Single-nuclei profiling of aged liver tissue from mice
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ABSTRACT:
PROVIDER: PRJNA1179314 | ENA |
REPOSITORIES: ENA
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Project description:The liver undergoes a slower aging process compared to other organs owing to its unique regenerative ability. Mammalian liver aging commonly manifests as impaired metabolic performance, reduced organ volume and blood/bile flow, altered cellular and organelle composition, and delayed regenerative ability after toxic insults. Although aging-induced degenerative changes in liver structure and function are not necessarily pathologic, these are associated with an increased risk and susceptibility to chronic liver diseases. However, little is known about the molecular mechanisms driving the morphological changes and functional decline of the aging liver. For an unbiased characterization of aging-driven changes in major cell types of the liver, we employed single-nucleus RNA sequencing (snRNA-seq). A total of 41,568 nuclei isolated from young and aged livers reflected the expected cell diversity of the liver. Analysis of the snRNA-seq dataset revealed that aged livers had altered percentages of hepatocytes across all zones and that aged hepatocytes were associated with zone-specific alterations in expression of genes involved in aging, senescence, and inflammation.
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Project description:Aging is accompanied by a loss of muscle mass and function, termed sarcopenia, causing numerous morbidities and economic burdens in human populations. Mechanisms implicated in age-related sarcopenia include inflammation, muscle stem cell depletion, mitochondrial dysfunction and loss of motor neurons, but whether there are key drivers of sarcopenia is not yet known. To gain deeper insights into age-related sarcopenia, we performed transcriptome profiling on lower limb muscle biopsies from 72 young, old and sarcopenic subjects using bulk RNA-seq (N = 72) and single-nuclei RNA-seq (N = 17). Using this combined approach, we discovered novel changes in gene expression that occur with age and sarcopenia in multiple cell types comprising mature skeletal muscle. Notably, we found increased expression of the genes MYH8 and PDK4, and decreased expression of the gene IGFN1, in old muscle. We also identified a small population of nuclei that express CDKN1A, present only in aged samples, consistent with P21CIP1 senescence in this subpopulation. Our findings identify unique cellular sub-populations populations in aged and sarcopenic skeletal muscle, which will facilitate the development of new therapeutic strategies to combat age-related sarcopenia.
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Project description:Abstract The liver is the largest solid organ and a primary metabolic hub. In recent years, intact cell nuclei were used to perform single-nuclei RNA-seq (snRNA-seq) for tissues difficult to dissociate and for flash-frozen archived tissue samples to discover unknown and rare cell sub-populations. In this study, we performed snRNA-seq of a liver sample to identify sub-populations of cells based on nuclear transcriptomics. In 4,282 single nuclei we detected on average 1,377 active genes and we identified seven major cell types. We integrated data from 94,286 distal interactions (p<0.05) for 7,682 promoters from a targeted chromosome conformation capture technique (HiCap) and mass spectrometry (MS) proteomics for the same liver sample. We observed a reasonable correlation between proteomics and in silico bulk snRNA-seq (r=0.47) using tissue-independent gene-specific protein abundancy estimation factors. We specifically looked at genes of medical importance. The DPYD gene is involved in the pharmacogenetics of fluoropyrimidines toxicity and some of its variants are analyzed for clinical purposes. We identified a new putative polymorphic regulatory element, which may contribute to variation in toxicity. Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer and we investigated all known risk genes. We identified a complex regulatory landscape for the SLC2A2 gene with 16 candidate enhancers. Three of them harbor somatic motif breaking and other mutations in HCC in the Pan Cancer Analysis of Whole Genomes dataset and are candidates to contribute to malignancy. Our results highlight the potential of a multi-omics approach in the study of human diseases.
2020-12-21 | PXD017610 | Pride
Project description:To investigate the differentially expressed RNA levels in the liver of aged LoxP and SIRT2-KOhep mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of liver of aged LoxP and SIRT2-KOhep mice
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Project description:Uninjured Mouse Liver Nuclei – Henderson Lab 1
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