Studying iPSCs from a hibernating mammal reveals molecular mechanisms of cold resistance in neural tissues
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE93935
PROVIDER: PRJNA362861 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5195260_1.fastq.gz | Fastqsanger.gz | |||
| SRR5195260_2.fastq.gz | Fastqsanger.gz | |||
| SRR5195261_1.fastq.gz | Fastqsanger.gz | |||
| SRR5195261_2.fastq.gz | Fastqsanger.gz | |||
| SRR5195252_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:To explore the cold resistant feature of ground squirrel neuron cells, we compared transcriptomes of human and ground squirrel iPSC derived neurons in the response to cold treatment. We identified several key pathways that are critical for the maintenance of neuronal microtubule cytoskeleton integrity at low temperature.
2018-03-22 | GSE93935 | GEO
Project description:During the winter, hibernating mammals undergo extreme changes in physiology which allow them to survive without access to food. These animals enter a state of torpor, which is characterized by a decreased metabolism, near-freezing body temperatures, and a dramatically reduced heart rate. The neurochemical basis of this regulation is largely unknown. Based on prior evidence suggesting that the peptide-rich hypothalamus plays critical roles in hibernation, we hypothesized that changes in specific cell-cell signaling peptides (neuropeptides and peptide hormones) underlie physiological changes during torpor/arousal cycles. To test this hypothesis, we used a mass spectrometry-based peptidomics approach to examine seasonal changes of endogenous peptides that occur in the hypothalamus and pituitary of a model hibernating mammal, the thirteen-lined ground squirrel (Ictidomys tridecemlineatus). In the pituitary, we observed changes in a number of distinct peptide hormones as animals prepare for torpor in October, exit torpor in March, and progress from Spring (March) to Fall (August). In the hypothalamus, we observed an overall increase in neuropeptides in October (pre-torpor), a decrease as the animal enters torpor, and an increase in a subset of neuropeptides during normothermic interbout arousals. Notable changes were observed for feeding regulatory peptides from NPY and proSAAS prohormones, opioid peptides from PENK, PDYN, and POMC prohormones, and a number of peptides without well-established functions. In contrast to transcriptome and antibody-based measurements, our mass spectrometry-based approach allowed the identification and measurement of the final processed forms of these peptides after extensive post-translational modifications. Overall, our study provides critical insight into changes in endogenous peptides in the hypothalamus and pituitary during mammalian hibernation that were not available from transcriptome measurements. Understanding the molecular basis underlying the hibernation phenotype may pave the way for future efforts to employ hibernation-like strategies for organ preservation, combating obesity, and treatments for stroke.
2023-07-10 | PXD040033 | Pride
Project description:We report the application of the Illumina/Solexa sequencing-by-synthesis platform to analysis differential expression genes of two key tissues (brain and adipose tissue) during hibernation vs. aroused state, with a hibernating bat species (Myotis ricketti) as model. Total of 12272 genes were identified including 11291 genes in brain and 10691 genes in adipose tissue. Chi-square test indicated that 1943 and 3673 genes in brain and adipose tissues respectively reached the significant level (P ⤠0.01), including 1243 up-regulated and 700 down-regulated genes in hibernating brain and 2621 up-regulated and 1052 down-regulated genes in hibernating adipose tissue. This study provide opportunity to in-deep analysis the molecular mechanism of hibernating regualtion.
2018-12-31 | GSE29052 | GEO
Project description:Mammalian hibernation is a complex phenotype involving metabolic rate reduction, bradycardia, profound hypothermia, and a reliance on stored fat that allows the animal to survive for months without food in a state of suspended animation. To determine the genes responsible for this phenotype in the thirteen-lined ground squirrel (Ictidomys tridecemlineatus) we used the Roche 454 platform to sequence mRNA isolated at six points throughout the year from three key tissues: heart, skeletal muscle, and white adipose tissue (WAT). Deep sequencing generated approximately 3.7 million cDNA reads from 18 samples (6 time points ×3 tissues) with a mean read length of 335 bases. Of these, 3,125,337 reads were assembled into 140,703 contigs. Approximately 90% of all sequences were matched to proteins in the human UniProt database. The total number of distinct human proteins matched by ground squirrel transcripts was 13,637 for heart, 12,496 for skeletal muscle, and 14,351 for WAT. Extensive mitochondrial RNA sequences enabled a novel approach of using the transcriptome to construct the complete mitochondrial genome for I. tridecemlineatus. Seasonal and activity-specific changes in mRNA levels that met our stringent false discovery rate cutoff (1.0 × 10(-11)) were used to identify patterns of gene expression involving various aspects of the hibernation phenotype. Among these patterns are differentially expressed genes encoding heart proteins AT1A1, NAC1 and RYR2 controlling ion transport required for contraction and relaxation at low body temperatures. Abundant RNAs in skeletal muscle coding ubiquitin pathway proteins ASB2, UBC and DDB1 peak in October, suggesting an increase in muscle proteolysis. Finally, genes in WAT that encode proteins involved in lipogenesis (ACOD, FABP4) are highly expressed in August, but gradually decline in expression during the seasonal transition to lipolysis.
| S-EPMC3203946 | biostudies-literature
Project description:We report the application of the Illumina/Solexa sequencing-by-synthesis platform to identify microRNA, which invovled in bat hibernating regualtion, in brain and adipose tissue. Total 866 microRNAs (including 477 novels) were identified and 269 microRNAs showed significant expression differences during hibernation, including 183 in brain and 199 in adipose tissue. Expressed pattern analysis indicated that two-thirds of differential expressed microRNAs showed down-regulated during hibernation in both tissues. This study will provide clules to in-deep analysis the molecular mechanism of hibernating regualtion. Identification of microRNA on hibernating regulation in 2 different tissues and 2 physiological states of bat.
