The Ultrastructural Signature of Human Embryonic Stem Cells

Cytoplasmic nucleoporin assemblage: the cellular artwork in physiology and disease

Nucleoporins, essential proteins building the nuclear pore, are pivotal for ensuring nucleocytoplasmic transport. While traditionally confined to the nuclear envelope, emerging evidence indicates their presence in various cytoplasmic structures, suggesting potential non-transport-related roles. This review consolidates findings on cytoplasmic nucleoporin assemblies across different states, including normal physiological conditions, stress, and pathology, exploring their structural organization, formation dynamics, and functional implications. We summarize the current knowledge and the latest concepts on the regulation of nucleoporin homeostasis, aiming to enhance our understanding of their unexpected roles in physiological and pathological processes.

Nuclear envelope assembly and dynamics during development

The nuclear envelope (NE) protects but also organizes the eukaryotic genome. In this review we will discuss recent literature on how the NE disassembles and reassembles, how it varies in surface area and protein composition and how this translates into chromatin organization and gene expression in the context of animal development.

Spatiotemporal Epigenetic Control of the Histone Gene Chromatin Landscape during the Cell Cycle

Higher-order genomic organization supports the activation of histone genes in response to cell cycle regulatory cues that epigenetically mediates stringent control of transcription at the G1/S-phase transition. Histone locus bodies (HLBs) are dynamic, non-membranous, phase-separated nuclear domains where the regulatory machinery for histone gene expression is organized and assembled to support spatiotemporal epigenetic control of histone genes. HLBs provide molecular hubs that support synthesis and processing of DNA replication-dependent histone mRNAs. These regulatory microenvironments support long-range genomic interactions among non-contiguous histone genes within a single topologically associating domain (TAD). HLBs respond to activation of the cyclin E/CDK2/NPAT/HINFP pathway at the G1/S transition. HINFP and its coactivator NPAT form a complex within HLBs that controls histone mRNA transcription to support histone protein synthesis and packaging of newly replicated DNA. Loss of HINFP compromises H4 gene expression and chromatin formation, which may result in DNA damage and impede cell cycle progression. HLBs provide a paradigm for higher-order genomic organization of a subnuclear domain that executes an obligatory cell cycle-controlled function in response to cyclin E/CDK2 signaling. Understanding the coordinately and spatiotemporally organized regulatory programs in focally defined nuclear domains provides insight into molecular infrastructure for responsiveness to cell signaling pathways that mediate biological control of growth, differentiation phenotype, and are compromised in cancer.

Architectural control of mesenchymal stem cell phenotype through nuclear actin

There is growing appreciation that architectural components of the nucleus regulate gene accessibility by altering chromatin organization. While nuclear membrane connector proteins link the mechanosensitive actin cytoskeleton to the nucleoskeleton, actin's contribution to the inner architecture of the nucleus remains enigmatic. Control of actin transport into the nucleus, plus the presence of proteins that control actin structure (the actin tool-box) within the nucleus, suggests that nuclear actin may support biomechanical regulation of gene expression. Cellular actin structure is mechanoresponsive: actin cables generated through forces experienced at the plasma membrane transmit force into the nucleus. We posit that dynamic actin remodeling in response to such biomechanical cues provides a novel level of structural control over the epigenetic landscape. We here propose to bring awareness to the fact that mechanical forces can promote actin transfer into the nucleus and control structural arrangements as illustrated in mesenchymal stem cells, thereby modulating lineage commitment.

Lysine-Specific Demethylase 1 (LSD1) epigenetically controls osteoblast differentiation

Epigenetic mechanisms regulate osteogenic lineage differentiation of mesenchymal stromal cells. Histone methylation is controlled by multiple lysine demethylases and is an important step in controlling local chromatin structure and gene expression. Here, we show that the lysine-specific histone demethylase Kdm1A/Lsd1 is abundantly expressed in osteoblasts and that its suppression impairs osteoblast differentiation and bone nodule formation in vitro. Although Lsd1 knockdown did not affect global H3K4 methylation levels, genome-wide ChIP-Seq analysis revealed high levels of Lsd1 at gene promoters and its binding was associated with di- and tri-methylation of histone 3 at lysine 4 (H3K4me2 and H3K4me3). Lsd1 binding sites in osteoblastic cells were enriched for the Runx2 consensus motif suggesting a functional link between the two proteins. Importantly, inhibition of Lsd1 activity decreased osteoblast activity in vivo. In support, mesenchymal-targeted knockdown of Lsd1 led to decreased osteoblast activity and disrupted primary spongiosa ossification and reorganization in vivo. Together, our studies demonstrate that Lsd1 occupies Runx2-binding cites at H3K4me2 and H3K4me3 and its activity is required for proper bone formation.

