DDIT4 regulates mesenchymal stem cell fate by mediating between HIF1α and mTOR signalling

Regulation Mechanisms and Maintenance Strategies of Stemness in Mesenchymal Stem Cells

Stemness pertains to the intrinsic ability of mesenchymal stem cells (MSCs) to undergo self-renewal and differentiate into multiple lineages, while simultaneously impeding their differentiation and preserving crucial differentiating genes in a state of quiescence and equilibrium. Owing to their favorable attributes, including uncomplicated isolation protocols, ethical compliance, and ease of procurement, MSCs have become a focal point of inquiry in the domains of regenerative medicine and tissue engineering. As age increases or ex vivo cultivation is prolonged, the functionality of MSCs decreases and their stemness gradually diminishes, thereby limiting their potential therapeutic applications. Despite the existence of several uncertainties surrounding the comprehension of MSC stemness, considerable advancements have been achieved in the clarification of the potential mechanisms that lead to stemness loss, as well as the associated strategies for stemness maintenance. This comprehensive review provides a systematic overview of the factors influencing the preservation of MSC stemness, the molecular mechanisms governing it, the strategies for its maintenance, and the therapeutic potential associated with stemness. Finally, we underscore the obstacles and prospective avenues in present investigations, providing innovative perspectives and opportunities for the preservation and therapeutic utilization of MSC stemness.

Faecalibacterium prausnitzii promotes intestinal epithelial IL-18 production through activation of the HIF1α pathway

Introduction

Intestinal epithelial cells produce interleukin-18 (IL-18), a key factor in promoting epithelial barrier integrity. Here, we analyzed the potential role of gut bacteria and the hypoxia-inducible factor 1α (HIF1α) pathway in regulating mucosal IL18 expression in inflammatory bowel disease (IBD).

Methods

Mucosal samples from patients with IBD (n = 760) were analyzed for bacterial composition, IL18 levels and HIF1α pathway activation. Wild-type Caco-2 and CRISPR/Cas9-engineered Caco-2-HIF1A-null cells were cocultured with Faecalibacterium prausnitzii in a "Human oxygen-Bacteria anaerobic" in vitro system and analyzed by RNA sequencing.

Results

Mucosal IL18 mRNA levels correlated positively with the abundance of mucosal-associated butyrate-producing bacteria, in particular F. prausnitzii, and with HIF1α pathway activation in patients with IBD. HIF1α-mediated expression of IL18, either by a pharmacological agonist (dimethyloxallyl glycine) or F. prausnitzii, was abrogated in Caco-2-HIF1A-null cells.

Conclusion

Butyrate-producing gut bacteria like F. prausnitzii regulate mucosal IL18 expression in a HIF1α-dependent manner that may aid in mucosal healing in IBD.

Mining host candidate regulators of schistosomiasis-induced liver fibrosis in response to artesunate therapy through transcriptomics approach

BACKGROUND

Artesunate (ART) has been reported to have an antifibrotic effect in various organs. The underlying mechanism has not been systematically elucidated. We aimed to clarify the effect of ART on liver fibrosis induced by Schistosoma japonicum (S. japonicum) in an experimentally infected rodent model and the potential underlying mechanisms.

METHODS

The effect of ART on hepatic stellate cells (HSCs) was assessed using CCK-8 and Annexin V-FITC/PI staining assays. The experimental model of liver fibrosis was established in the Mongolian gerbil model infected with S. japonicum cercariae and then treated with 20 mg/kg or 40 mg/kg ART. The hydroxyproline (Hyp) content, malondialdehyde (MDA) content, superoxide dismutase (SOD) and glutathione peroxidase (GPX) activities in liver tissue were measured and histopathological changes of liver tissues were observed. Whole-transcriptome RNA sequencing (RNA-seq) of the liver tissues was performed. Differentially expressed genes (DEGs) were identified using bioinformatic analysis and verified by quantitative PCR (qPCR) and western blot assay.

