Van Keymeulen, Alexandra, Dong, Haidong, Series Editor, Radeke, Heinfried H., Series Editor, Rezaei, Nima, Series Editor, Steinlein, Ortrud, Series Editor, Xiao, Junjie, Series Editor, Rosenhouse-Dantsker, Avia, Series Editor, Gerlai, Robert, Series Editor, Sørlie, Therese, editor, and Clarke, Robert B., editor
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- 2025
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8. Investigating the basis of lineage decisions and developmental trajectories in the dorsal spinal cord through pseudotime analyses.
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Gupta, Sandeep, Heinrichs, Eric, Novitch, Bennett G, and Butler, Samantha J
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Biological Sciences ,Biomedical and Clinical Sciences ,Neurosciences ,Genetics ,Neurodegenerative ,Stem Cell Research ,Chronic Pain ,Pain Research ,Underpinning research ,1.1 Normal biological development and functioning ,Neurological ,Animals ,Mice ,Spinal Cord ,Cell Lineage ,Interneurons ,Cell Differentiation ,Gene Expression Regulation ,Developmental ,Single-Cell Analysis ,Mouse Embryonic Stem Cells ,RNA-Seq ,Cell fate ,Dorsal spinal cord ,Pseudotime ,Sensory interneurons ,Single-cell RNA-Seq analysis ,Stem cells ,Medical and Health Sciences ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
Dorsal interneurons (dIs) in the spinal cord encode the perception of touch, pain, heat, itchiness and proprioception. Previous studies using genetic strategies in animal models have revealed important insights into dI development, but the molecular details of how dIs arise as distinct populations of neurons remain incomplete. We have developed a resource to investigate dI fate specification by combining a single-cell RNA-Seq atlas of mouse embryonic stem cell-derived dIs with pseudotime analyses. To validate this in silico resource as a useful tool, we used it to first identify genes that are candidates for directing the transition states that lead to distinct dI lineage trajectories, and then validated them using in situ hybridization analyses in the developing mouse spinal cord in vivo. We have also identified an endpoint of the dI5 lineage trajectory and found that dIs become more transcriptionally homogeneous during terminal differentiation. This study introduces a valuable tool for further discovery about the timing of gene expression during dI differentiation and demonstrates its utility in clarifying dI lineage relationships.
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- 2024
9. The role of Golgi complex proteins in cell division and consequences of their dysregulation.
- Author
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Iannitti, Roberta, Mascanzoni, Fabiola, Colanzi, Antonino, and Spano, Daniela
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SPINDLE apparatus ,CELL polarity ,GOLGI apparatus ,CELL division ,MEIOSIS - Abstract
The GC (Golgi complex) plays a pivotal role in the trafficking and sorting of proteins and lipids until they reach their final destination. Additionally, the GC acts as a signalling hub to regulate a multitude of cellular processes, including cell polarity, motility, apoptosis, DNA repair and cell division. In light of these crucial roles, the GC has garnered increasing attention, particularly given the evidence that a dysregulation of GC-regulated signalling pathways may contribute to the onset of various pathological conditions. This review examines the functions of the GC and GC-localised proteins in regulating cell cycle progression, in both mitosis and meiosis. It reviews the involvement of GC-resident proteins in the formation and orientation of the spindle during cell division. In light of the roles played by the GC in controlling cell division, this review also addresses the involvement of the GC in cancer development. Furthermore, TCGA (The Cancer Genome Atlas) database has been queried in order to retrieve information on the genetic alterations and the correlation between the expression of GC-localised proteins and the survival of cancer patients. The data presented in this review highlight the relevance of the GC in regulating cell cycle progression, cellular differentiation and tumourigenesis. [ABSTRACT FROM AUTHOR]
- Published
- 2025
- Full Text
- View/download PDF
10. Deep conservation complemented by novelty and innovation in the insect eye ground plan.
- Author
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Ke Gao, Donati, Antoine, Ainsworth, Julia, Di Wu, Terner, Eleanor R., and Perry, Michael W.
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TRANSCRIPTION factors , *COLOR vision , *DEVELOPMENTAL programs , *GENE knockout , *BEETLES - Abstract
A spectacular diversity of forms and features allow species to thrive in different environments, yet some structures remain relatively unchanged. Insect compound eyes are easily recognizable despite dramatic differences in visual abilities across species. It is unknown whether distant insect species use similar or different mechanisms to pattern their eyes or what types of genetic changes produce diversity of form and function. We find that flies, mosquitos, butterflies, moths, beetles, wasps, honeybees, and crickets use homologous developmental programs to pattern their retinas. Transcription factor expression can be used to establish homology of different photoreceptor (PR) types across the insects: Prospero (Pros) for R7, Spalt (Sal) for R7+R8, and Defective proventriculus (Dve) for R1-6. Using gene knockout (CRISPR/Cas9) in houseflies, butterflies, and crickets and gene knockdown (RNAi) in beetles, we found that like Drosophila, EGFR and Sevenless (Sev) signaling pathways are required to recruit motion and color vision PRs, though Drosophila have a decreased reliance on Sev signaling relative to other insects. Despite morphological and physiological variation across species, retina development passes through a highly conserved phylotypic stage when the unit eyes (ommatidia) are first patterned. This patterning process likely represents an "insect eye ground plan" that is established by an ancient developmental program. We identify three types of developmental patterning modifications (ground plan modification, nonstochastic patterns, and specialized regions) that allow for the diversification of insect eyes. We suggest that developmental divergence after the ground plan is established is responsible for the exceptional diversity observed across insect visual systems. [ABSTRACT FROM AUTHOR]
- Published
- 2025
- Full Text
- View/download PDF
11. Structural changes shaping the Drosophila ellipsoid body ER-neurons during development and aging.
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Koch, Sandra, Kandimalla, Pratyush, Padilla, Eddie, Kaur, Sabrina, Kaur, Rabina, Nguyen, My, Nelson, Annie, Khalsa, Satkartar, Younossi-Hartenstein, Amelia, and Hartenstein, Volker
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NEURAL circuitry , *CELL analysis , *YOUNG adults , *CELLULAR aging , *NEURON development - Abstract
The ellipsoid body (EB) of the insect brain performs pivotal functions in controlling navigation. Input and output of the EB is provided by multiple classes of R-neurons (now referred to as ER-neurons) and columnar neurons which interact with each other in a stereotypical and spatially highly ordered manner. The developmental mechanisms that control the connectivity and topography of EB neurons are largely unknown. One indispensable prerequisite to unravel these mechanisms is to document in detail the sequence of events that shape EB neurons during their development. In this study, we analyzed the development of the Drosophila EB. In addition to globally following the ER-neuron and columnar neuron (sub)classes in the spatial context of their changing environment we performed a single cell analysis using the multi-color flip out (MCFO) system to analyze the developmental trajectory of ER-neurons at different pupal stages, young adults (4d) and aged adults (∼60d). We show that the EB develops as a merger of two distinct elements, a posterior and anterior EB primordium (prEBp and prEBa, respectively. ER-neurons belonging to different subclasses form growth cones and filopodia that associate with the prEBp and prEBa in a pattern that, from early pupal stages onward, foreshadows their mature structure. Filopodia of all ER-subclasses are initially much longer than the dendritic and terminal axonal branches they give rise to, and are pruned back during late pupal stages. Interestingly, extraneous branches, particularly significant in the dendritic domain, are a hallmark of ER-neuron structure in aged brains. Aging is also associated with a decline in synaptic connectivity from columnar neurons, as well as upregulation of presynaptic protein (Brp) in ER-neurons. Our findings advance the EB (and ER-neurons) as a favorable system to visualize and quantify the development and age-related decline of a complex neuronal circuitry. [Display omitted] • Growth cones and filopodia of ER-neurons were analyzed during development. • ER-neurons show type-specific characteristics that foreshadow their later morphology. • The dendritic domain of ER-neurons displays ectopic branches in aged brains. • Synaptic connectivity between ER-neurons and their targets declines in aged brains. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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12. The many faces of H3.3 in regulating chromatin in embryonic stem cells and beyond.
