Proteomics provides insights into the inhibition of Chinese hamster V79 cell proliferation in the deep underground environment

Progress in biological and medical research in the deep underground: an update

As the growing population of individuals residing or working in deep underground spaces for prolonged periods, it has become imperative to understand the influence of factors in the deep underground environment (DUGE) on living systems. Heping Xie has conceptualized the concept of deep underground medicine to identify factors in the DUGE that can have either detrimental or beneficial effects on human health. Over the past few years, an increasing number of studies have explored the molecular mechanisms that underlie the biological impacts of factors in the DUGE on model organisms and humans. Here, we present a summary of the present landscape of biological and medical research conducted in deep underground laboratories and propose promising avenues for future investigations in this field. Most research demonstrates that low background radiation can trigger a stress response and affect the growth, organelles, oxidative stress, defense capacity, and metabolism of cells. Studies show that residing and/or working in the DUGE has detrimental effects on human health. Employees working in deep mines suffer from intense discomfort caused by high temperature and humidity, which increase with depth, and experience fatigue and sleep disturbance. The negative impacts of the DUGE on human health may be induced by changes in the metabolism of specific amino acids; however, the cellular pathways remain to be elucidated. Biological and medical research must continue in deep underground laboratories and mines to guarantee the safe probing of uncharted depths as humans utilize the deep underground space.

Radiation dose rate effects: what is new and what is needed?

Despite decades of research to understand the biological effects of ionising radiation, there is still much uncertainty over the role of dose rate. Motivated by a virtual workshop on the "Effects of spatial and temporal variation in dose delivery" organised in November 2020 by the Multidisciplinary Low Dose Initiative (MELODI), here, we review studies to date exploring dose rate effects, highlighting significant findings, recent advances and to provide perspective and recommendations for requirements and direction of future work. A comprehensive range of studies is considered, including molecular, cellular, animal, and human studies, with a focus on low linear-energy-transfer radiation exposure. Limits and advantages of each type of study are discussed, and a focus is made on future research needs.

Transcriptome analysis of lipid metabolism in response to cerium stress in the oleaginous microalga Nannochloropsis oculata

Nannochloropsis oculata can accumulate large amounts of lipids under rare earth element (REE) conditions. However, the lipid accumulation mechanism responsible for REE stress has not been elucidated. In this study, the effects of cerium (the most abundant REE) on the growth and lipid accumulation of N. oculata were investigated. The de novo transcriptome data of N. oculata under cerium conditions were subsequently collected and analyzed. The results showed that N. oculata exhibited good cerium-resistance ability, showed slightly decrease in biomass but significantly increase in lipid content (55.8 % dry cell weight) under 6.0 mg/L cerium condition. Meanwhile, about 83.4 % cerium was biological fixated. Through transcriptome analysis, we found that the inhibited photosynthesis and carbon fixation pathways coupled with the stress-sensitive expression of ribosome biogenesis genes acclimatized the cells to REE stress. The active glycolysis pathway accelerated carbon flux to pyruvate and acetyl-CoA, and the upregulation of glycerol kinase and phosphatidate cytidylyltransferase genes further induced lipid accumulation. In addition, cerium downregulated the acyl-CoA oxidase and triacylglycerol lipase genes, which inhibited the degradation of lipids. Therefore, different responses to cerium demonstrate how N. oculata cells adapt to REE stress, and this knowledge may be used to extend our understanding of triacylglycerol (TAG) and the synthesis of other important metabolites.

Urine metabolomics analysis of sleep quality in deep-underground miners: A pilot study

Background

In previous questionnaire surveys of miners, sleep disorders were found among underground workers. The influence of the special deep-underground environment and its potential mechanism are still unclear. Therefore, this study intends to utilize LC-MS metabolomics to study the potential differences between different environments and different sleep qualities.

Methods

Twenty-seven miners working at 645-1,500 m deep wells were investigated in this study, and 12 local ground volunteers were recruited as the control group. The Pittsburgh Sleep Quality Index (PSQI) was used to examine and evaluate the sleep status of the subjects in the past month, and valuable basic information about the participants was collected. PSQI scores were obtained according to specific calculation rules, and the corresponding sleep grouping and subsequent analysis were carried out. Through liquid chromatography-mass spectrometry (LC-MS) non-targeted metabolomics analysis, differences in metabolism were found by bioinformatics analysis in different environments.

