Naked mole rat cells show resistance to iPSC reprogramming and signs of more stable epigenome
ABSTRACT: Naked mole rat (NMR) is a valuable model for aging and cancer research due to its exceptional longevity and resistance to tumorigenesis. In an effort to generate NMR induced pluripotent stem cells (iPSCs) we observed that reprogramming efficiency of NMR fibroblasts in repsonse to OSKM overexpression was drasticaly lower than that of mouse fibroblasts. To understand the cause of NMR resistance to reprogramming we screened for factors that improve reprogramming effciency. We identified that expression of SV40 Large T (LT) dramatically improved reprogramming of NMR fibroblasts. Inactivation of Rb alone, but not p53, was suffcient to improve reprogramming effciency suggesting that NMR chromatin structure is refractory to reprogramming. Analysis of global histone landscape using quantitative mass spectrometry revealed that NMR fibroblasts had higer levels of repressive H3K27 methylation marks, and lower levels of activating H3K27 acetylation mark than the mouse fibroblasts. Furthermore, the NMR cells had lower levels of permissive H2A.Z acetylation marks. ChIP showed that of E-cadherin had repressive H3K9me3 histone mark in the NMR, but was poised with a bivalent H3K4me3/H3K27me3 in the mouse. Expression of LT reduced the levels of H3K9me3 mark on E-cadherin promoter. ATAC-seq revealed that NMR had more open chromatin globally, however, NMR promoters were more closed than mouse promoters. Expression of LT antigen led to massive opening of the NMR promoters including gene promoters required for reprogramming. Cumulatively, these data suggest that NMR has more stable epigenome than mouse, which resists reprogramming and may contribute to NMR longevity and cancer resistance. Overall design: ATAC-seq in mouse and naked mole rate fibroblast cell lines.
Project description:The goal was to find genes which are differentially expressed between the naked mole-rat (Heterocephalus glaber) and the wild-type mice liver tissue. The genes which are most differentially expressed may provide a clue for the remarkable differences between naked mole-rat and mouse in terms of longevity, cancer resistance and adaptation to subterranean environments. Analysis of 2 mRNA samples, one pooled from 3 wild-type mice liver tissue and another pooled from 3 naked mole-rat liver tissue.
Project description:We compared RNA-seq expression patterns in liver, an organ with high oxidative metabolism and abundant spontaneous DNA damage, from humans, naked mole rats, and mice, differing in maximum lifespan over a range of ~100, 30, and 3 years, respectively, for 130 genes involved in DNA repair. The results show that the longer-lived species, human and naked mole rat, share higher expression of these DNA repair genes, including core genes in several DNA repair pathways. A more systematic approach of signaling pathway analysis (SPA) indicates statistically significant upregulation of several DNA repair signaling pathways in human and naked mole rat compared with mouse. Overall design: Compare steady-state RNA levels from 3 samples each of adult liver tissue of human, naked mole rat, and mouse. Mouse samples available in the Short Reads Archive: SRX871336, SRX871370, SRX871395 (SRP053350) and BioProject PRJNA274780.
Project description:Deep sequencing of mRNA from naked mole rat Analysis of ploy(A)+ RNA of different specimens: brain, kidney, liver from new born , 4 years old , 20 years old and 4 years old hypoxia-exposed naked mole rat
Project description:Deep sequencing of mRNA from naked mole rat Overall design: Analysis of ploy(A)+ RNA of different specimens: brain, kidney, liver from new born , 4 years old , 20 years old and 4 years old hypoxia-exposed naked mole rat
Project description:Mammals display wide range of variation in their lifespan. Investigating the molecular networks that distinguish long- from short-lived species has proven useful to identify determinants of longevity. Here, we compared the liver of long-lived naked mole-rats (NMRs) and the phylogenetically closely related, shorter-lived, guinea pigs using an integrated omic approach. We found that NMRs livers display a unique expression pattern of mitochondrial proteins that result in distinct metabolic features of their mitochondria. For instance, we observed a generally reduced respiration rate associated with lower protein levels of respiratory chain components, particularly complex I, and increased capacity to utilize fatty acids. Interestingly, we show that the same molecular networks are affected during aging in both NMR and humans, supporting a direct link to the extraordinary longevity of both species. Finally, we identified a novel longevity pathway and validated it experimentally in the nematode C. elegans.
Project description:Cancer resistance is a major cause for longevity of the naked mole-rat. Recent liver transcriptome analysis in this animal compared to wild-derived mice revealed higher expression of alpha2-macroglobulin (A2M) and cell adhesion molecules, which contribute to the naked mole-rat’s cancer resistance. Notably, A2M is known to dramatically decrease with age in humans. We hypothesize that this might facilitate tumour development. Here we found that A2M modulates tumour cell adhesion, migration and growth by inhibition of tumour promoting signalling pathways, e.g. PI3K / AKT, SMAD and up-regulated PTEN via down-regulation of miR-21, in vitro and in tumour xenografts. A2M increases the expression of CD29 and CD44 but did not evoke EMT. Transcriptome analysis of A2M-treated tumour cells, xenografts and mouse liver demonstrated a multifaceted regulation of tumour promoting signalling pathways indicating a less tumorigenic environment mediated by A2M. By virtue of these multiple actions the naturally occurring A2M has strong potential as a novel therapeutic agent. Overall design: 11 samples: 5 treated with PBS, 6 treated with A2M
Project description:Comparison of gene expression level by Illumina sequencing of naked mole-rat liver from breeders and non-breeders. Overall design: 23 liver samples, 5-6 animals per group, 4 groups: 1) female non-breeder, 2) female breeder, 3) male non-breeder, 4) male breeder
Project description:Comparison of gene expression level by Illumina sequencing of naked mole-rat liver from young and old animals. We identified differentially expressed genes and provide functional profiles, which give insights into the aging process of long-lived rodents. Overall design: 9 liver samples; 2 groups: 1) 6 young animals, 2) 3 old animals