Improve cellular fitness of human stem cell-derived islets under hypoxia
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PROVIDER: PRJNA1095907 | ENA |
REPOSITORIES: ENA
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Project description:Stem cell-derived islet (SC-islet) cell therapy holds immense potential for the treatment of Type 1 Diabetes. However, low oxygen supply leads to cell dysfunction post-transplantation, especially in subcutaneous spaces and encapsulation devices. The response of SC-islets to hypoxia and effective strategies to alleviate its detrimental effects remain poorly understood. This study investigates the impact of hypoxia on SC-islets and elucidate the dynamics of hypoxia-induced stress. We performed transcriptional profiling of human SC-islets exposed to hypoxic conditions, and drew the transcriptomic and epigenetic profiles of single cells. Our findings demonstrate that β cells within SC-islets gradually undergo a decline in cell identity and metabolic function in response to hypoxia. The loss of expression from immediate early genes, specifically EGR1, FOS, and JUN, results in the downregulation of key transcription factors (TFs) that are essential for maintaining SC-islet cell identity under hypoxic conditions. By comparing SC-islets under low and high oxygen conditions, we identified genes that play a role in maintaining the fitness of SC-islets in a low-oxygen environment. Notably, the expression of EDN3, a potent vasoconstrictor gene that is enriched in native pancreatic β cells, significantly aids in preserving β cell identity under hypoxic conditions. Elevated expression of EDN3 in SC-islets effectively mitigated the deleterious effects of hypoxia by modulating genes involved in SC-islet maturation including genes associated with glucose sensing and regulation in β cells. These insights improve the understanding of SC-islets under hypoxic conditions, offering a potential point of intervention for future clinical applications in the treatment of Type 1 Diabetes
2025-03-24 | GSE263130 | GEO
Project description:Stem cell-derived islet cell therapy can effectively treat type 1 diabetes, but its efficacy is hindered by low oxygen supply post-transplantation, particularly in subcutaneous spaces and encapsulation devices, leading to cell dysfunction. The response to hypoxia and effective strategies to alleviate its detrimental effects remain poorly understood. Here, we show that beta cells within stem cell-derived islets gradually undergo a decline in cell identity and metabolic function in hypoxia. This is linked to reduced expression of immediate early genes (EGR1, FOS, and JUN), which downregulates key beta cell transcription factors. We further identified genes important for maintaining beta cell fitness in hypoxia, with EDN3 as a potent player. Elevated EDN3 expression preserves beta cell identity and function in hypoxia by modulating genes involved in beta cell maturation, glucose sensing and regulation. These insights improve the understanding of hypoxias impact on stem cell-derived islets, offering a potential intervention for clinical applications.
2025-04-03 | MSV000097523 | MassIVE
Project description:MYC and hypoxia gene clusters are the two most commonly recurring transcriptional programs in heterogenous tumors. Understanding the cellular fitness of MYC-driven cancer cells in normoxia and hypoxia may lead to identification of distinct cancer cell vulnerabilities. Using genome-wide CRISPR screenings of MYC-driven liver cancer cells cultured over 4 weeks in 21% and 1% oxygen in monolayer, and 21% oxygen in 3D spheroid, we not only identify over 600 essential genes under all three conditions but also context-specific fitness genes and pathways. Knockout of VHL-HIF1 pathway results in incompatible fitness defects under 21% oxygen versus 1% oxygen or 3D. Genetic deletion of each of the mitochondrial respiratory complex I-V has distinct cellular fitness outcomes. Notably, the organogenesis signaling pathways such as TGF-SMAD specifically limits the uncontrolled cell proliferation of 3D spheroids while inactivation of epigenetic modifiers (Bcor, Kmt2d, Mettl3 and Mettl14) has opposite outcomes in monolayer versus 3D. We also discover distinct metabolic requirement for fatty acid and cholesterol synthesis in three conditions. Chemical perturbations using 125 FDA approved oncology drugs reveal that MYC-driven liver cancer cells have different sensitivity to inhibition of tyrosine kinase receptors under hypoxia and 3D. Our resource study highlights unique epigenetic and metabolic dependency of MYC-driven cancer cells in different tumor environmental settings.