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Cohen, Lea R.Z. and Meshorer, Eran
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EMBRYONIC stem cells , *HETEROCHROMATIN , *GENE silencing , *CHROMATIN , *GENETIC transcription - Abstract
H3.3 is a highly conserved nonreplicative histone variant. In mammalian cells, H3.3 is enriched in both active chromatin and suppressed heterochromatin. H3.3 is associated with development and cell fate maintenance. H3.3 is also involved in heterochromatin formation and silencing of developmental genes. Multiple H3.3 mutations cause cancer or neurodegeneration. H3.3 is a highly conserved nonreplicative histone variant. H3.3 is enriched in promoters and enhancers of active genes, but it is also found within suppressed heterochromatin, mostly around telomeres. Accordingly, H3.3 is associated with seemingly contradicting functions: It is involved in development, differentiation, reprogramming, and cell fate, as well as in heterochromatin formation and maintenance, and the silencing of developmental genes. The emerging view is that different cellular contexts and histone modifications can promote opposing functions for H3.3. Here, we aim to provide an update with a focus on H3.3 functions in early mammalian development, considering the context of embryonic stem cell maintenance and differentiation, to finally conclude with emerging roles in cancer development and cell fate transition and maintenance. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
13. Pulmonary Epithelium Cell Fate Determination: Chronic Obstructive Pulmonary Disease, Lung Cancer, or Both.
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Xu, Yu, Li, Mengxia, and Bai, Li
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CELL determination ,CHRONIC obstructive pulmonary disease ,LUNG cancer ,DNA damage ,CELL communication ,LUNGS - Abstract
The concurrence of chronic obstructive pulmonary disease (COPD) and lung cancer has been widely reported and extensively addressed by pulmonologists and oncologists. However, most studies have focused on shared risk factors, DNA damage pathways, immune microenvironments, inflammation, and imbalanced proteases/antiproteases. In the present review, we explore the association between COPD and lung cancer in terms of airway pluripotent cell fate determination and discuss the various cell types and signaling pathways involved in the maintenance of lung epithelium homeostasis and their involvement in the pathogenesis of co-occurring COPD and lung cancer. [ABSTRACT FROM AUTHOR]
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- 2024
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14. LMNA-Related Dilated Cardiomyopathy: Single-Cell Transcriptomics during Patient-Derived iPSC Differentiation Support Cell Type and Lineage-Specific Dysregulation of Gene Expression and Development for Cardiomyocytes and Epicardium-Derived Cells with Lamin A/C Haploinsufficiency
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Zaragoza, Michael V, Bui, Thuy-Anh, Widyastuti, Halida P, Mehrabi, Mehrsa, Cang, Zixuan, Sha, Yutong, Grosberg, Anna, and Nie, Qing
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Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Stem Cell Research ,Cardiovascular ,Rare Diseases ,Pediatric ,Stem Cell Research - Induced Pluripotent Stem Cell - Human ,Regenerative Medicine ,Human Genome ,Stem Cell Research - Induced Pluripotent Stem Cell ,Heart Disease ,2.1 Biological and endogenous factors ,Good Health and Well Being ,Induced Pluripotent Stem Cells ,Humans ,Cardiomyopathy ,Dilated ,Lamin Type A ,Myocytes ,Cardiac ,Cell Differentiation ,Haploinsufficiency ,Female ,Transcriptome ,Pericardium ,Cell Lineage ,Single-Cell Analysis ,Gene Expression Regulation ,Mutation ,Adult ,nuclear lamina ,disease modeling ,stem cells ,single-cell RNA-seq ,differentially expressed genes ,epigenetics ,X-inactivation ,genomic imprinting ,pluripotency ,cell fate ,Biological sciences ,Biomedical and clinical sciences - Abstract
LMNA-related dilated cardiomyopathy (DCM) is an autosomal-dominant genetic condition with cardiomyocyte and conduction system dysfunction often resulting in heart failure or sudden death. The condition is caused by mutation in the Lamin A/C (LMNA) gene encoding Type-A nuclear lamin proteins involved in nuclear integrity, epigenetic regulation of gene expression, and differentiation. The molecular mechanisms of the disease are not completely understood, and there are no definitive treatments to reverse progression or prevent mortality. We investigated possible mechanisms of LMNA-related DCM using induced pluripotent stem cells derived from a family with a heterozygous LMNA c.357-2A>G splice-site mutation. We differentiated one LMNA-mutant iPSC line derived from an affected female (Patient) and two non-mutant iPSC lines derived from her unaffected sister (Control) and conducted single-cell RNA sequencing for 12 samples (four from Patients and eight from Controls) across seven time points: Day 0, 2, 4, 9, 16, 19, and 30. Our bioinformatics workflow identified 125,554 cells in raw data and 110,521 (88%) high-quality cells in sequentially processed data. Unsupervised clustering, cell annotation, and trajectory inference found complex heterogeneity: ten main cell types; many possible subtypes; and lineage bifurcation for cardiac progenitors to cardiomyocytes (CMs) and epicardium-derived cells (EPDCs). Data integration and comparative analyses of Patient and Control cells found cell type and lineage-specific differentially expressed genes (DEGs) with enrichment, supporting pathway dysregulation. Top DEGs and enriched pathways included 10 ZNF genes and RNA polymerase II transcription in pluripotent cells (PP); BMP4 and TGF Beta/BMP signaling, sarcomere gene subsets and cardiogenesis, CDH2 and EMT in CMs; LMNA and epigenetic regulation, as well as DDIT4 and mTORC1 signaling in EPDCs. Top DEGs also included XIST and other X-linked genes, six imprinted genes (SNRPN, PWAR6, NDN, PEG10, MEG3, MEG8), and enriched gene sets related to metabolism, proliferation, and homeostasis. We confirmed Lamin A/C haploinsufficiency by allelic expression and Western blot. Our complex Patient-derived iPSC model for Lamin A/C haploinsufficiency in PP, CM, and EPDC provided support for dysregulation of genes and pathways, many previously associated with Lamin A/C defects, such as epigenetic gene expression, signaling, and differentiation. Our findings support disruption of epigenomic developmental programs, as proposed in other LMNA disease models. We recognized other factors influencing epigenetics and differentiation; thus, our approach needs improvement to further investigate this mechanism in an iPSC-derived model.
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- 2024
15. Hepatocyte differentiation requires anisotropic expansion of bile canaliculi.
- Author
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Bebelman, Maarten P., Belicova, Lenka, Gralinska, Elzbieta, Jumel, Tobias, Lahree, Aparajita, Sommer, Sarah, Shevchenko, Andrej, Zatsepin, Timofei, Kalaidzidis, Yannis, Vingron, Martin, and Zerial, Marino
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CELL polarity , *BILE ducts , *GENE expression profiling , *REGULATOR genes , *PROGENITOR cells - Abstract
During liver development, bipotential progenitor cells called hepatoblasts differentiate into hepatocytes or cholangiocytes. Hepatocyte differentiation is uniquely associated with multi-axial polarity, enabling the anisotropic expansion of apical lumina between adjacent cells and formation of a three-dimensional network of bile canaliculi. Cholangiocytes, the cells forming the bile ducts, exhibit the vectorial polarity characteristic of epithelial cells. Whether cell polarization feeds back on the gene regulatory pathways governing hepatoblast differentiation is unknown. Here, we used primary mouse hepatoblasts to investigate the contribution of anisotropic apical expansion to hepatocyte differentiation. Silencing of the small GTPase Rab35 caused isotropic lumen expansion and formation of multicellular cysts with the vectorial polarity of cholangiocytes. Gene expression profiling revealed that these cells express reduced levels of hepatocyte markers and upregulate genes associated with cholangiocyte identity. Timecourse RNA sequencing demonstrated that loss of lumen anisotropy precedes these transcriptional changes. Independent alterations in apical lumen morphology induced either by modulation of the subapical actomyosin cortex or by increased intraluminal pressure caused similar transcriptional changes. These findings suggest that cell polarity and lumen morphogenesis feed back to hepatoblast-to-hepatocyte differentiation. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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16. A Snapshot of Early Transcriptional Changes Accompanying the Pro-Neural Phenotype Switch by NGN2, ASCL1, SOX2, and MSI1 in Human Fibroblasts: An RNA-Seq Study.
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Samoilova, Ekaterina M., Chudakova, Daria A., Dashinimaev, Erdem B., Snezhkina, Anastasiya V., Kudryashova, Olga M., Lipatova, Anastasia V., Soboleva, Alesya V., Vorob'yev, Pavel O., Valuev-Elliston, Vladimir T., Zakirova, Natalia F., Ivanov, Alexander V., and Baklaushev, Vladimir P.
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SOMATIC cells , *NEURAL crest , *PHENOTYPIC plasticity , *PHENOTYPES , *TRANSCRIPTION factors - Abstract
Direct pro-neural reprogramming is a conversion of differentiated somatic cells to neural cells without an intermediate pluripotency stage. It is usually achieved via ectopic expression (EE) of certain transcription factors (TFs) or other reprogramming factors (RFs). Determining the transcriptional changes (TCs) caused by particular RFs in a given cell line enables an informed approach to reprogramming initiation. Here, we characterized TCs in the human fibroblast cell line LF1 on the 5th day after EE of the single well-known pro-neural RFs NGN2, ASCL1, SOX2, and MSI1. As assessed by expression analysis of the bona fide neuronal markers nestin and beta-III tubulin, all four RFs initiated pro-neuronal phenotype conversion; analysis by RNA-seq revealed striking differences in the resulting TCs, although some pathways were overlapping. ASCL1 and SOX2 were not sufficient to induce significant pro-neural phenotype switches using our EE system. NGN2 induced TCs indicative of cell phenotype changes towards neural crest cells, neural stem cells, mature neurons, as well as radial glia, astrocytes, and oligodendrocyte precursors and their mature forms. MSI1 mainly induced a switch towards early stem-like cells, such as radial glia. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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17. Melatonin regulates endoplasmic reticulum stress in diverse pathophysiological contexts: A comprehensive mechanistic review.
