Restoring Mitochondrial Quantity and Quality to Reverse Warburg Effect and Drive Tumor Differentiation
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PROVIDER: PRJNA1214678 | ENA |
REPOSITORIES: ENA
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Project description:Restoring Mitochondrial Quantity and Quality to Reverse Warburg Effect and Drive Tumor Differentiation
| PRJNA1216192 | ENA
Project description:Reduced mitochondrial quality and quantity in tumors is associated with dedifferentiation and increased malignancy. However, it remains unclear how to restore mitochondrial quantity and quality in tumors, and whether mitochondrial restoration can drive tumor differentiation. Our study shows that restoring mitochondrial function using retinoic acid (RA) to boost mitochondrial biogenesis and a mitochondrial uncoupler to enhance respiration synergistically drives neuroblastoma differentiation and inhibits proliferation. U-13C-glucose/glutamine isotope tracing revealed a metabolic shift from the pentose phosphate pathway to oxidative phosphorylation, accelerating the TCA cycle and switching substrate preference from glutamine to glucose. These effects were reversed by ETC inhibitors or in ρ0 cells lacking mtDNA, emphasizing the necessity of mitochondrial function for differentiation. Dietary RA and uncoupler treatment promoted tumor differentiation in an orthotopic neuroblastoma xenograft model, evidenced by neuropil production and Schwann cell recruitment. Single-cell RNA sequencing analysis of the orthotopic xenografts revealed that this strategy effectively eliminated the stem cell population, promoted differentiation, and increased mitochondrial gene signatures along the differentiation trajectory, which could potentially significantly improve patient outcomes. Collectively, our findings establish a mitochondria-centric therapeutic strategy for inducing tumor differentiation, suggesting that maintaining/driving differentiation in tumor requires not only ATP production but also continuous ATP consumption and sustained ETC activity.
2025-01-31 | GSE287773 | GEO
Project description:Reduced mitochondrial quality and quantity in tumors is associated with dedifferentiation and increased malignancy. However, it remains unclear how to restore mitochondrial quantity and quality in tumors, and whether mitochondrial restoration can drive tumor differentiation. Our study shows that restoring mitochondrial function using retinoic acid (RA) to boost mitochondrial biogenesis and a mitochondrial uncoupler to enhance respiration synergistically drives neuroblastoma differentiation and inhibits proliferation. U-13C-glucose/glutamine isotope tracing revealed a metabolic shift from the pentose phosphate pathway to oxidative phosphorylation, accelerating the TCA cycle and switching substrate preference from glutamine to glucose. These effects were reversed by ETC inhibitors or in ρ0 cells lacking mtDNA, emphasizing the necessity of mitochondrial function for differentiation. Dietary RA and uncoupler treatment promoted tumor differentiation in an orthotopic neuroblastoma xenograft model, evidenced by neuropil production and Schwann cell recruitment. Single-cell RNA sequencing analysis of the orthotopic xenografts revealed that this strategy effectively eliminated the stem cell population, promoted differentiation, and increased mitochondrial gene signatures along the differentiation trajectory, which could potentially significantly improve patient outcomes. Collectively, our findings establish a mitochondria-centric therapeutic strategy for inducing tumor differentiation, suggesting that maintaining/driving differentiation in tumor requires not only ATP production but also continuous ATP consumption and sustained ETC activity.
2025-01-29 | GSE288099 | GEO
Project description:We investigated the contentious role of mitochondrial reactive oxygen species (ROS) on mitochondrial DNA (mtDNA) quality and quantity in female reproductive aging. By conditionally knocking out the Sod2 gene in female mouse germline, we observed increased mitochondrial ROS and decreased oocyte quality, primarily due to impacts on OXPHOS complex II and mtDNA encoded mRNA levels. Interestingly, we found no increased mtDNA mutations, but alterations in mtDNA quantity, indicating the susceptibility of mtDNA to the mitochondrial ROS during reproductive aging. Notably, when we further decreased the basal level of mtDNA quantity by deactivating the mtSSB protein in Sod2 conditional knockout females, we observed an exacerbation of reproductive aging effects. This highlights the crucial role of mtDNA quantity in mitigating the impact of oxidative stress on fertility.
2024-09-09 | GSE251734 | GEO
Project description:The Guthrie 903 card archived dried blood spots (DBS) are a unique but terminal resource amenable for individual and population wide genomic profiling. The limited amounts of DBS-derived genomic DNA (gDNA) can be whole-genome amplified (WGA) producing sufficient gDNA for genomic applications, albeit with variable success, and optimizing the isolation of high-quality DNA from these finite, low-yield specimens is essential. Visual automated fluorescence electrophoresis (VAFE) is a novel QC technology affording precise quality, quantity and molecular weight of double-stranded DNA from a single microliter of sample. The VAFE QC data were correlated with subsequent sample performance in PCR, sequencing, and high-density comparative genome hybridization array.