2024-06-26 | GSE240980 | GEO
Project description:MYC and hypoxia gene clusters are the two most commonly recurring transcriptional programs in heterogenous tumors. Understanding the cellular fitness of MYC-driven cancer cells in normoxia and hypoxia may lead to identification of distinct cancer cell vulnerabilities. Using genome-wide CRISPR screenings of MYC-driven liver cancer cells cultured over 4 weeks in 21% and 1% oxygen in monolayer, and 21% oxygen in 3D spheroid, we not only identify over 600 essential genes under all three conditions but also context-specific fitness genes and pathways. Knockout of VHL-HIF1 pathway results in incompatible fitness defects under 21% oxygen versus 1% oxygen or 3D. Genetic deletion of each of the mitochondrial respiratory complex I-V has distinct cellular fitness outcomes. Notably, the organogenesis signaling pathways such as TGF-SMAD specifically limits the uncontrolled cell proliferation of 3D spheroids while inactivation of epigenetic modifiers (Bcor, Kmt2d, Mettl3 and Mettl14) has opposite outcomes in monolayer versus 3D. We also discover distinct metabolic requirement for fatty acid and cholesterol synthesis in three conditions. Chemical perturbations using 125 FDA approved oncology drugs reveal that MYC-driven liver cancer cells have different sensitivity to inhibition of tyrosine kinase receptors under hypoxia and 3D. Our resource study highlights unique epigenetic and metabolic dependency of MYC-driven cancer cells in different tumor environmental settings.
2024-06-26 | GSE262074 | GEO
Project description:<p>Biosynthetic gene clusters (BGCs) encoding the production of bacteriocins are widespread among bacterial isolates and are important genetic determinants of competitive fitness within a given habitat. Staphylococci produce a tremendous diversity of compounds, and the corresponding BGCs are frequently associated with mobile genetic elements, suggesting gain and loss of biosynthetic capacity. Pharmaceutical biology has shown that compound production in heterologous hosts is often challenging, and many BGC recipients initially produce small amounts of compound or show reduced growth rates. To assess whether transfer of BGCs between closely related Staphylococcus aureus strains can be instantly effective or requires elaborate metabolic adaptation, we investigated the intraspecies transfer of a BGC encoding the ribosomally synthesized and posttranslationally modified peptide (RiPP) micrococcin P1 (MP1). We found that acquisition of the BGC by S. aureus RN4220 enabled immediate MP1 production but also imposed a metabolic burden, which was relieved after prolonged cultivation by adaptive mutation. We used a multiomics approach to study this phenomenon and found adaptive evolution to select for strains with increased activity of the tricarboxylic acid cycle (TCA), which enhanced metabolic fitness and levels of compound production. Metabolome analysis revealed increases of central metabolites, including citrate and α-ketoglutarate in the adapted strain, suggesting metabolic adaptation to overcome the BGC-associated growth defects. Our results indicate that BGC acquisition requires genetic and metabolic predispositions, allowing the integration of bacteriocin production into the cellular metabolism. Inappropriate metabolic characteristics of recipients can entail physiological burdens, negatively impacting the competitive fitness of recipients within natural bacterial communities.</p><p><strong>IMPORTANCE:</strong> Human microbiomes are critically associated with human health and disease. Importantly, pathogenic bacteria can hide in human-associated communities and can cause disease when the composition of the community becomes unbalanced. Bacteriocin-producing commensals are able to displace pathogens from microbial communities, suggesting that their targeted introduction into human microbiomes might prevent pathogen colonization and infection. However, to develop probiotic approaches, strains are needed that produce high levels of bioactive compounds and retain cellular fitness within mixed bacterial communities. Our work offers insights into the metabolic burdens associated with the production of the bacteriocin micrococcin P1 and highlights evolutionary strategies that increase cellular fitness in the context of production. Metabolic adaptations are most likely broadly relevant for bacteriocin producers and need to be considered for the future development of effective microbiome editing strategies.</p>