RESULTS

ART significantly inhibited the proliferation and induce the apoptosis of HSCs in a dose-dependent manner. In vivo, Hyp content decreased significantly in the ART-H group compared to the model (MOD) group and GPX activity was significantly higher in the ART-H group than in the MOD group. Besides, ART treatment significantly reduced collagen production (p <0.05). A total of 158 DEGs and 44 differentially expressed miRNAs related to ART-induced anti-schistosomiasis liver fibrosis were identified. The qPCR and western blot results of selected DEGs were consistent with the sequencing results. These DEGs were implicated in key pathways such as immune and inflammatory response, integrin-mediated signaling and toll-like receptor signaling pathways.

CONCLUSION

ART is effective against liver fibrosis using Mongolian gerbil model induced by S. japonicum infection. We identified host candidate regulators of schistosomiasis-induced liver fibrosis in response to ART through transcriptomics approach.

Cell plasticity in regeneration in the stomach and beyond

Recent studies using cell lineage-tracing techniques, organoids, and single-cell RNA sequencing analyses have revealed: 1) adult organs use cell plasticity programs to recruit progenitor cells to regenerate tissues after injury, and 2) plasticity is far more common than previously thought, even in homeostasis. Here, we focus on the complex interplay of normal stem cell differentiation and plasticity in homeostasis and after injury, using the gastric epithelium as a touchstone. We also examine common features of regenerative programs and discuss the evolutionarily conserved, stepwise process of paligenosis which reprograms mature cells into progenitors that can repair damaged tissue. Finally, we discuss how conserved plasticity programs may help us better understand pathological processes like metaplasia.

Histone deacetylase 4 reverses cellular senescence via DDIT4 in dermal fibroblasts

Histone deacetylases (HDACs) remove acetyl groups from lysine chains on histones and other proteins and play a crucial role in epigenetic regulation and aging. Previously, we demonstrated that HDAC4 is consistently downregulated in aged and ultraviolet (UV)-irradiated human skin in vivo. Cellular senescence is a permanent cell cycle arrest induced by various stressors. To elucidate the potential role of HDAC4 in the regulation of cellular senescence and skin aging, we established oxidative stress- and UV-induced cellular senescence models using primary human dermal fibroblasts (HDFs). RNA sequencing after overexpression or knockdown of HDAC4 in primary HDFs identified candidate molecular targets of HDAC4. Integrative analyses of our current and public mRNA expression profiles identified DNA damage-inducible transcript 4 (DDIT4) as a critical senescence-associated factor regulated by HDAC4. Indeed, DDIT4 and HDAC4 expressions were downregulated during oxidative stress- and UV-induced senescence. HDAC4 overexpression rescued the senescence-induced decrease in DDIT4 and senescence phenotype, which were prevented by DDIT4 knockdown. In addition, DDIT4 overexpression reversed changes in senescence-associated secretory phenotypes and aging-related genes, suggesting that DDIT4 mediates the reversal of cellular senescence via HDAC4. Collectively, our results identify DDIT4 as a promising target regulated by HDAC4 associated with cellular senescence and epigenetic skin aging.

Gene Ontology Groups and Signaling Pathways Regulating the Process of Avian Satellite Cell Differentiation

Modern science is becoming increasingly committed to environmentally friendly solutions, mitigating the impact of the developing human civilisation on the environment. One of the leading fields aimed at sustainable agriculture is in vitro meat production. Cellular agriculture aims to provide a source of animal-free meat products, which would decrease worldwide nutritional dependency on animal husbandry, thereby reducing the significant impact of this industry on Earth’s climate. However, while some studies successfully produced lab-based meat on a small scale, scalability of this approach requires significant optimisation of the methodology in order to ensure its viability on an industrial scale. One of the methodological promises of in vitro meat production is the application of cell suspension-based bioreactors. Hence, this study focused on a complex transcriptomic comparison of adherent undifferentiated, differentiated and suspension-cultured myosatellite cells, aiming to determine the effects of different culture methods on their transcriptome. Modern next-generation sequencing (RNAseq) was used to determine the levels of transcripts in the cultures’ cell samples. Then, differential expression and pathway analyses were performed using bionformatical methods. The significantly regulated pathways included: EIF2, mTOR, GP6, integrin and HIFα signalling. Differential regulation of gene expression, as well as significant enrichment and modulation of pathway activity, suggest that suspension culture potentially promotes the ex vivo-associated loss of physiological characteristics and gain of plasticity. Therefore, it seems that suspension cultures, often considered the desired method for in vitro meat production, require further investigation to fully elucidate their effect on myosatellite cells and, therefore, possibly enable their easier scalability to ensure suitability for industrial application.