2013-07-01 | GSE44249 | GEO
Project description:The Guthrie 903 card archived dried blood spots (DBS) are a unique but terminal resource amenable for individual and population wide genomic profiling. The limited amounts of DBS-derived genomic DNA (gDNA) can be whole-genome amplified (WGA) producing sufficient gDNA for genomic applications, albeit with variable success, and optimizing the isolation of high-quality DNA from these finite, low-yield specimens is essential. Visual automated fluorescence electrophoresis (VAFE) is a novel QC technology affording precise quality, quantity and molecular weight of double-stranded DNA from a single microliter of sample. The VAFE QC data were correlated with subsequent sample performance in PCR, sequencing, and high-density comparative genome hybridization array. The Swedish Repository of DBS samples collected on Guthrie 903 cards for neonatal screening of inborn diseases provided deidentified 3mm blood spot punches. There were total of eight (8) samples representing two (2) decades; 1970s: 1975, 1976, 1977, 1978; 1980s: 1980, 1982, 1984, 1986. gDNA was extracted and whole genome amplified prior to aCGH experiments using control female reference genomic DNA. The objective was to show that large rearrangements (e.g. loss of chrX in male samples) can be detected in WGA gDNA from blood spots >30 years old.
2013-07-01 | E-GEOD-44249 | biostudies-arrayexpress
Project description:In order to clarify if there is a tradeoff between quantity and quality of oocytes retrieved after ovarian stimulation, we compared the protein expression of mouse oocytes and embryos with vs without a background of ovarian stimulation using gonadotropins, administered according to the standard protocol in use since more than 50 years (PMID 13185277; PMID 13475597). The data we gathered contribute to a more complete understanding of embryonic gene expression, by taking into account the effect of the commonly used superovulation.
2021-12-15 | PXD021331 | Pride
Project description:In order to clarify if there is a tradeoff between quantity and quality of oocytes retrieved after ovarian stimulation, we compared the protein expression of mouse oocytes and embryos with vs without a background of ovarian stimulation using gonadotropins, administered according to the standard protocol in use since more than 50 years (PMID 13185277; PMID 13475597). The data we gathered contribute to a more complete understanding of embryonic gene expression, by taking into account the effect of the commonly used superovulation.
2021-12-14 | PXD026347 | Pride
Project description:The type and the amount of dietary fat have a significant influence on the metabolic pathways involved in the development of obesity, metabolic syndrome, diabetes type 2 and cardiovascular diseases. However, it is unknown to what extent this modulation is achieved through DNA methylation. We assessed the effects of cholesterol intake, the proportion of energy intake derived from fat, the ratio of polyunsaturated fatty acids (PUFA) to saturated fatty acids (SFA), the ratio of monounsaturated fatty acids (MUFA) to SFA, and the ratio of (MUFA+PUFA) to SFA on genome-wide DNA methylation patterns in normal-weight and obese children. We determined the genome-wide methylation profile in blood of 69 Greek preadolescents (~10 y old), as well as their dietary intake for two consecutive weekdays and one weekend day. The methylation levels of four sites and a CpG island were significantly correlated with total fat intake. The methylation levels of 13 islands and 16 sites were significantly correlated with PUFA/SFA; of 35 islands and 158 sites with MUFA/SFA; and of 50 islands and 130 sites with (MUFA+PUFA)/SFA. We found significant gene enrichment in 26 pathways for PUFA/SFA, including the leptin pathway, and a significant enrichment in three pathways for (MUFA+PUFA)/SFA. Our results suggest that the quality, and to a lesser extent the quantity of fat intake, influences DNA methylation, including genes involved in metabolism. Thus, specific changes in DNA methylation may play an important role in the mechanisms involved in the physiological responses to different types of dietary fat.
2014-05-09 | GSE57484 | GEO
Project description:The type and the amount of dietary fat have a significant influence on the metabolic pathways involved in the development of obesity, metabolic syndrome, diabetes type 2 and cardiovascular diseases. However, it is unknown to what extent this modulation is achieved through DNA methylation. We assessed the effects of cholesterol intake, the proportion of energy intake derived from fat, the ratio of polyunsaturated fatty acids (PUFA) to saturated fatty acids (SFA), the ratio of monounsaturated fatty acids (MUFA) to SFA, and the ratio of (MUFA+PUFA) to SFA on genome-wide DNA methylation patterns in normal-weight and obese children. We determined the genome-wide methylation profile in blood of 69 Greek preadolescents (~10 y old), as well as their dietary intake for two consecutive weekdays and one weekend day. The methylation levels of four sites and a CpG island were significantly correlated with total fat intake. The methylation levels of 13 islands and 16 sites were significantly correlated with PUFA/SFA; of 35 islands and 158 sites with MUFA/SFA; and of 50 islands and 130 sites with (MUFA+PUFA)/SFA. We found significant gene enrichment in 26 pathways for PUFA/SFA, including the leptin pathway, and a significant enrichment in three pathways for (MUFA+PUFA)/SFA. Our results suggest that the quality, and to a lesser extent the quantity of fat intake, influences DNA methylation, including genes involved in metabolism. Thus, specific changes in DNA methylation may play an important role in the mechanisms involved in the physiological responses to different types of dietary fat. Bisulphite converted DNA from 22 boys were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2.Both obese and normal-weight indiviudals were included.
2014-05-09 | E-GEOD-57484 | biostudies-arrayexpress