Transcriptome sequencing of the naked mole rat (Heterocephalus glaber) and identification of hypoxia tolerance genes

ABSTRACT The naked mole rat (NMR; Heterocephalus glaber) is a small rodent species found in regions of Kenya, Ethiopia and Somalia. It has a high tolerance for hypoxia and is thus considered one of the most important natural models for studying hypoxia tolerance mechanisms. The various mechanisms underlying the NMR's hypoxia tolerance are beginning to be understood at different levels of organization, and next-generation sequencing methods promise to expand this understanding to the level of gene expression. In this study, we examined the sequence and transcript abundance data of the muscle transcriptome of NMRs exposed to hypoxia using the Illumina HiSeq 2500 system to clarify the possible genomic adaptive responses to the hypoxic underground surroundings. The RNA-seq raw FastQ data were mapped against the NMR genome. We identified 2337 differentially expressed genes (DEGs) by comparison of the hypoxic and control groups. Functional annotation of the DEGs by gene ontology (GO) analysis revealed enrichment of hypoxia stress-related GO categories, including ‘biological regulation’, ‘cellular process’, ‘ion transport’ and ‘cell-cell signaling’. Enrichment of DEGs in signaling pathways was analyzed against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to identify possible interactions between DEGs. The results revealed significant enrichment of DEGs in focal adhesion, the mitogen-activated protein kinase (MAPK) signaling pathway and the glycine, serine and threonine metabolism pathway. Furthermore, inhibition of DEGs (STMN1, MAPK8IP1 and MAPK10) expression induced apoptosis and arrested cell growth in NMR fibroblasts following hypoxia. Thus, this global transcriptome analysis of NMRs can provide an important genetic resource for the study of hypoxia tolerance in mammals. Furthermore, the identified DEGs may provide important molecular targets for biomedical research into therapeutic strategies for stroke and cardiovascular diseases.

I have a BSc in veterinary medicine, and an MSc in zoology. My PhD is in molecular genetics, where under the mentorship of Dr Shuhan Sun, I am studying the mechanisms underlying naked mole rat hypoxia tolerance. I am also investigating the role of H2O2 treatment or serum deprivation in autophagy and apoptosis in naked mole rat skin fibroblasts. Furthermore, I am exploring the role of the PI3K/Akt signaling pathway in regulating autophagy and apoptosis of naked mole rat hepatic stellate cells under hypoxic condition. The lab specifically focusses on the mechanism of anti-aging, hypoxia resistance in the naked mole rat.
How would you explain the main findings of your paper to non-scientific family and friends?
Genes that control cell proliferation, apoptosis (cell death) and metabolism are differentially expressed in response to hypoxic stress (low oxygen conditions). The protective roles that these genes play are the same as the emergency departments' roles when a crisis happens. Some signaling pathway involved in cell proliferation and apoptosis are activated when cells are exposed to hypoxia. This is like many departments working together to deal with the crisis. In this paper, we report how naked mole rat muscle genes are expressed under continuous hypoxic stress. We mapped the reads against the naked mole rat genome and annotated the genes that were differentially expressed in response to hypoxic stress.
"We found that the temporal expression pattern of the DEGs varied greatly according to the length of time that naked mole rats were exposed to hypoxic stress." What are the potential implications of these results for your field of research?
The identified differentially expressed genes in our work provide an important genetic resource for further analyses of mammalian tolerance to hypoxia and molecular targets for the prevention of ischemic diseases.

What has surprised you the most while conducting your research?
The results that indicated hypoxia-dependent focal adhesion is required for cellular communication and activation of the MAPK signaling pathway involved in cell proliferation, apoptosis and metabolism are the most surprising. We explored the transcriptomic changes of naked mole rat muscle in response to hypoxic stress over time and identified numerous differentially expressed genes (DEGs) with primary involvement in cell adhesion, cell-cell signaling, and metabolism. Furthermore, we found that the temporal expression pattern of the DEGs varied greatly according to the length of time that naked mole rats were exposed to hypoxic stress. We also identified a greater number of upregulated DEGs at 8 h or 12 h compared with those at 1 h or 4 h. These findings suggest that gene expression in naked mole rat muscle is highly coordinated in response to hypoxic shock at 1 h or 4 h and hypoxic stress at 8 h or 12 h.

What changes do you think could improve the professional lives of early-career scientists?
More availability to journal articles through open access, earlier and more opportunities to learn relevant experimental techniques. Because the process of learning experimental techniques in which they can well know how the results were obtained can deepen their understanding of the results in the articles. It is often difficult for early career scientists to understand the experimental results and the conclusions in the articles written with a non-native languages.  After I complete my PhD, I will take up a position as a research scientist in the Department of Medical Genetics here at The Second Military Medical University. I will remain in the field of aging research using the natural model of the anti-aging naked mole rat.