METTL3-Mediated m6A RNA Modification Regulates Corneal Injury Repair

Limbal stem cells are essential for continuous corneal regeneration and injury repair. METTL3-catalyzed N6-methyladenosine (m⁶A) mRNA modifications are involved in many biological processes and play a specific role in stem cell regeneration, while the role of m⁶A modifications in corneal injury repair remains unknown. In this study, we generated a limbal stem cell-specific METTL3 knockout mouse model and studied the role of m⁶A in repairing corneal injury caused by alkali burn. The results showed that METTL3 knockout in the limbal stem cells promotes the in vivo cell proliferation and migration, leading to the fast repair of corneal injury. In addition, m⁶A modification profiling identified stem cell regulatory factors AHNAK and DDIT4 as m⁶A targets. Our study reveals the essential functions of m⁶A RNA modification in regulating injury repair and provides novel insights for clinical therapy of corneal diseases.

Histone demethylase KDM4A plays an oncogenic role in nasopharyngeal carcinoma by promoting cell migration and invasion

Compelling evidence has indicated the vital role of lysine-specific demethylase 4 A (KDM4A), hypoxia-inducible factor-1α (HIF1α) and the mechanistic target of rapamycin (mTOR) signaling pathway in nasopharyngeal carcinoma (NPC). Therefore, we aimed to investigate whether KDM4A affects NPC progression by regulating the HIF1α/DDIT4/mTOR signaling pathway. First, NPC and adjacent tissue samples were collected, and KDM4A protein expression was examined by immunohistochemistry. Then, the interactions among KDM4A, HIF1α and DDIT4 were assessed. Gain- and loss-of-function approaches were used to alter KDM4A, HIF1α and DDIT4 expression in NPC cells. The mechanism of KDM4A in NPC was evaluated both in vivo and in vitro via RT-qPCR, Western blot analysis, MTT assay, Transwell assay, flow cytometry and tumor formation experiments. KDM4A, HIF1α, and DDIT4 were highly expressed in NPC tissues and cells. Mechanistically, KDM4A inhibited the enrichment of histone H3 lysine 9 trimethylation (H3K9me3) in the HIF1α promoter region and thus inhibited the methylation of HIF1α to promote HIF1α expression, thus upregulating DDIT4 and activating the mTOR signaling pathway. Overexpression of KDM4A, HIF1α, or DDIT4 or activation of the mTOR signaling pathway promoted SUNE1 cell proliferation, migration, and invasion but inhibited apoptosis. KDM4A silencing blocked the mTOR signaling pathway by inhibiting the HIF1α/DDIT4 axis to inhibit the growth of SUNE1 cells in vivo. Collectively, KDM4A silencing could inhibit NPC progression by blocking the activation of the HIF1α/DDIT4/mTOR signaling pathway by increasing H3K9me3, highlighting a promising therapeutic target for NPC.

High expression of DNA damage-inducible transcript 4 (DDIT4) is associated with advanced pathological features in the patients with colorectal cancer

DNA damage-inducible transcript 4 (DDIT4) is induced in various cellular stress conditions. This study was conducted to investigate expression and prognostic significance of DDIT4 protein as a biomarker in the patients with colorectal cancer (CRC). PPI network and KEGG pathway analysis were applied to identify hub genes among obtained differentially expressed genes in CRC tissues from three GEO Series. In clinical, expression of DDIT4 as one of hub genes in three subcellular locations was evaluated in 198 CRC tissues using immunohistochemistry method on tissue microarrays. The association between DDIT4 expression and clinicopathological features as well as survival outcomes were analyzed. Results of bioinformatics analysis indicated 14 hub genes enriched in significant pathways according to KEGG pathways analysis among which DDIT4 was selected to evaluate CRC tissues. Overexpression of nuclear DDIT4 protein was found in CRC tissues compared to adjacent normal tissues (P = 0.003). Furthermore, higher nuclear expression of DDIT4 was found to be significantly associated with the reduced tumor differentiation and advanced TNM stages (all, P = 0.009). No significant association was observed between survival outcomes and nuclear expression of DDIT4 in CRC cases. Our findings indicated higher nuclear expression of DDIT4 was significantly associated with more aggressive tumor behavior and more advanced stage of disease in the patients with CRC.