2015-12-31 | E-GEOD-29053 | biostudies-arrayexpress
Project description:Objectives: While cardiac scar tissue is damaged irreversibly, hibernating myocardium is characterized by reversible contractile dysfunction. Limited data are available in humans regarding the molecular biology of hibernating myocardium. The aim of this study was to identify new molecular mechanisms distinctive for human hibernating myocardium by gene expression analysis. Results: Of 4,171 transcripts examined, we identified 86 to be differentially expressed. Twentyone genes showed an increased and 65 genes a decreased expression in hibernating myocardium. Functional clustering revealed major changes in the expression of genes associated with transcription, protein modification and phosphorylation, regulation of apoptosis and intercellular communication. Besides the reported upregulation of ß-adrenergic receptor kinase-1 in heart failure, we observed new gene expression patterns, such as the upregulation of fas-activated serine/threonine kinase (FAST) or reduced expression of desmoplakin. Downregulation of desmoplakin in cardiomyocytes from hibernating myocardium was also seen on the protein level, consistent with a role of this protein in the development of a dilative cardiomyopathy. Conclusions: Gene expression analysis of hibernating myocardium provided novel insights into the molecular mechanisms underlying ischemic heart failure. Dysfunction of desmosomes may contribute to impaired contractility and dilative tissue remodeling. Keywords: disease state analysis
2007-07-01 | GSE4704 | GEO
Project description:We report the application of the Illumina/Solexa sequencing-by-synthesis platform to identify microRNA, which invovled in bat hibernating regualtion, in brain and adipose tissue. Total 866 microRNAs (including 477 novels) were identified and 269 microRNAs showed significant expression differences during hibernation, including 183 in brain and 199 in adipose tissue. Expressed pattern analysis indicated that two-thirds of differential expressed microRNAs showed down-regulated during hibernation in both tissues. This study will provide clules to in-deep analysis the molecular mechanism of hibernating regualtion.
2015-12-31 | GSE29053 | GEO
Project description:Title: Gene expression profiling of human heart samples: a comparison between normal and hibernating myocardium.<br/> Description: The aim of this project is to investigate the changes in global gene<br/> expression in hibernating,(preserved wall thickness, impaired <br/> contractility at rest, recruitable with low dose dobutamine <br/> and 50% transmural hyperenhancement with gadolinium) and normal myocardium,<br/> (preserved myocardial wall thickness, normal contractility, no significant improvement in functional recruitability with dobutamine and no cardiac fibrosis seen).
2006-12-31 | E-MIMR-27 | biostudies-arrayexpress
Project description:Hibernating American black bears have significantly different clotting parameters than their active summer counterparts, affording them innate protection against venous thromboembolism (VTE) despite prolonged periods of immobility. Physiologic changes that occur during hibernation are thought to result from differential gene expression, rather than novel genes, and there is increasing evidence miRNAs may play an important role this regulation. We propose that significant differences exist in miRNA expression in the plasma of hibernating black bears compared to their active counter parts (summer), which lead to critical gene regulation responsible for auto-anticoagulation during hibernation. Methods: Blood was collected from 21 American black bears in the Northern Michigan Peninsula in summer 2017 and winter 2018 (11 active, 10 hibernating). Plasma was extracted Results: Fifteen miRNAs were differentially expressed in the plasma of hibernating black bears. Nine miRNAs were significantly downregulated (miR10b-3p, miR-136-3p, miR-181c-5p , miR-200a-3p, miR-200b-5p, miR-200c-3p, miR-320b, miR-320c and miR-320d) and six miRNAs were significantly upregulated (miR-15a-5p, miR-15b-3p, miR-15b-5p, miR-16-5p, miR-92a-3p, miR-150-5p) during hibernation. Twelve miRNAs had no identifiable targets, but miR-200a-3p, miR-200b-5p and miR-200c-3p found to be targets of SERPINC1, the gene responsible for the production of antithrombin (AT). Conclusions: Several miRNAs were differentially expressed in hibernating bears (12). Most importantly miR-200a-3p, miR-200b-5p and miR-200c-3p were all downregulated in hibernation and associated with increased expression of SERPINC1 and production of AT. AT is a powerful anticoagulant and this finding may explain the hibernating black bears ability to achieve auto-anticoagulation and protection from VTE.
2020-09-01 | GSE124398 | GEO
Project description:Hibernating mammals cease feeding during the winter and rely primarily on stored lipids to fuel alternating periods of torpor and arousal. How hibernators manage large fluxes of lipids and sterols over the annual hibernation cycle is poorly understood. The aim of this study was to investigate lipid and cholesterol transport and storage in ground squirrels studied in spring, summer, and several hibernation states. Cholesterol levels in total plasma, HDL and LDL particles were elevated in hibernators compared with spring or summer squirrels. Hibernation increased plasma apolipoprotein A-I expression and HDL particle size. Expression of cholesterol 7 alpha-hydroxylase was 13-fold lower in hibernators than in active season squirrels. Plasma triglycerides were reduced by fasting in spring but not summer squirrels. In hibernators plasma ?-hydroxybutyrate was elevated during torpor whereas triglycerides were low relative to normothermic states. We conclude that the switch to a lipid-based metabolism during winter, coupled with reduced capacity to excrete cholesterol creates a closed system in which efficient use of lipoproteins is essential for survival.
| S-EPMC3240636 | biostudies-literature