Interactions between ALS-linked FUS and nucleoporins are associated with defects in the nucleocytoplasmic transport pathway

Nucleocytoplasmic transport (NCT) decline occurs with aging and neurodegeneration. Here, we investigated the NCT pathway in models of amyotrophic lateral sclerosis-fused in sarcoma (ALS-FUS). Expression of ALS-FUS led to a reduction in NCT and nucleoporin (Nup) density within the nuclear membrane of human neurons. FUS and Nups were found to interact independently of RNA in cells and to alter the phase-separation properties of each other in vitro. FUS-Nup interactions were not localized to nuclear pores, but were enriched in the nucleus of control neurons versus the cytoplasm of mutant neurons. Our data indicate that the effect of ALS-linked mutations on the cytoplasmic mislocalization of FUS, rather than on the physiochemical properties of the protein itself, underlie our reported NCT defects. An aberrant interaction between mutant FUS and Nups is underscored by studies in Drosophila, whereby reduced Nup expression rescued multiple toxic FUS-induced phenotypes, including abnormal nuclear membrane morphology in neurons.

Ultrastructural heterogeneity of the mitochondrial population in rat embryonic and induced pluripotent stem cells

Even though rats are popular model animals, the ultrastructure of their pluripotent cells, that is, embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), remains unexplored, although fine structure of pluripotent stem cells of mice and humans and its changes during differentiation have been investigated well. In the present study, we carried out ultrastructural and morphometric analyses of three lines of rat ESCs and two lines of rat iPSCs. The rat pluripotent stem cells were found to have the main typical morphological features of pluripotent cells: large nuclei of irregular or nearly round shape, scanty cytoplasm with few membrane organelles, and a poorly developed Golgi apparatus and endoplasmic reticulum. The cytoplasm of the rat pluripotent cells contains clusters of glycogen, previously described in human ESCs. To identify possible differences between rat ESCs and iPSCs, we performed a morphometric analysis of cell parameters. The mean area of cells and nuclei, the nuclear/cytoplasmic ratio, distributions of glycogen and diversity of mitochondria showed marked variations among the lines of rat pluripotent stem cells and were more pronounced than variations between rat ESCs and iPSCs as separate types of pluripotent stem cells. We noted morphological heterogeneity of the mitochondrial population in the rat pluripotent stem cells. The cells contained three types of mitochondria differing in the structure of cristae and in matrix density, and our morphometric analysis revealed differences in cristae structure.

3D chromatin architecture and epigenetic regulation in cancer stem cells

Dedifferentiation of cell identity to a progenitor-like or stem cell-like state with increased cellular plasticity is frequently observed in cancer formation. During this process, a subpopulation of cells in tumours acquires a stem cell-like state partially resembling to naturally occurring pluripotent stem cells that are temporarily present during early embryogenesis. Such characteristics allow these cancer stem cells (CSCs) to give rise to the whole tumour with its entire cellular heterogeneity and thereby support metastases formation while being resistant to current cancer therapeutics. Cancer development and progression are demarcated by transcriptional dysregulation. In this article, we explore the epigenetic mechanisms shaping gene expression during tumorigenesis and cancer stem cell formation, with an emphasis on 3D chromatin architecture. Comparing the pluripotent stem cell state and epigenetic reprogramming to dedifferentiation in cellular transformation provides intriguing insight to chromatin dynamics. We suggest that the 3D chromatin architecture could be used as a target for re-sensitizing cancer stem cells to therapeutics.

Regulation of Genomic Output and (Pluri)potency in Regeneration

Regeneration is a remarkable phenomenon that has been the subject of awe and bafflement for hundreds of years. Although regeneration competence is found in highly divergent organisms throughout the animal kingdom, recent advances in tools used for molecular and genomic characterization have uncovered common genes, molecular mechanisms, and genomic features in regenerating animals. In this review we focus on what is known about how genome regulation modulates cellular potency during regeneration. We discuss this regulation in the context of complex tissue regeneration in animals, from Hydra to humans, with reference to ex vivo-cultured cell models of pluripotency when appropriate. We emphasize the importance of a detailed molecular understanding of both the mechanisms that regulate genomic output and the functional assays that assess the biological relevance of such molecular characterizations.

Correlation of TERT and Stem Cell Markers in the Context of Human Breast Cancer

BACKGROUND

Telomerase reverse transcriptase (TERT) has a well-known role in carcinogenesis due to its functions in inducing cell immortality and preventing senescence. In this study, the relationships between TERT and a panel of known stem cell markers was examined in order to direct future enquiries into the role of 'stem-ness' in human breast cancer.