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de Almeida Chuffa, Luiz Gustavo, Seiva, Fábio Rodrigues Ferreira, Silveira, Henrique S., Cesário, Roberta Carvalho, da Silva Tonon, Karolina, Simão, Vinicius Augusto, Zuccari, Debora Aparecida P. C., and Reiter, Russel J.
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UNFOLDED protein response , *ENDOPLASMIC reticulum , *INSULIN resistance , *CELL death , *HOMEOSTASIS - Abstract
The endoplasmic reticulum (ER) is crucial for protein quality control, and disruptions in its function can lead to various diseases. ER stress triggers an adaptive response called the unfolded protein response (UPR), which can either restore cellular homeostasis or induce cell death. Melatonin, a safe and multifunctional compound, shows promise in controlling ER stress and could be a valuable therapeutic agent for managing the UPR. By regulating ER and mitochondrial functions, melatonin helps maintain cellular homeostasis via reduction of oxidative stress, inflammation, and apoptosis. Melatonin can directly or indirectly interfere with ER‐associated sensors and downstream targets of the UPR, impacting cell death, autophagy, inflammation, molecular repair, among others. Crucially, this review explores the mechanistic role of melatonin on ER stress in various diseases including liver damage, neurodegeneration, reproductive disorders, pulmonary disease, cardiomyopathy, insulin resistance, renal dysfunction, and cancer. Interestingly, while it alleviates the burden of ER stress in most pathological contexts, it can paradoxically stimulate ER stress in cancer cells, highlighting its intricate involvement in cellular homeostasis. With numerous successful studies using in vivo and in vitro models, the continuation of clinical trials is imperative to fully explore melatonin's therapeutic potential in these conditions. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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18. Growth pattern of de novo small clusters of colorectal cancer is regulated by Notch signaling at detachment.
- Author
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Lin, Yi‐Kai, Coppo, Roberto, Onuma, Kunishige, Endo, Hiroko, Kondo, Jumpei, Iwabuchi, Sadahiro, Hashimoto, Shinichi, Itatani, Yoshiro, Obama, Kazutaka, and Inoue, Masahiro
- Abstract
Cancer cell clusters have a higher capacity for metastasis than single cells, suggesting cancer cell clusters have biological properties different from those of single cells. The nature of de novo cancer cell clusters that are newly formed from tumor masses is largely unknown. Herein, we generated small cell clusters from colorectal cancer organoids and tracked the growth patterns of the clusters up to four cells. Growth patterns were classified into actively growing and poorly growing spheroids (PG). Notch signaling was robustly activated in small clusters immediately after dissociation, and Notch signaling inhibition markedly increased the proportion of PG spheroids. Only a limited number of PG spheroids grew under growth‐permissive conditions in vitro, but xenograft tumors derived from Notch inhibited clusters showed growth rates comparable to those of untreated spheroids. Thus, de novo clusters are composed of cells with interchangeable growth fates, which are regulated in a context‐dependent manner by Notch signaling. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
19. The single RRM domain‐containing protein SARP1 is required for establishment of the separation zone in Arabidopsis.
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Yun, Ju, Lee, Inhye, Lee, Jae Ho, Kim, Seonghwan, Jung, Su Hyun, Oh, Sung Aeong, Lee, Jiyoun, Park, Soon Ki, Soh, Moon‐Soo, Lee, Yuree, and Kwak, June M.
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TRANSCRIPTION factors , *CELL separation , *ABSCISSION (Botany) , *CELL size , *ARABIDOPSIS thaliana - Abstract
Summary: Abscission is the shedding of plant organs in response to developmental and environmental cues. Abscission involves cell separation between two neighboring cell types, residuum cells (RECs) and secession cells (SECs) in the floral abscission zone (AZ) in Arabidopsis thaliana. However, the regulatory mechanisms behind the spatial determination that governs cell separation are largely unknown.The class I KNOTTED‐like homeobox (KNOX) transcription factor BREVIPEDICELLUS (BP) negatively regulates AZ cell size and number in Arabidopsis. To identify new players participating in abscission, we performed a genetic screen by activation tagging a weak complementation line of bp‐3. We identified the mutant ebp1 (enhancer of BP1) displaying delayed floral organ abscission.The ebp1 mutant showed a concaved surface in SECs and abnormally stacked cells on the top of RECs, in contrast to the precisely separated surface in the wild‐type. Molecular and histological analyses revealed that the transcriptional programming during cell differentiation in the AZ is compromised in ebp1. The SECs of ebp1 have acquired REC‐like properties, including cuticle formation and superoxide production.We show that SEPARATION AFFECTING RNA‐BINDING PROTEIN1 (SARP1) is upregulated in ebp1 and plays a role in the establishment of the cell separation layer during floral organ abscission in Arabidopsis. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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20. Reproducibly oriented cell divisions pattern the prothallus to set up dorsoventrality and de novo meristem formation in Marchantia polymorpha.
- Author
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Wallner, Eva-Sophie and Dolan, Liam
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TRANSCRIPTION factors , *CELL division , *STEM cells , *CELL aggregation , *MERISTEMS - Abstract
Land plant bodies develop from stem cells located in meristems. However, we know little about how meristems initiate from non-meristematic cells. The haploid body of bryophytes develops from unicellular spores in isolation from the parental plant, which allows all stages of development to be observed. We discovered that the Marchantia spore undergoes a series of reproducibly oriented cell divisions to generate a flat prothallus on which a meristem later develops de novo. The young sporeling comprises an early cell mass. One cell of the early cell mass elongates and undergoes a formative division that produces the prothalloblast, which initiates prothallus formation. A symmetric division of the prothalloblast followed by two transverse divisions generates a four-celled plate that expands into a flat disc through oblique divisions in three of the four plate-cell-derived quadrants. One quadrant gives rise to a flat flabellum. A notch with a meristem and apical stem cell develops at the margin of the flabellum. The transcription factor Marchantia class III homeodomain-leucine-zipper (MpC3HDZ) is a marker of the first flat prothallus structure and polarizes to the dorsal tissues of flabella and meristems. Mp c3hdz mutants are defective in setting up dorsoventrality and thallus body flatness. We report how a regular set of cell divisions forms the prothallus—the first dorsoventral structure—and how cells on the margin of the prothallus develop a dorsoventralized meristem de novo. [Display omitted] • Marchantia polymorpha develops meristems from single-celled spores • The sporeling forms a prothalloblast to initiate the first flat prothallus • A meristem is formed de novo on the flat prothallus flabellum • MpC3HDZ regulates dorsoventrality and marks the dorsal side of the prothallus Wallner and Dolan describe the cell division patterns that form the flat Marchantia prothallus from a single-celled spore. A meristem with an apical stem cell develops on the prothallus to initiate indeterminate thallus growth. The transcription factor MpC3HDZ marks the first flat structure and regulates dorsoventrality of the flat Marchantia body. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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21. Manipulating cell fate through reprogramming: approaches and applications.
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Masaki Yagi, Horng, Joy E., and Hochedlinger, Konrad
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INDUCED pluripotent stem cells , *PLURIPOTENT stem cells , *SOMATIC cells , *TRANSCRIPTION factors , *SMALL molecules - Abstract
Cellular plasticity progressively declines with development and differentiation, yet these processes can be experimentally reversed by reprogramming somatic cells to induced pluripotent stem cells (iPSCs) using defined transcription factors. Advances in reprogramming technology over the past 15 years have enabled researchers to study diseases with patient-specific iPSCs, gain fundamental insights into how cell identity is maintained, recapitulate early stages of embryogenesis using various embryo models, and reverse aspects of aging in cultured cells and animals. Here, we review and compare currently available reprogramming approaches, including transcription factor-based methods and small molecule-based approaches, to derive pluripotent cells characteristic of early embryos. Additionally, we discuss our current understanding of mechanisms that resist reprogramming and their role in cell identity maintenance. Finally, we review recent efforts to rejuvenate cells and tissues with reprogramming factors, as well as the application of iPSCs in deriving novel embryo models to study pre-implantation development. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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22. EnhancerNet: a predictive model of cell identity dynamics through enhancer selection.