Impact of exogenously applied trehalose on leaf biochemistry, achene yield and oil composition of sunflower under drought stress

This study was carried out to assess the influence of trehalose, a non-reducing disaccharide involved in improving plant stress tolerance, on two cultivars (Hysun 33 and FH 598) of sunflower (Helianthus annuus L.) grown under control and drought stress conditions. At pre-flowering stage, varying concentrations (10, 20 and 30 mM) of trehalose were applied to the foliage. Drought stress significantly suppressed the plant growth, total soluble proteins, chlorophyll, achene yield per plant, oil percentage, organic contents, as well as oil palmitic and linoleic acids in both sunflower cultivars. External application of trehalose significantly reduced RMP (relative membrane permeability), and the accumulation of H₂ O₂ (hydrogen peroxide), while a considerable improvement was recorded in shoot fresh and shoot and root dry weights, total soluble proteins, glycinebetaine, AsA (ascorbic acid), total phenolics, achene yield per plant, oil contents, inorganic and organic contents, and the activities of catalase (CAT), superoxide dismutase (SOD) and peroxidase (POD) enzymes under water-limited regimes. The cultivar Hysun 33 was superior to the other cultivar in plant growth, RMP, glycinebetaine, proline, achene yield per plant, oil contents, and palmitic and linoleic acids. Overall, foliar-applied trehalose improved plant growth, oxidative defense system, yield and oil composition of sunflower under drought stress conditions.

Identification of genes involved in neuronal cell death and recovery over time in rat axotomy and neurorrhaphy models through RNA sequencing

Facial nerves are frequently injured during cosmetic or other types of facial surgery. However, information on the genes involved in the damage and recovery of the facial nerves is limited. Here, we aimed to identify the genes affected by facial nerve injury and repair using next-generation sequencing. We established a rat axotomy model and a parallel epineurial neurorrhaphy model, in which gene expression was analyzed from 3 days to 8 weeks after surgery. We discovered that ARRB1, SGK1, and GSK3B genes associated with neuronal cell death were upregulated in the axotomy model. In contrast, MFRP, MDK, and ACE genes involved in neural recovery and regeneration exhibited higher expression in the neurorrhaphy model. In the present study, the analysis of the big data obtained from the next-generation sequencing (RNA-seq) technology reveals that the expression of genes involved in neuronal cell death is induced during nerve damage, and those associated with neural recovery are more abundantly expressed during repair processes. These results are considered to be useful for the establishment of the treatment of related diseases and basic research in various neuroscience fields by utilizing damage and recovery mechanism of facial nerves.

The self-renewal dental pulp stem cell microtissues challenged by a toxic dental monomer

Dental pulp stem cells (DPSCs) regenerate injured/diseased pulp tissue and deposit tertiary dentin. DPSCs stress response can be activated by exposing cells to the monomer triethyleneglycol dimethacrylate (TEGDMA) and inducing the DNA-damage inducible transcript 4 (DDIT4) protein expression. The goal of the present study was to determine the impact of TEGDMA on the ability of DPSCs to maintain their self-renewal capabilities, develop and preserve their 3D structures and deposit the mineral. Human primary and immortalized DPSCs were cultured in extracellular matrix/basement membrane (ECM/BM) to support stemness and to create multicellular interacting layers (microtissues). The microtissues were exposed to the toxic concentrations of TEGDMA (0.5 and 1.5 mmol/l). The DPSCs spatial architecture was assessed by confocal microscopy. Mineral deposition was detected by alizarin red staining and visualized by stereoscopy. Cellular self-renewal transcription factor SOX2 was determined by immunocytochemistry. The microtissue thicknesses/vertical growth, surface area of the mineralizing microtissues, the percentage of area covered by the deposited mineral, and the fluorescence intensity of the immunostained cells were quantified ImageJ. DDIT4 expression was determined by a single molecule RNA-FISH technique and the cell phenotype was determined morphologically. DDIT4 expression was correlated with the cytotoxic phenotype. TEGDMA affected the structures of developing and mature microtissues. It inhibited the deposition of the mineral in the matrix while not affecting the SOX2 expression. Our data demonstrate that DPSCs retained their self-renewal capacity although their other functions were impeded. Since the DPSCs pool remained preserved, properties effected by the irritant should be restored by a proper rescue therapy.