2022-11-09 | MTBLS5196 | MetaboLights
Project description:Horizontal transfer of bacteriocin biosynthesis genes requires metabolic adaptation to improve compound production and cellular fitness
| PRJNA857994 | ENA
Project description:Biosynthetic gene clusters (BGCs) encoding the production of bacteriocins are widespread amongst bacterial isolates and are important genetic determinants of competitive fitness among bacterial lineages within a given habitat. Staphylococci produce a tremendous diversity of compounds and the corresponding gene clusters (Staphylococcal Antibiosis Islands - SAbIs) are frequently associated with mobile genetic elements, suggesting acquisition and loss of biosynthetic capacity. Pharmaceutical biology has shown that compound production in heterologous hosts is often challenged by the lack of optimal precursor supplies. Accordingly, many recipients produce low compound amounts or show reduced growth rates. To assess whether transfer of SAbIs between closely related S. aureus strains has similar effects, we used as model the SAbI encoding the ribosomally synthesized and post-translationally modified peptide (RiPP) Micrococcin P1 (MP1). We found that acquisition of the SAbI by S. aureus RN4220 did allow immediate MP1 production but also imposed a metabolic burden. Adaptive evolution selected for strains with increased TCA-cycle activity, which enhanced metabolic fitness and levels of compound production. Metabolome analysis showed that the adaptive mutation increased the levels of central metabolites including citrate and α-ketoglutarate, and the increased availability of citrate turned out to be essential to overcome SAbI associated growth defects. Our results indicate that acquisition of SAbIs represents a blessing for the recipient strain as long as its genetic and metabolic predispositions allow integration of bacteriocin production into the cellular metabolism. This in turn may be crucial to ensure the competitive fitness of SAbI recipients within natural bacterial communities.
2022-11-21 | GSE208001 | GEO
Project description:Mesoderm specification under hypoxia
| PRJNA721233 | ENA
Project description:Rationale：Poor peri-implant osseointegration of dental implants in patients with type II diabetes has become a major clinical challenge in recent years. MSC (Mesenchymal stem cell)-derived exosomes may play an important role in peri-implant osseointegration, but the mechanism remains unclear. Enhancing the therapeutic effect of MSC-derived exosomes and exploring the potential mechanism can help provide a new therapeutic strategy to improve the clinical outcome of dental implant restorations in patients with type II diabetes. Methods：The exosomes derived from hypoxia (Hypo-exos) or normoxia (Nor-exos) preconditioned bone marrow mesenchymal stem cells (BMSCs) were co-cultured with BMSCs and human umbilical vein endothelial cells (HUVECs). The effect of exosomes on BMSCs cell proliferation was detected by CCK-8 assay and EdU assay, and the effect on angiogenesis ability of HUVECs was detected by wound healing assay, transwell migration assay, tube formation assay, enzyme-linked immunosorbent assay (ELISA), quantitative real-time polymerase chain reaction (qRT-PCR) and western blot. A diabetic rat dental implant model was also established and the effect of exosomes on implant osseointegration was evaluated through micro-CT scanning and histological analysis. The differentially expressed miRNAs between Hypo-exos and Nor-exos were identified by high-throughput miRNA sequencing. Subsequently, the target genes and their roles in regulating angiogenesis were predicted and analyzed by bioinformatics analysis and dual luciferase reporter assay. Results：In vitro experiments indicated that hypoxia preconditioning could elevate exosome production and promote cell proliferation of BMSCs and angiogenesis of HUVECs. Moreover, Hypo-exos promoted peri-implant osteogenesis in rats with diabetes. Further investigation revealed the vital involvement of the miR-106b-5p/HIF-1α axis in promoting peri-implant osseointegration. Conclusion: Exosomes derived from hypoxia-preconditioned BMSCs could improve the peri-implant osseointegration in rats with diabetes by promoting cell proliferation and angiogenesis, and the miR-106b-5p/ HIF-1α axis could be the underlying mechanism.
2024-09-04 | GSE275863 | GEO
Project description:Aspergillus fumigatus Colony Biofilm Morphology Impacts Hypoxia Fitness, Inflammation, and Disease Progression
| PRJNA551460 | ENA