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Karin, Omer
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TRANSCRIPTION factors , *IDENTITY (Psychology) , *CYTOLOGY , *STATISTICAL physics , *SYSTEMS biology - Abstract
Understanding how cell identity is encoded by the genome and acquired during differentiation is a central challenge in cell biology. I have developed a theoretical framework called EnhancerNet, which models the regulation of cell identity through the lens of transcription factor-enhancer interactions. I demonstrate that autoregulation in these interactions imposes a constraint on the model, resulting in simplified dynamics that can be parameterized from observed cell identities. Despite its simplicity, EnhancerNet recapitulates a broad range of experimental observations on cell identity dynamics, including enhancer selection, cell fate induction, hierarchical differentiation through multipotent progenitor states and direct reprogramming by transcription factor overexpression. The model makes specific quantitative predictions, reproducing known reprogramming recipes and the complex haematopoietic differentiation hierarchy without fitting unobserved parameters. EnhancerNet provides insights into how new cell types could evolve and highlights the functional importance of distal regulatory elements with dynamic chromatin in multicellular evolution. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
23. Observations of root hair patterning in soils: Insights from synchrotron-based X-ray computed microtomography.
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Duddek, Patrick, Papritz, Andreas, Ahmed, Mutez Ali, Lovric, Goran, and Carminati, Andrea
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X-ray computed microtomography , *HAIR growth , *SOIL structure , *SOIL particles , *CORN - Abstract
Background And Aims: Root hair emergence is affected by heterogeneities in water availability in the growth medium. Root hairs preferentially emerge into air, whereas their emergence into water is inhibited. Yet, these results were based either on destructive methods or on roots grown on an agar-air interface. Additionally, there is a lack of knowledge about the spatial distribution of root hairs as hairs elongate radially across the rhizosphere. Therefore, root hair growth in soils remains largely unexplored. Methods: Maize (Zea Mays L.) plants were grown in microcosms which were scanned with a synchrotron-based X-ray μ CT. The distribution of root hairs along the root epidermis and radially across the rhizosphere (i.e. as function of distance from the root epidermis) was analysed using spatial point pattern analysis. Results: While hairs emerged randomly in air-filled pores, their emergence was inhibited where the root was in contact with the soil matrix. As hairs elongated radially into the soil, they were preferentially located in the close proximity of soil particles. In maize, we rarely observed root hairs penetrating into soil aggregates. Conclusion: We conclude that in maize, root hairs grow in air-filled pores at the root-soil interface, where the flow of nutrients and water is impeded. Across the rhizosphere, hairs establish contact to the soil by growing in the proximity to soil particles. The effect of hairs on uptake processes, plant anchorage and rhizosheath formation might be limited (in maize) as they hardly penetrate into soil aggregates. [ABSTRACT FROM AUTHOR]
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- 2024
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24. What Is a Plant Cell Type in the Age of Single-Cell Biology? It's Complicated.
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Rusnak, Byron, Clark, Frances K., Vadde, Batthula Vijaya Lakshmi, and Roeder, Adrienne H.K.
- Abstract
One of the fundamental questions in developmental biology is how a cell is specified to differentiate as a specialized cell type. Traditionally, plant cell types were defined based on their function, location, morphology, and lineage. Currently, in the age of single-cell biology, researchers typically attempt to assign plant cells to cell types by clustering them based on their transcriptomes. However, because cells are dynamic entities that progress through the cell cycle and respond to signals, the transcriptome also reflects the state of the cell at a particular moment in time, raising questions about how to define a cell type. We suggest that these complexities and dynamics of cell states are of interest and further consider the roles signaling, stochasticity, cell cycle, and mechanical forces play in plant cell fate specification. Once established, cell identity must also be maintained. With the wealth of single-cell data coming out, the field is poised to elucidate both the complexity and dynamics of cell states. [ABSTRACT FROM AUTHOR]
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- 2024
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25. Structural Functions of 3D‐Printed Polymer Scaffolds in Regulating Cell Fates and Behaviors for Repairing Bone and Nerve Injuries.
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Zhang, Tongling, Shan, Wenpeng, Le Dot, Marie, and Xiao, Pu
- Subjects
- *
NERVOUS system injuries , *CELL differentiation , *CELLULAR control mechanisms , *BONE injuries , *CELL anatomy , *BONE regeneration - Abstract
Tissue repair and regeneration, such as bone and nerve restoration, face significant challenges due to strict regulations within the immune microenvironment, stem cell differentiation, and key cell behaviors. The development of 3D scaffolds is identified as a promising approach to address these issues via the efficiently structural regulations on cell fates and behaviors. In particular, 3D‐printed polymer scaffolds with diverse micro‐/nanostructures offer a great potential for mimicking the structures of tissue. Consequently, they are foreseen as promissing pathways for regulating cell fates, including cell phenotype, differentiation of stem cells, as well as the migration and the proliferation of key cells, thereby facilitating tissue repairs and regenerations. Herein, the roles of structural functions of 3D‐printed polymer scaffolds in regulating the fates and behaviors of numerous cells related to tissue repair and regeneration, along with their specific influences are highlighted. Additionally, the challenges and outlooks associated with 3D‐printed polymer scaffolds with various structures for modulating cell fates are also discussed. [ABSTRACT FROM AUTHOR]
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- 2024
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26. Revisiting trophectoderm-inner cell mass lineage segregation in the mammalian preimplantation embryo.
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Skory, Robin M
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MAMMALIAN embryos , *HUMAN embryos , *CELL polarity , *NON-coding RNA , *OVUM - Abstract
In the first days of life, cells of the mammalian embryo segregate into two distinct lineages, trophectoderm and inner cell mass. Unlike nonmammalian species, mammalian development does not proceed from predetermined factors in the oocyte. Rather, asymmetries arise de novo in the early embryo incorporating cues from cell position, contractility, polarity, and cell–cell contacts. Molecular heterogeneities, including transcripts and non-coding RNAs, have now been characterized as early as the 2-cell stage. However, it's debated whether these early heterogeneities bias cells toward one fate or the other or whether lineage identity arises stochastically at the 16-cell stage. This review summarizes what is known about early blastomere asymmetries and our understanding of lineage allocation in the context of historical models. Preimplantation development is reviewed coupled with what is known about changes in morphology, contractility, and transcription factor networks. The addition of single-cell atlases of human embryos has begun to reveal key differences between human and mouse, including the timing of events and core transcription factors. Furthermore, the recent generation of blastoid models will provide valuable tools to test and understand fate determinants. Lastly, new techniques are reviewed, which may better synthesize existing knowledge with emerging data sets and reconcile models with the regulative capacity unique to the mammalian embryo. [ABSTRACT FROM AUTHOR]
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- 2024
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27. Vitamin D receptor cross-talk with p63 signaling promotes epidermal cell fate.
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Oda, Yuko, Wong, Christian, Oh, Dennis, Meyer, Mark, Pike, J, and Bikle, Daniel
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Cell fate ,Epigenetics ,Keratinocytes ,wounding ,P63 ,Vitamin D ,Vitamin D receptor ,Animals ,Mice ,Receptors ,Calcitriol ,Receptor Cross-Talk ,Epidermis ,Keratinocytes ,Epidermal Cells ,Cell Differentiation ,Transcription Factors ,Vitamin D - Abstract
The vitamin D receptor with its ligand 1,25 dihydroxy vitamin D3 (1,25D3) regulates epidermal stem cell fate, such that VDR removal from Krt14 expressing keratinocytes delays re-epithelialization of epidermis after wound injury in mice. In this study we deleted Vdr from Lrig1 expressing stem cells in the isthmus of the hair follicle then used lineage tracing to evaluate the impact on re-epithelialization following injury. We showed that Vdr deletion from these cells prevents their migration to and regeneration of the interfollicular epidermis without impairing their ability to repopulate the sebaceous gland. To pursue the molecular basis for these effects of VDR, we performed genome wide transcriptional analysis of keratinocytes from Vdr cKO and control littermate mice. Ingenuity Pathway analysis (IPA) pointed us to the TP53 family including p63 as a partner with VDR, a transcriptional factor that is essential for proliferation and differentiation of epidermal keratinocytes. Epigenetic studies on epidermal keratinocytes derived from interfollicular epidermis showed that VDR is colocalized with p63 within the specific regulatory region of MED1 containing super-enhancers of epidermal fate driven transcription factor genes such as Fos and Jun. Gene ontology analysis further implicated that Vdr and p63 associated genomic regions regulate genes involving stem cell fate and epidermal differentiation. To demonstrate the functional interaction between VDR and p63, we evaluated the response to 1,25(OH)2D3 of keratinocytes lacking p63 and noted a reduction in epidermal cell fate determining transcription factors such as Fos, Jun. We conclude that VDR is required for the epidermal stem cell fate orientation towards interfollicular epidermis. We propose that this role of VDR involves cross-talk with the epidermal master regulator p63 through super-enhancer mediated epigenetic dynamics.