MATERIALS AND METHODS

Breast cancer tissues (n=124) and adjacent normal tissues (n=30) underwent reverse transcription and quantitative polymerase chain reaction. Transcript levels were analyzed for the correlation with that of TERT.

RESULTS

A significant direct correlation was found in cancerous tissue between TERT and BMI1 proto-oncogene polycomb ring finger 4 (BMI1; n=88, p<0.001), nestin (NES; n=88, p<0.001), POU domain, class 5, transcription factor 1 (POU5F1; n=88, p<0.001), aldehyde dehydrogenase 1 family member A2 (ALDH1A2; n=87, p=0.0298), cyclin-dependent kinase inhibitor 1A (CDKN1A; n=88, p<0.001), integrin subunit beta 1 (ITGNB1; n=88, p<0.001), integrin subunit alpha 6 (ITGA6; n=88, p<0.001), cluster of differentiation antigen 24 (CD24; n=88, p=0.0114), MET proto-oncogene (MET; n=78, p<0.001) and noggin (NOG; n=88, p<0.001).

CONCLUSION

The evidence presented in this article of possible interactions between TERT and a discrete subset of known stem cell markers would significantly contribute to further enquiries regarding clonal dynamics in the context of human breast cancer.

Gene regulation through dynamic actin control of nuclear structure

Bone marrow mesenchymal stem cells exist in a multipotential state, where osteogenic and adipogenic genomes are silenced in heterochromatin at the inner nuclear leaflet. Physical force, generated in the marrow space during dynamic exercise exerts control overexpression of differentiation. Mesenchymal stem cells experience mechanical force through their cytoskeletal attachments to substrate, inducing signaling that alters gene expression. The generated force is further transferred from the cytoskeleton to the nucleoskeleton through tethering of actin to Linker of Nucleus and Cytoskeleton (LINC) complexes. Forces exerted on LINC alter the shape and placement of the nucleus within the cell, and are ultimately transferred into the nucleus. LINC complexes transverse the nuclear membrane and connect to the internal nucleoskeleton that is made up of lamin filaments and actin. Force transfer through LINC thus causes structural rearrangements of the nuclear scaffolding upon which chromosomes are arranged. Gene availability is not only modulated through heterochromatin remodeling enzymes and active transcription factors but also by control of nucleoskeletal structure and nuclear enzymes that mediate actin polymerization in the nucleus. Nuclear actin structure may be affected by similar force-activated pathways as those controlling the cytoplasmic actin cytoskeleton and represent a critical determinant of mesenchymal stem cell lineage commitment.

Impact statement

Gene expression is controlled by nuclear structure which is modulated by both internal and external forces exerted on the nucleoskeleton. Extracellular forces experienced through the actin cytoskeleton are transmitted to the internal nucleoskeleton via Linker of Nucleus and Cytoskeleton (LINC) protein connections. LINC complexes directly alter nuclear shape and entry of molecules that regulate transcription. New mechanistic models indicate that nuclear actin is a dynamic component of the filamentous nucleoskeleton and modified by an intranuclear “actin toolbox”, a set of enzymes that regulate linear and branched polymerization of nuclear actin. External stimulation of both biomechanical and biochemical pathways alters nuclear actin structure and has profound effects on gene expression by controlling chromatin architecture and transcription factor access to gene targets. The available data indicate that nucleoskeletal control of gene expression is critical for self-renewal and mesenchymal lineage-allocation in stem cells.

NANOG Is Required for the Long-Term Establishment of Avian Somatic Reprogrammed Cells

Somatic reprogramming, which was first identified in rodents, remains poorly described in non-mammalian species. Here, we generated avian reprogrammed cells by reprogramming of chicken and duck primary embryonic fibroblasts. The efficient generation of long-term proliferating cells depends on the method of delivery of reprogramming factors and the addition of NANOG and LIN28 to the canonical OCT4, SOX2, KLF4, and c-MYC gene combination. The reprogrammed cells were positive for several key pluripotency-associated markers including alkaline phosphatase activity, telomerase activity, SSEA1 expression, and specific cell cycle and epigenetic markers. Upregulated endogenous pluripotency-associated genes included POU5F3 (POUV) and KLF4, whereas cells failed to upregulate NANOG and LIN28A. However, cells showed a tumorigenic propensity when injected into recipient embryos. In conclusion, although the somatic reprogramming process is active in avian primary cells, it needs to be optimized to obtain fully reprogrammed cells with similar properties to those of chicken embryonic stem cells.

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NANOG is required for avian somatic reprogramming

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NANOG is necessary for long-term establishment of avian reprogrammed cells

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Avian reprogrammed cells express pluripotency markers

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Avian cells are only partially reprogrammed