Similar Datasets
Project description:Single cell transcriptomics of yound and aged naked mole-rat (NMR) epidermal cells
| PRJNA640800 | ENA
Project description:The naked mole-rat (NMR), Heterocephalus glaber, is a mouse-sized subterranean rodent native to East Africa. Research on NMRs is intensifying in an effort to gain leverage from their unusual physiology, long-life span and cancer resistance for the development of new theraputics. Few studies have attempted to explain the reasons behind the NMR’s cancer resistance, but most prominently Tian et al. reported that NMR cells produce high-molecular weight hyaluronan as a potential cause for the NMR’s cancer resistance. Tian et al. have shown that NMR cells are resistant to transformation by SV40 Large T Antigen (SV40LT) and oncogenic HRAS (HRASG12V), a combination of oncogenes sufficient to transform mouse and rat fibroblasts. We have developed a number of lentiviral vectors to deliver both these oncogenes and generated 106 different cell lines from five different tissues and eleven different NMRs, and report here that contrary to Tian et al.’s observation, NMR cells are susceptible to oncogenic transformation by SV40LT and HRASG12V. Our data thus point to a non-cell autonomous mechanism underlying the remarkable cancer resistance of NMRs. Identifying these non-cell autonomous mechanisms could have significant implications on our understanding of human cancer development.
2020-06-12 | E-MTAB-8932 | biostudies-arrayexpress
Project description:The immune system consists of a network of specialized cells and processes that protect the organism from diseases and regulates tissue repair. Natural killer (NK) cells and the αβ and γδ T cells comprise the cytotoxic arm of the immune system and have evolved to detect and eradicate cells infected with pathogens and affected by malignancies, in order to prevent their spread and subsequent tissue damage. The naked mole-rat (NMR; Heterocephalus glaber) exhibits an unusually long lifespan relative to its body size, remarkable cancer resistance, and a surprising absence of NK cells, likely lost during its evolution. So far, little is known about NMR T cells in terms of the subsets they comprise, the evolution of the genes that regulate their function, the diversity of their clonotypes, and the organ in which they mature – the thymus. Using single-cell RNA sequencing (scRNA-seq), we find that NMRs have a large population of circulating γδT cells, comprising two subsets, one with an activated cytotoxic profile. Using comparative genomics, we find that the NMR genome maintains a large diversity of γ and δ variable T-cell receptor (TCR) regions, relative to that in other mammalian genomes. We devise a novel TCR scRNA-seq approach, which reveals that the NMR cytotoxic γδT-cell subset harbors a dominant clonotype, and that, in contrast to mouse, the clonotypic diversity of NMR CD8 αβT cells is significantly lower than that of its CD4 αβT cells. The latter suggests that NMRs have evolved under a relaxed intracellular pathogenic selective pressure, consistent with the loss of their NK cells. We corroborate this by showing that the genomic diversity of NMR MHC-I genes, relative to that of MHC-II genes, is considerably smaller than in other mammalian genomes. In line with these findings, we further show that NMR thymi in early life are considerably smaller compared to mouse thymi, yet by middle age thymi of both species show equivalent signs of involution. Our study thus sheds significant light on NMR T cells and moves us one step closer towards understanding the contributions of the immune system to the remarkable longevity and cancer resistance of this species.
2023-11-30 | GSE214390 | GEO
Project description:The naked mole-rat (NMR) is an exceptionally long-lived rodent that does not show increased mortality with age, uniquely defining NMR as a demographically non-aging mammal. Here, we performed bisulfite sequencing on over one hundred NMR blood samples differing in age, assessing more than 3 million common CpG sites. We observed an information loss of the NMR methylome during aging suggesting that NMR ages. Unsupervised clustering based on the 758 CpG sites whose methylation level strongly correlate with age suggests an age-related shift of the NMR methylome. We also developed an epigenetic aging clock that accurately predicts the NMR age spread across the genome. Based on the clock, NMRs age much slower than mice and much faster than humans, consistent with their known maximum lifespans. We further found that patterns of age-related methylation changes of aging clock sites in Tert and Prpf19 showed differences between NMRs and mice. Together, the data indicate that NMRs, like other mammals, epigenetically age even in the absence of demographic aging of this species.
2021-12-19 | GSE179039 | GEO
Project description: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.
2017-06-21 | GSE83585 | GEO
Project description:The role of CD44 in naked-mole rats (NMR) oligodendrocyte progenitor cells (OPCs) were evaluated by comparing the transcriptome of control and CD44-knockdown NMR OPCs.
2022-03-31 | E-MTAB-9166 | biostudies-arrayexpress
Project description:This study compares the transcriptional response to hypoxia in liver of the hypoxia-tolerant naked mole rat (NMR) and the hypoxia-sensitive rat.
2019-11-14 | GSE71612 | GEO
Project description:The naked mole rat (NMR), a long-lived and cancer resistant rodent, is highly resistant to hypoxia. Here, using robust cellular models wherein the mouse telomeric protein TRF1 is substituted by the NMR TRF1 or its mutant forms, we show that TRF1 supports maximal glycolytic capacity under low oxygen, shows increased nuclear localization and association with telomeres, and protects telomeres from replicative stress. We pinpoint this evolutionary gain of metabolic function to specific amino acid changes in the homodimerization domain of this protein. We further find that NMR TRF1 accelerates telomere shortening. These findings reveal an evolutionary strategy to adapt telomere biology for metabolic control under an extreme environment.
2021-03-02 | GSE163064 | GEO
Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from many tissues of the naked mole rat We generated DNA methylation data from n=289 tissues. All tissues except for skin biopsies and blood were obtained from frozen tissue collection that were euthanized for other studies. Skin biopsies (2 mm punch) were collected from the backs of the animals under local anesthesia. Blood samples were collected from the tails. The n=3 induced pluripotent stem cells from NMR were generated as described in (Tan et al 2017., PMID: 29107597). As control set for the iPS study, we used n=3 fibroblasts samples. Genomic DNA was extracted using Qiagen DNeasy Blood and Tissue kit and quantified using Nanodrop and Qubit.als
2021-10-18 | GSE174777 | GEO
Project description:Naked mole rats (NMRs, Heterocephalus glaber) are long-lived mammals that possess a natural resistance to cancer and other age-related pathologies, maintaining a healthy life span for >30 years. We report application of RNAseq technology to analyze changes in the skin transcriptome of NMRs during aging. RNAseq analyses reveal that the transcript levels of several longevity-associated (Igfbp3, Igf2bp3, Ing2) and tumor-suppressor genes (Btg2, Cdkn1a, Cdkn2c, Dnmt3a, Hic1, Socs3, Sfrp1, Sfrp5, Thbs1, Tsc1, Zfp36) are increased in aged versus young NMR skin. Overall, these data suggest that specific features in the NMR skin aging transcriptome might contribute to the resistance of NMRs to spontaneous skin carcinogenesis and provide a platform for further investigations of NMRs as a model organism for studying the biology and disease resistance of human skin.
2022-04-26 | GSE200736 | GEO