- Published
- 2023
28. Gene expression changes in blastocyst hatching affect embryo implantation success in mice
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Liyou An, Liang Zhang, Yulin Wu, Yadi Teng, Zihan Liu, Meixiang Ma, Miaolong Li, Xinrong Peng, and Chenxi Liu
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mouse blastocyst ,hatching ,gene expression ,implantation ,cell fate ,Biology (General) ,QH301-705.5 - Abstract
In mammalian embryonic development, blastocyst hatching is essential for normal implantation and development of the fetus. We reported previously that blastocysts hatching out of the zona pellucida (ZP) exhibited site preferences that were associated with pregnancy outcomes. To characterize these site differences, we analyzed the transcriptomes in the following developing mouse blastocysts within 16 h of hatching: expanding (E), hatching from the A-site (A), B-site (B), and C-site (C), hatched (H), and non-hatching (N). By principal component analysis and hierarchical cluster analysis, we determined that the gene expression profiles of A and B blastocysts, which resulted in good fertility, clustered closely. C and N blastocysts, which resulted in poor fertility, clustered closely, but distantly from A and B. Embryos hatched at B- vs. C-sites, with good vs. poor pregnancy, showed 178 differentially expressed genes (DEGs), mainly involved in immunity, which correlated positively with birth rate. These DEGs were primarily regulated by transcription factors TCF24 and DLX3. During blastocyst hatching, immune-related genes were regulated, such as Ptgs1, Lyz2, Il-α, Cfb (upregulated) and Cd36 (downregulated). By immunofluorescence staining, we found C3 and IL-1β on the extra-luminal surface of the trophectoderm of the hatched blastocyst, suggesting that they play a role in maternal-fetal interactions. As the blastocysts developed from the expanding to the fully hatched state, 307 DEGs were either upregulated by transcription factor ATOH8 or downregulated by SPIC to switch on immune pathways. Based on the hatching outcome, we identified three transcription patterns in developing blastocysts, with complex changes in the transcriptional regulation network of failed hatched blastocysts vs. successfully hatched blastocysts. We developed a LASSO regression-based model using DEGs Lyz2, Cd36, Cfb, and Cyp17a1 to predict implantation success. This study revealed the diverse, multidimensional developmental fates of blastocysts during short-term hatching and indicated that the immune properties of the embryo had a major effect on blastocyst hatching outcomes. We suggest that transcriptional changes and their regulation during the development of the preimplantation blastocyst affect implantation. This study contributes to our understanding of the role of transcriptional changes in mammalian embryonic development during hatching and their effect on maternal-fetal interactions.
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- 2025
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29. Cell–cell heterogeneity in phosphoenolpyruvate carboxylase biases early cell fate priming in Dictyostelium discoideum
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Kenichi Abe, Hidenori Hashimura, Haruka Hiraoka, Shoko Fujishiro, Narufumi Kameya, Kazuteru Taoka, Satoshi Kuwana, Masashi Fukuzawa, and Satoshi Sawai
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PEPC ,cell fate ,cell metabolism ,cell heterogeneity ,cell differentiation ,Dictyostelium discoideum ,Biology (General) ,QH301-705.5 - Abstract
Glucose metabolism is a key factor characterizing the cellular state during multicellular development. In metazoans, the metabolic state of undifferentiated cells correlates with growth/differentiation transition and cell fate determination. Notably, the cell fate of the Amoebozoa species Dictyostelium discoideum is biased by the presence of glucose and is also correlated with early differences in intracellular ATP. However, the relationship between early cell–cell heterogeneity, cell differentiation, and the metabolic state is unclear. To address the link between glucose metabolism and cell differentiation in D. discoideum, we studied the role of phosphoenolpyruvate carboxylase (PEPC), a key enzyme in the PEP-oxaloacetate-pyruvate node, a core junction that dictates the metabolic flux of glycolysis, the TCA cycle, and gluconeogenesis. We demonstrate that there is cell–cell heterogeneity in PEPC promoter activity in vegetative cells, which depends on nutrient conditions, and that cells with high PEPC promoter activity differentiate into spores. The PEPC null mutant exhibited an aberrantly high prestalk/prespore ratio, and the spore mass of the fruiting body was glassy and consisted of immature spores. Furthermore, the PEPC null mutant had high ATP levels and low mitochondrial membrane potential. Our results suggest the importance of cell–cell heterogeneity in the levels of metabolic enzymes during early cell fate priming.
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- 2025
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30. The role of Golgi complex proteins in cell division and consequences of their dysregulation
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Roberta Iannitti, Fabiola Mascanzoni, Antonino Colanzi, and Daniela Spano
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Golgi complex ,mitosis ,meiosis ,cell fate ,cancer ,Biology (General) ,QH301-705.5 - Abstract
The GC (Golgi complex) plays a pivotal role in the trafficking and sorting of proteins and lipids until they reach their final destination. Additionally, the GC acts as a signalling hub to regulate a multitude of cellular processes, including cell polarity, motility, apoptosis, DNA repair and cell division. In light of these crucial roles, the GC has garnered increasing attention, particularly given the evidence that a dysregulation of GC-regulated signalling pathways may contribute to the onset of various pathological conditions. This review examines the functions of the GC and GC-localised proteins in regulating cell cycle progression, in both mitosis and meiosis. It reviews the involvement of GC-resident proteins in the formation and orientation of the spindle during cell division. In light of the roles played by the GC in controlling cell division, this review also addresses the involvement of the GC in cancer development. Furthermore, TCGA (The Cancer Genome Atlas) database has been queried in order to retrieve information on the genetic alterations and the correlation between the expression of GC-localised proteins and the survival of cancer patients. The data presented in this review highlight the relevance of the GC in regulating cell cycle progression, cellular differentiation and tumourigenesis.
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- 2025
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31. MicroRNAs as Regulators of Radiation-Induced Oxidative Stress
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Branislav Kura, Patricia Pavelkova, Barbora Kalocayova, Margita Pobijakova, and Jan Slezak
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apoptosis ,cell fate ,microRNA ,oxidative stress ,radiation ,ROS ,Biology (General) ,QH301-705.5 - Abstract
microRNAs (miRNAs) represent small RNA molecules involved in the regulation of gene expression. They are implicated in the regulation of diverse cellular processes ranging from cellular homeostasis to stress responses. Unintended irradiation of the cells and tissues, e.g., during medical uses, induces various pathological conditions, including oxidative stress. miRNAs may regulate the expression of transcription factors (e.g., nuclear factor erythroid 2 related factor 2 (Nrf2), nuclear factor kappa B (NF-κB), tumor suppressor protein p53) and other redox-sensitive genes (e.g., mitogen-activated protein kinase (MAPKs), sirtuins (SIRTs)), which trigger and modulate cellular redox signaling. During irradiation, miRNAs mainly act with reactive oxygen species (ROS) to regulate the cell fate. Depending on the pathway involved and the extent of oxidative stress, this may lead to cell survival or cell death. In the context of radiation-induced oxidative stress, miRNA-21 and miRNA-34a are among the best-studied miRNAs. miRNA-21 has been shown to directly target superoxide dismutase (SOD), or NF-κB, whereas miRNA-34a is a direct regulator of NADPH oxidase (NOX), SIRT1, or p53. Understanding the mechanisms underlying radiation-induced injury including the involvement of redox-responsive miRNAs may help to develop novel approaches for modulating the cellular response to radiation exposure.
- Published
- 2024
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32. Macrophage-derived extracellular vesicles regulate skeletal stem/progenitor Cell lineage fate and bone deterioration in obesity
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Chen He, Chen Hu, Wen-Zhen He, Yu-Chen Sun, Yangzi Jiang, Ling Liu, Jing Hou, Kai-Xuan Chen, Yu-Rui Jiao, Mei Huang, Min Huang, Mi Yang, Qiong Lu, Jie Wei, Chao Zeng, Guang-Hua Lei, and Chang-Jun Li
- Subjects
Obesity-induced bone deterioration ,Macrophage-derived extracellular vesicles ,Skeletal stem/progenitor cells ,Cell fate ,Aptamer ,Cell-specific targeting ,Materials of engineering and construction. Mechanics of materials ,TA401-492 ,Biology (General) ,QH301-705.5 - Abstract
Obesity-induced chronic inflammation exacerbates multiple types of tissue/organ deterioration and stem cell dysfunction; however, the effects on skeletal tissue and the underlying mechanisms are still unclear. Here, we show that obesity triggers changes in the microRNA profile of macrophage-secreted extracellular vesicles, leading to a switch in skeletal stem/progenitor cell (SSPC) differentiation between osteoblasts and adipocytes and bone deterioration. Bone marrow macrophage (BMM)-secreted extracellular vesicles (BMM-EVs) from obese mice induced bone deterioration (decreased bone volume, bone microstructural deterioration, and increased adipocyte numbers) when administered to lean mice. Conversely, BMM-EVs from lean mice rejuvenated bone deterioration in obese recipients. We further screened the differentially expressed microRNAs in obese BMM-EVs and found that among the candidates, miR-140 (with the function of promoting adipogenesis) and miR-378a (with the function of enhancing osteogenesis) coordinately determine SSPC fate of osteogenic and adipogenic differentiation by targeting the Pparα-Abca1 axis. BMM miR-140 conditional knockout mice showed resistance to obesity-induced bone deterioration, while miR-140 overexpression in SSPCs led to low bone mass and marrow adiposity in lean mice. BMM miR-378a conditional depletion in mice led to obesity-like bone deterioration. More importantly, we used an SSPC-specific targeting aptamer to precisely deliver miR-378a-3p-overloaded BMM-EVs to SSPCs via an aptamer-engineered extracellular vesicle delivery system, and this approach rescued bone deterioration in obese mice. Thus, our study reveals the critical role of BMMs in mediating obesity-induced bone deterioration by transporting selective extracellular-vesicle microRNAs into SSPCs and controlling SSPC fate.