DNA damage repair response in mesenchymal stromal cells: From cellular senescence and aging to apoptosis and differentiation ability

Mesenchymal stromal cells (MSCs) are heterogeneous and contain several populations, including stem cells. MSCs' secretome has the ability to induce proliferation, differentiation, chemo-attraction, anti-apoptosis, and immunomodulation activities in stem cells. Moreover, these cells recognize tissue damage caused by drugs, radiation (e.g., Ultraviolet, infra-red) and oxidative stress, and respond in two ways: either MSCs differentiate into particular cell lineages to preserve tissue homeostasis, or they release a regenerative secretome to activate tissue repairing mechanisms. The maintenance of MSCs in quiescence can increase the incidence and accumulation of various forms of genomic modifications, particularly upon environmental insults. Thus, dysregulated DNA repair pathways can predispose MSCs to senescence or apoptosis, reducing their stemness and self-renewal properties. For instance, DNA damage can impair telomere replication, activating DNA damage checkpoints to maintain MSC function. In this review, we aim to summarize the role of DNA damage and associated repair responses in MSC senescence, differentiation and programmed cell death.

Regulated in Development and DNA Damage Responses 1 Prevents Dermal Adipocyte Differentiation and Is Required for Hair Cycle-Dependent Dermal Adipose Expansion

Dermal white adipose tissue (dWAT) expansion is associated with important homeostatic and pathologic processes in skin. Even though mTOR/protein kinase B signaling is important for adipogenesis, the role of regulated development of DNA damage responses 1 (REDD1), a negative regulator of mTOR/protein kinase B, is poorly understood. Loss of REDD1 in mice resulted in reduction of body mass, total fat, size of gonadal white adipose tissue, and interscapular brown adipose tissue. Inguinal subcutaneous white adipose tissue and dWAT in REDD1 knockouts were expanded compared with wild type mice. Size and number of mature adipocytes in dWAT were also increased in adult REDD1 knockouts. This dWAT phenotype was established around postnatal day 18 and did not depend on the hair growth cycle. Numbers of adipocyte precursor cells were lower in REDD1 knockout skin. In vitro analysis revealed increased differentiation of skin-derived REDD1 knockout adipocyte precursor cells as indicated by higher lipid accumulation and increased adipogenic marker expression. 3T3L1 cells overexpressing REDD1 had decreased sensitivity to differentiation. Overall, our findings indicate that REDD1 silencing induced expansion of dWAT through hypertrophy and hyperplasia. This REDD1-dependent mechanism of adipogenesis could be used to preferentially target skin-associated adipose tissue for therapeutic purposes.

The Tumor Suppressor PTEN as Molecular Switch Node Regulating Cell Metabolism and Autophagy: Implications in Immune System and Tumor Microenvironment

Recent studies conducted over the past 10 years evidence the intriguing role of the tumor suppressor gene Phosphatase and Tensin Homolog deleted on Chromosome 10 PTEN in the regulation of cellular energy expenditure, together with its capability to modulate proliferation and survival, thus expanding our knowledge of its physiological functions. Transgenic PTEN mice models are resistant to oncogenic transformation, present decreased adiposity and reduced cellular glucose and glutamine uptake, together with increased mitochondrial oxidative phosphorylation. These acquisitions led to a novel understanding regarding the role of PTEN to counteract cancer cell metabolic reprogramming. Particularly, PTEN drives an “anti-Warburg state” in which less glucose is taken up, but it is more efficiently directed to the mitochondrial Krebs cycle. The maintenance of cellular homeostasis together with reduction of metabolic stress are controlled by specific pathways among which autophagy, a catabolic process strictly governed by mTOR and PTEN. Besides, a role of PTEN in metabolic reprogramming and tumor/stroma interactions in cancer models, has recently been established. The genetic inactivation of PTEN in stromal fibroblasts of mouse mammary glands, accelerates breast cancer initiation and progression. This review will discuss our novel understanding in the molecular connection between cell metabolism and autophagy by PTEN, highlighting novel implications regarding tumor/stroma/immune system interplay. The newly discovered action of PTEN opens innovative avenues for investigations relevant to counteract cancer development and progression.