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- 2024
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33. Intermediate filaments at a glance.
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Coelho-Rato, Leila S., Parvanian, Sepideh, Salajkova, Sarka Andrs, Medalia, Ohad, and Eriksson, John E.
- Abstract
Intermediate filaments (IFs) comprise a large family of versatile cytoskeletal proteins, divided into six subtypes with tissue-specific expression patterns. IFs have a wide repertoire of cellular functions, including providing structural support to cells, as well as active roles in mechanical support and signaling pathways. Consequently, defects in IFs are associated with more than 100 diseases. In this Cell Science at a Glance article, we discuss the established classes of IFs and their general features, their functions beyond structural support, and recent advances in the field. We also highlight their involvement in disease and potential use as clinical markers of pathological conditions. Finally, we provide our view on current knowledge gaps and the future directions of the IF field. [ABSTRACT FROM AUTHOR]
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- 2024
- Full Text
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34. Reconstruction of single-cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition.
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Yu-Chen Cheng, Yun Zhang, Tripathi, Shubham, Harshavardhan, B. V., Jolly, Mohit Kumar, Schiebinger, Geoffrey, Levine, Herbert, McDonald, Thomas O., and Michor, Franziska
- Subjects
- *
EPITHELIAL-mesenchymal transition , *GENE expression , *RNA sequencing , *CELL cycle , *CELL lines - Abstract
Exploring the complexity of the epithelial-to-mesenchymal transition (EMT) unveils a diversity of potential cell fates; however, the exact timing and mechanisms by which early cell states diverge into distinct EMT trajectories remain unclear. Studying these EMT trajectories through single-cell RNA sequencing is challenging due to the necessity of sacrificing cells for each measurement. In this study, we employed optimal-transport analysis to reconstruct the past trajectories of different cell fates during TGF-beta-induced EMT in the MCF10A cell line. Our analysis revealed three distinct trajectories leading to low EMT, partial EMT, and high EMT states. Cells along the partial EMT trajectory showed substantial variations in the EMT signature and exhibited pronounced stemness. Throughout this EMT trajectory, we observed a consistent downregulation of the EED and EZH2 genes. This finding was validated by recent inhibitor screens of EMT regulators and CRISPR screen studies. Moreover, we applied our analysis of early-phase differential gene expression to gene sets associated with stemness and proliferation, pinpointing ITGB4, LAMA3, and LAMB3 as genes differentially expressed in the initial stages of the partial versus high EMT trajectories. We also found that CENPF, CKS1B, and MKI67 showed significant upregulation in the high EMT trajectory. While the first group of genes aligns with findings from previous studies, our work uniquely pinpoints the precise timing of these upregulations. Finally, the identification of the latter group of genes sheds light on potential cell cycle targets for modulating EMT trajectories. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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35. Cohesin composition and dosage independently affect early development in zebrafish.
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Labudina, Anastasia A., Meier, Michael, Gimenez, Gregory, Tatarakis, David, Ketharnathan, Sarada, Mackie, Bridget, Schilling, Thomas F., Antony, Jisha, and Horsfield, Julia A.
- Subjects
- *
COHESINS , *MESODERM , *BRACHYDANIO , *GENE expression , *WNT signal transduction , *CELL cycle - Abstract
Cohesin, a chromatin-associated protein complex with four core subunits (Smc1a, Smc3, Rad21 and either Stag1 or 2), has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed 'cohesinopathies' are characterized by germline variants of cohesin or its regulators that do not entirely eliminate cohesin function. However, it is not clear whether mutations in individual cohesin subunits have independent developmental consequences. Here, we show that zebrafish rad21 or stag2b mutants independently influence embryonic tailbud development. Both mutants have altered mesoderm induction, but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2b mutants have narrower notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single-cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2b, but not rad21, mutants. Our results suggest that mutations altering the quantity versus composition of cohesin have independent developmental consequences, with implications for the understanding and management of cohesinopathies. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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36. Influence of DNA-methylation at multiple stages of limb chondrogenesis.
- Author
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Pérez-Maldonado, Mario Alberto, González-González, Ximena Alexandra, Chimal-Monroy, Jesús, and Marín-Llera, Jessica Cristina
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- *
CHONDROGENESIS , *CELL differentiation , *CELL adhesion , *DNA methylation , *GENETIC regulation , *CARTILAGE regeneration , *CELLULAR control mechanisms - Abstract
Precise regulation of gene expression is of utmost importance during cell fate specification. DNA methylation is a key epigenetic mechanism that plays a significant role in the regulation of cell fate by recruiting repression proteins or inhibiting the binding of transcription factors to DNA to regulate gene expression. Limb development is a well-established model for understanding cell fate decisions, and the formation of skeletal elements is coordinated through a sequence of events that control chondrogenesis spatiotemporally. It has been established that epigenetic control participates in cartilage maturation. However, further investigation is required to determine its role in the earliest stages of chondrocyte differentiation. This study investigates how the DNA methylation environment affects cell fate divergence during the early chondrogenic events. Our research has shown for the first time that inhibiting DNA methylation in interdigital tissue with 5-azacytidine results in the formation of an ectopic digit. This discovery suggested that DNA methylation dynamics could regulate the fate of cells between chondrogenesis and cell death during autopod development. Our in vitro findings indicate that DNA methylation at the early stages of chondrogenesis is integral in regulating condensation by controlling cell adhesion and proapoptotic genes. As a result, the dynamics of methylation and demethylation are crucial in governing chondrogenesis and cell death during different stages of limb chondrogenesis. [Display omitted] • Chondrogenic and death cell fate control during digit formation depends on methylation and demethylation dynamics. • An ectopic digit is induced in the interdigital tissue after the global DNA methylation is inhibited. • When chondrogenic fate is triggered, the inhibition of global DNA methylation enhances chondrogenesis. • Global DNA hypomethylated state constrains nodule formation in mesodermal progenitor cells by controlling cell condensation. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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37. Mechanisms of regeneration: to what extent do they recapitulate development?
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Aztekin, Can
- Subjects
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REGENERATION (Biology) , *TRANSCRIPTOMES , *BIOLOGY , *MORPHOGENESIS , *CRISPRS - Abstract
One of the enduring debates in regeneration biology is the degree to which regeneration mirrors development. Recent technical advances, such as single-cell transcriptomics and the broad applicability of CRISPR systems, coupled with new model organisms in research, have led to the exploration of this longstanding concept from a broader perspective. In this Review, I outline the historical parallels between development and regeneration before focusing on recent research that highlights how dissecting the divergence between these processes can uncover previously unreported biological mechanisms. Finally, I discuss how these advances position regeneration as a more dynamic and variable process with expanded possibilities for morphogenesis compared with development. Collectively, these insights into mechanisms that orchestrate morphogenesis may reshape our understanding of the evolution of regeneration, reveal hidden biology activated by injury, and offer non-developmental strategies for restoring lost or damaged organs and tissues. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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38. Notch 信号通路调控间充质干细胞的增殖与分化.
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王雪淞, 周 林, 李林材, 邹征伟, 唐兴坤, 卢文明, 陈文杰, 汪 月, and 叶俊松
- Subjects
- *
NOTCH genes , *NOTCH signaling pathway , *MESENCHYMAL stem cell differentiation , *BIOLOGICAL evolution , *MESENCHYMAL stem cells , *MEMBRANE proteins - Abstract
BACKGROUND: It was found that the ligands and receptors of Notch are both cell membrane surface proteins, which are important proteins to mediate intercellular communication, and the Notch signaling pathway plays a crucial regulatory role in the proliferation and differentiation of mesenchymal stem cells. OBJECTIVE: To review the regulatory mechanism of the Notch signaling pathway on the proliferation and differentiation of mesenchymal stem cells, summarize and clarify the research advance in how the Notch signaling pathway regulates the proliferation and differentiation of mesenchymal stem cells, and provide theoretical support for the future use of stem cells to treat various related diseases. METHODS: By using the computer, the first author searched the relevant studies involving Notch signaling pathway regulation of mesenchymal stem cell proliferation and differentiation on CNKI, Wanfang, VIP, PubMed, Web of Science, and Nature databases with Chinese search terms “mesenchymal stem cells, Notch, Notch signaling pathway, proliferation, differentiation” and the English search terms “mesenchymal stem cells, MSC, Notch, Notch signaling pathway, proliferation, differentiation”. Part of the literature was searched in combination with the literature tracing method. Finally, 87 articles were included in the review analysis. RESULTS AND CONCLUSION: (1) Notch signaling pathway is a conserved signaling pathway in multicellular organisms, which plays an important role in regulating cell differentiation, proliferation, apoptosis, and the cell cycle by mediating communication between neighboring cells through receptor-ligand binding. (2) Mesenchymal stem cells are a class of adult stem cells with self-proliferative and multi-directional differentiation potential, which can be regulated by external signaling pathways to affect their proliferation and differentiation. Notch signaling pathway, as one of them, when Notch ligands are activated, the Notch proteins will undergo two protein hydrolysis cleavages to release Notch intracellular structural domain NICD, which then enters the nucleus and thus promotes the transcription of target genes to regulate the proliferation and differentiation of mesenchymal stem cells from different sources, such as bone marrow, adipose, and umbilical cord. However, the specific mechanisms that regulate the proliferation and differentiation of mesenchymal stem cells from different tissue sources of the same species are different. (3) The Notch signaling pathway can regulate the differentiation of mesenchymal stem cells into different target cells, but due to different target cells, the expression levels of receptors or ligands in the Notch signaling pathway vary. (4) Clinical targeting of the Notch signaling pathway to promote mesenchymal stem cells for the treatment of various refractory diseases, such as aplastic anemia, severe joint injuries, ischemic strokes, and myocardial infarctions, has a promising application. (5) By exploring the Notch signaling pathway via regulating the expression levels of its receptors and ligands in bone marrow mesenchymal stem cells from rat, mouse, and human, it can be found that the Notch signaling pathway expression levels in the proliferation and differentiation of mesenchymal stem cells from different species origins are also different. (6) The role of mesenchymal stem cells in tissue engineering has been gradually highlighted due to their advantages of safety, low immune rejection, and wide therapeutic prospects. The Notch signaling pathway regulates the proliferation and differentiation of mesenchymal stem cells with a wide range of influencing factors, and subsequent studies should further optimize the influencing factor variables and explore the standardized studies of regulating the proliferation and differentiation of mesenchymal stem cells. [ABSTRACT FROM AUTHOR]
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- 2024
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39. Cadmium toxicity and autophagy: a review.
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Shao, Yueting, Zheng, Liting, and Jiang, Yiguo
- Abstract
Cadmium (Cd) is an important environmental pollutant that poses a threat to human health and represents a critical component of air pollutants, food sources, and cigarette smoke. Cd is a known carcinogen and has toxic effects on the environment and various organs in humans. Heavy metals within an organism are difficult to biodegrade, and those that enter the respiratory tract are difficult to remove. Autophagy is a key mechanism for counteracting extracellular (microorganisms and foreign bodies) or intracellular (damaged organelles and proteins that cannot be degraded by the proteasome) stress and represents a self-protective mechanism for eukaryotes against heavy metal toxicity. Autophagy maintains cellular homeostasis by isolating and gathering information about foreign chemicals associated with other molecular events. However, autophagy may trigger cell death under certain pathological conditions, including cancer. Autophagy dysfunction is one of the main mechanisms underlying Cd-induced cytotoxicity. In this review, the toxic effects of Cd-induced autophagy on different human organ systems were evaluated, with a focus on hepatotoxicity, nephrotoxicity, respiratory toxicity, and neurotoxicity. This review also highlighted the classical molecular pathways of Cd-induced autophagy, including the ROS-dependent signaling pathways, endoplasmic reticulum (ER) stress pathway, Mammalian target of rapamycin (mTOR) pathway, Beclin-1 and Bcl-2 family, and recently identified molecules associated with Cd. Moreover, research directions for Cd toxicity regarding autophagic function were proposed. This review presents the latest theories to comprehensively reveal autophagy behavior in response to Cd toxicity and proposes novel potential autophagy-targeted prevention and treatment strategies for Cd toxicity and Cd-associated diseases in humans. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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40. Molecular Genetics of Stomatal Development in Arabidopsis
- Author
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Saiz-Pérez, Josué, Fenoll, Carmen, Mena, Montaña, Lüttge, Ulrich, Series Editor, Cánovas, Francisco M., Series Editor, Pretzsch, Hans, Series Editor, Risueño, María-Carmen, Series Editor, Leuschner, Christoph, Series Editor, and Risueño Almeida, María Carmen, editor
- Published
- 2024
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41. Astrocyte Development in the Rodent
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Xie, Yajun, Harwell, Corey C., Garcia, A. Denise R., Verkhratsky, Alexej, Series Editor, Blanco-Suarez, Elena, editor, and Farhy-Tselnicker, Isabella, editor
- Published
- 2024
- Full Text
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42. Neurotrophic factor Neuritin modulates T cell electrical and metabolic state for the balance of tolerance and immunity
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Hong Yu, Hiroshi Nishio, Joseph Barbi, Marisa Mitchell-Flack, Paolo DA Vignali, Ying Zheng, Andriana Lebid, Kwang-Yu Chang, Juan Fu, Makenzie Higgins, Ching-Tai Huang, Xuehong Zhang, Zhiguang Li, Lee Blosser, Ada Tam, Charles Drake, and Drew Pardoll
- Subjects
electric state ,metabolism ,Treg ,effector T cell ,autoimmunity ,cell fate ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
The adaptive T cell response is accompanied by continuous rewiring of the T cell’s electric and metabolic state. Ion channels and nutrient transporters integrate bioelectric and biochemical signals from the environment, setting cellular electric and metabolic states. Divergent electric and metabolic states contribute to T cell immunity or tolerance. Here, we report in mice that neuritin (Nrn1) contributes to tolerance development by modulating regulatory and effector T cell function. Nrn1 expression in regulatory T cells promotes its expansion and suppression function, while expression in the T effector cell dampens its inflammatory response. Nrn1 deficiency in mice causes dysregulation of ion channel and nutrient transporter expression in Treg and effector T cells, resulting in divergent metabolic outcomes and impacting autoimmune disease progression and recovery. These findings identify a novel immune function of the neurotrophic factor Nrn1 in regulating the T cell metabolic state in a cell context-dependent manner and modulating the outcome of an immune response.
- Published
- 2024
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43. Opening and changing: mammalian SWI/SNF complexes in organ development and carcinogenesis
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Fadia Abu Sailik, Bright Starling Emerald, and Suraiya Anjum Ansari
- Subjects
chromatin remodelling ,cancer ,gene expression ,cell fate ,Biology (General) ,QH301-705.5 - Abstract
The switch/sucrose non-fermentable (SWI/SNF) subfamily are evolutionarily conserved, ATP-dependent chromatin-remodelling complexes that alter nucleosome position and regulate a spectrum of nuclear processes, including gene expression, DNA replication, DNA damage repair, genome stability and tumour suppression. These complexes, through their ATP-dependent chromatin remodelling, contribute to the dynamic regulation of genetic information and the maintenance of cellular processes essential for normal cellular function and overall genomic integrity. Mutations in SWI/SNF subunits are detected in 25% of human malignancies, indicating that efficient functioning of this complex is required to prevent tumourigenesis in diverse tissues. During development, SWI/SNF subunits help establish and maintain gene expression patterns essential for proper cellular identity and function, including maintenance of lineage-specific enhancers. Moreover, specific molecular signatures associated with SWI/SNF mutations, including disruption of SWI/SNF activity at enhancers, evasion of G0 cell cycle arrest, induction of cellular plasticity through pro-oncogene activation and Polycomb group (PcG) complex antagonism, are linked to the initiation and progression of carcinogenesis. Here, we review the molecular insights into the aetiology of human malignancies driven by disruption of the SWI/SNF complex and correlate these mechanisms to their developmental functions. Finally, we discuss the therapeutic potential of targeting SWI/SNF subunits in cancer.