Treatment with synthetic glucocorticoid impairs bone metabolism, as revealed by in vivo imaging of osteoblasts and osteoclasts in medaka fish

Glucocorticoids (GCs) play an important role in the stress reaction and function in the development of multiple tissues in our body. When given chronically in supraphysiologic doses, GCs are associated with orthodontic tooth movement, with serious side effects and particularly adverse effects on bone metabolism. However, the effects of steroids on bone cell dynamics are incompletely understood. Therefore, in this present study we examined the participation of osteoblasts and osteoclasts in osterix-DsRed/TRAP-EGFP double transgenic (Tg) medaka treated with synthetic GCs. Chronic continuous administration of prednisolone (PN) significantly reduced the fluorescence signals in the whole body of both osterix-DsRed and TRAP-EGFP medaka at 18 days, and those of the pharyngeal bone and tooth region at 32 days. To examine the capacity of the medaka for fracture healing during chronic administration of PN, we caused a fracture of a part of the bony fin ray at 18 days after the initiation of PN continuous administration. The bone fracture healing was significantly delayed by 32 days, accompanied by decreased signal area of both osterix-DsRed and TRAP-EGFP compared with that of the control. Next, to investigate the effect of acute administration of GC on the fracture healing, we started administration of dexamethasone (DX) immediately after the bone fracture, and this administration lasted during the 11 days of fracture healing. The results showed that the TRAP-EGFP-positive osteoclasts were reduced in area, but not the osterix-DsRed-positive osteoblasts. Lastly, to confirm the function of the glucocorticoid receptor in bone healing, we generated glucocorticoid receptor 2-deficient medaka (gr2^-/-). The fluorescent signal area of osterix-DsRed and TRAP-EGFP were increased at bone fracture sites in these fish, and DX treatment of them decreased the TRAP-EGFP signal area compared with that for the control fish. Our results indicate that GRs negatively regulated osteoclast recruitment and the accumulation of osteoblasts in bone fracture healing.

Metabolism as an early predictor of DPSCs aging

Tissue resident adult stem cells are known to participate in tissue regeneration and repair that follows cell turnover, or injury. It has been well established that aging impedes the regeneration capabilities at the cellular level, but it is not clear if the different onset of stem cell aging between individuals can be predicted or prevented at an earlier stage. Here we studied the dental pulp stem cells (DPSCs), a population of adult stem cells that is known to participate in the repair of an injured tooth, and its properties can be affected by aging. The dental pulp from third molars of a diverse patient group were surgically extracted, generating cells that had a high percentage of mesenchymal stem cell markers CD29, CD44, CD146 and Stro1 and had the ability to differentiate into osteo/odontogenic and adipogenic lineages. Through RNA seq and qPCR analysis we identified homeobox protein, Barx1, as a marker for DPSCs. Furthermore, using high throughput transcriptomic and proteomic analysis we identified markers for DPSC populations with accelerated replicative senescence. In particular, we show that the transforming growth factor-beta (TGF-β) pathway and the cytoskeletal proteins are upregulated in rapid aging DPSCs, indicating a loss of stem cell characteristics and spontaneous initiation of terminal differentiation. Importantly, using metabolic flux analysis, we identified a metabolic signature for the rapid aging DPSCs, prior to manifestation of senescence phenotypes. This metabolic signature therefore can be used to predict the onset of replicative senescence. Hence, the present study identifies Barx1 as a DPSCs marker and dissects the first predictive metabolic signature for DPSCs aging.