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- 2024
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44. Fatty acid synthase (FASN) signalome: A molecular guide for precision oncology
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Javier A. Menendez, Elisabet Cuyàs, Jose Antonio Encinar, Travis Vander Steen, Sara Verdura, Àngela Llop‐Hernández, Júlia López, Eila Serrano‐Hervás, Sílvia Osuna, Begoña Martin‐Castillo, and Ruth Lupu
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cell fate ,ferroptosis ,immunotherapy ,metastasis ,mitochondrial priming ,molecular glues ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
The initial excitement generated more than two decades ago by the discovery of drugs targeting fatty acid synthase (FASN)‐catalyzed de novo lipogenesis for cancer therapy was short‐lived. However, the advent of the first clinical‐grade FASN inhibitor (TVB‐2640; denifanstat), which is currently being studied in various phase II trials, and the exciting advances in understanding the FASN signalome are fueling a renewed interest in FASN‐targeted strategies for the treatment and prevention of cancer. Here, we provide a detailed overview of how FASN can drive phenotypic plasticity and cell fate decisions, mitochondrial regulation of cell death, immune escape and organ‐specific metastatic potential. We then present a variety of FASN‐targeted therapeutic approaches that address the major challenges facing FASN therapy. These include limitations of current FASN inhibitors and the lack of precision tools to maximize the therapeutic potential of FASN inhibitors in the clinic. Rethinking the role of FASN as a signal transducer in cancer pathogenesis may provide molecularly driven strategies to optimize FASN as a long‐awaited target for cancer therapeutics.
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- 2024
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45. Mechanically guided cell fate determination in early development
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Alasaadi, Delan N. and Mayor, Roberto
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- 2024
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46. Asymmetric division of stem cells and its cancer relevance
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Chao, Shanshan, Yan, Huiwen, and Bu, Pengcheng
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- 2024
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47. The dynamics of Notch signaling in the neuron-glia switch: a balancing act.
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Ashfield, Lauren R.
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- *
OLIGODENDROGLIA , *CENTRAL nervous system , *EMBRYOLOGY , *SIGNALS & signaling , *PROSENCEPHALON - Abstract
A recent study by Tran et al. (Tran LN, Loew SK, Franco SJ. J Neurosci 43: 6854–6871, 2023) investigated the cellular processes underlying the timing and regulation of oligodendrocyte production, focusing on the role of Notch signaling in the dorsal forebrain of mouse embryos. They found that although Notch signaling is required to specify oligodendrocyte precursor cell fate during embryonic development, overexpression prevents oligodendrogenesis through several mechanisms. This critical review highlights their findings and offers suggestions for future research investigating the precise spatiotemporal control of Notch signaling throughout the development of the central nervous system. [ABSTRACT FROM AUTHOR]
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- 2024
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48. ARGONAUTE10 controls cell fate specification and formative cell divisions in the Arabidopsis root.
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El Arbi, Nabila, Schürholz, Ann-Kathrin, Handl, Marlene U, Schiffner, Alexei, Hidalgo Prados, Inés, Schnurbusch, Liese, Wenzl, Christian, Zhao, Xin'Ai, Zeng, Jian, Lohmann, Jan U, and Wolf, Sebastian
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CELL differentiation , *CELL division , *ARABIDOPSIS , *PHENOTYPIC plasticity , *CELL proliferation , *ROOT growth , *WNT signal transduction - Abstract
A key question in plant biology is how oriented cell divisions are integrated with patterning mechanisms to generate organs with adequate cell type allocation. In the root vasculature, a gradient of miRNA165/6 controls the abundance of HD-ZIP III transcription factors, which in turn control cell fate and spatially restrict vascular cell proliferation to specific cells. Here, we show that vascular development requires the presence of ARGONAUTE10, which is thought to sequester miRNA165/6 and protect HD-ZIP III transcripts from degradation. Our results suggest that the miR165/6-AGO10-HDZIP III module acts by buffering cytokinin responses and restricting xylem differentiation. Mutants of AGO10 show faster growth rates and strongly enhanced survival under severe drought conditions. However, this superior performance is offset by markedly increased variation and phenotypic plasticity in sub-optimal carbon supply conditions. Thus, AGO10 is required for the control of formative cell division and coordination of robust cell fate specification of the vasculature, while altering its expression provides a means to adjust phenotypic plasticity. Synopsis: In the Arabidopsis root vascular tissue, a gradient of miRNA165/6 controls the abundance of HD-ZIP III transcription factors, which in turn control cell fate and spatially restrict vascular cell proliferation to specific cells. This work shows that vascular development requires ARGONAUTE10 to sequester miRNA165/6, thus protecting HD-ZIP III transcripts from degradation. AGO10 controls formative cell divisions in the centre of the root stele, with its loss leading to ectopic xylem strands, increased procambial cell number, and enhanced root growth. Consistent with a role in protecting HD-ZIP III transcripts from miRNA165/6-mediated degradation, AGO10 is mostly expressed in the centre of the meristematic stele. AGO10 promotes HD-ZIP III activity to suppress cytokinin responses in the stele. AGO10 mutants outperform the wild type under water-limiting conditions. However, AGO10 is required for phenotypic robustness upon reduced carbon availability. AGO10 sequesters miRNA165/6 to suppress cytokinin-dependent responses in the root apical meristem. [ABSTRACT FROM AUTHOR]
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- 2024
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49. Neuropilin‐1 regulates renin synthesis in juxtaglomerular cells.
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Shen, Yunzhu, Lotenberg, Kenza, Zaworski, Jeremy, Broeker, Katharina A.‐E., Vasseur, Florence, Louedec, Liliane, Placier, Sandrine, Frère, Perrine, Verpont, Marie‐Christine, Galichon, Pierre, Buob, David, Hadchouel, Juliette, Terzi, Fabiola, Chatziantoniou, Christos, and Calmont, Amélie
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FATE mapping (Genetics) , *MYELIN proteins , *RENIN , *KNOCKOUT mice , *CELL physiology - Abstract
Renin is the key enzyme of the systemic renin–angiotensin–aldosterone system, which plays an essential role in regulating blood pressure and maintaining electrolyte and extracellular volume homeostasis. Renin is mainly produced and secreted by specialized juxtaglomerular (JG) cells in the kidney. In the present study, we report for the first time that the conserved transmembrane receptor neuropilin‐1 (NRP1) participates in the development of JG cells and plays a key role in renin production. We used the myelin protein zero‐Cre (P0‐Cre) to abrogate Nrp1 constitutively in P0‐Cre lineage‐labelled cells of the kidney. We found that the P0‐Cre precursor cells differentiate into renin‐producing JG cells. We employed a lineage‐tracing strategy combined with RNAscope quantification and metabolic studies to reveal a cell‐autonomous role for NRP1 in JG cell function. Nrp1‐deficient animals displayed abnormal levels of tissue renin expression and failed to adapt properly to a homeostatic challenge to sodium balance. These findings provide new insights into cell fate decisions and cellular plasticity operating in P0‐Cre–expressing precursors and identify NRP1 as a novel key regulator of JG cell maturation. Key points: Renin is a centrepiece of the renin–angiotensin–aldosterone system and is produced by specialized juxtaglomerular cells (JG) of the kidney.Neuropilin‐1 (NRP1) is a conserved membrane‐bound receptor that regulates vascular and neuronal development, cancer aggressiveness and fibrosis progression.We used conditional mutagenesis and lineage tracing to show that NRP1 is expressed in JG cells where it regulates their function.Cell‐specific Nrp1 knockout mice present with renin paucity in JG cells and struggle to adapt to a homeostatic challenge to sodium balance.The results support the versatility of renin‐producing cells in the kidney and may open new avenues for therapeutic approaches. [ABSTRACT FROM AUTHOR]
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- 2024
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50. Biomolecular Condensates Decipher Molecular Codes of Cell Fate: From Biophysical Fundamentals to Therapeutic Practices.
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Sun, Xing, Zhou, Yangyang, Wang, Zhiyan, Peng, Menglan, Wei, Xianhua, Xie, Yifang, Wen, Chengcai, Liu, Jing, and Ye, Mao
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- *
SIGNALS & signaling - Abstract
Cell fate is precisely modulated by complex but well-tuned molecular signaling networks, whose spatial and temporal dysregulation commonly leads to hazardous diseases. Biomolecular condensates (BCs), as a newly emerging type of biophysical assemblies, decipher the molecular codes bridging molecular behaviors, signaling axes, and clinical prognosis. Particularly, physical traits of BCs play an important role; however, a panoramic view from this perspective toward clinical practices remains lacking. In this review, we describe the most typical five physical traits of BCs, and comprehensively summarize their roles in molecular signaling axes and corresponding major determinants. Moreover, establishing the recent observed contribution of condensate physics on clinical therapeutics, we illustrate next-generation medical strategies by targeting condensate physics. Finally, the challenges and opportunities for future medical development along with the rapid scientific and technological advances are highlighted. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
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