Results

Between the deep-underground and ground (DUvsG) group, 316 differential metabolites were identified and 125 differential metabolites were identified in the good sleep quality vs. poor sleep quality (GSQvsPSQ) group. The metabolic pathways of Phenylalanine, tyrosine and tryptophan biosynthesis (p = 0.0102) and D-Glutamine and D-glutamate metabolism (p = 0.0241) were significantly enriched in DUvsG. For GSQvsPSQ group, Butanoate metabolism was statistically significant (p = 0.0276). L-Phenylalanine, L-Tyrosine and L-Glutamine were highly expressed in the deep-underground group. Acetoacetic acid was poorly expressed, and 2-hydroxyglutaric acid was highly expressed in good sleep quality.

Conclusions

The influence of the underground environment on the human body is more likely to induce specific amino acid metabolism processes, and regulate the sleep-wake state by promoting the production of excitatory neurotransmitters. The difference in sleep quality may be related to the enhancement of glycolytic metabolism, the increase in excitatory neurotransmitters and the activation of proinflammation. L-phenylalanine, L-tyrosine and L-glutamine, Acetoacetic acid and 2-hydroxyglutaric acid may be potential biomarkers correspondingly.

Electronic cigarette liquids impair metabolic cooperation and alter proteomic profiles in V79 cells

Background

Although still considered a safer alternative to classical cigarettes, growing body of work points to harmful effects of electronic cigarettes (e-cigarettes) affecting a range of cellular processes. The biological effect of e-cigarettes needs to be investigated in more detail considering their widespread use.

Methods

In this study, we treated V79 lung fibroblasts with sub-cytotoxic concentration of e-cigarette liquids, with and without nicotine. Mutagenicity was evaluated by HPRT assay, genotoxicity by comet assay and the effect on cellular communication by metabolic cooperation assay. Additionally, comprehensive proteome analysis was performed via high resolution, parallel accumulation serial fragmentation-PASEF mass spectrometry.

Results

E-cigarette liquid concentration used in this study showed no mutagenic or genotoxic effect, however it negatively impacted metabolic cooperation between V79 cells. Both e-cigarette liquids induced significant depletion in total number of proteins and impairment of mitochondrial function in treated cells. The focal adhesion proteins were upregulated, which is in accordance with the results of metabolic cooperation assay. Increased presence of posttranslational modifications (PTMs), including carbonylation and direct oxidative modifications, was observed. Data are available via ProteomeXchange with identifier PXD032071.

Conclusions

Our study revealed impairment of metabolic cooperation as well as significant proteome and PTMs alterations in V79 cells treated with e-cigarette liquid warranting future studies on e-cigarettes health impact.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12931-022-02102-w.

Chinese hamster V79 cells' dependence on background ionizing radiation for optimal growth

The study of depriving cells from background ionizing radiation for the past decades has provided valuable insights into its role in cellular homeostasis control. To explore the existence of such response in eukaryotic cells, we grew Chinese hamster (Cricetulus griseus) V79 cells for 23 days using three different dose rates: 0.91 (below background), 35 (surface control) and 72 nGy h^-1 (underground KCl-amended control). We did not observe a significant difference in cell number during the course of the experiment. However, cells grown at below background showed significantly lower viability compared to those grown at both control levels after 5 days of incubation and lasted, intermittently, for up to 21 days. We also observed a clear differentiation between the underground and the surface controls that could be explained by the variety of radiation sources present during cell growth under unshielded conditions. To explore the molecular mechanisms for these responses we performed transcriptome analysis on samples collected on days 2 and 5, but only samples from day 5 resulted in significant regulation. Gene enrichment analysis revealed two control-dependent general transcriptional responses. When compared the underground-KCl control, below-background cells showed the upregulation of processes intended for the response to drugs, metals and mechanical stimuli. In comparison, the response relative to the surface control was characterized by the upregulation of responses to organic substances and abiotic stimuli involved in the regulation of signaling, as well as to cell proliferation and homeostatic control of the number of cell processes.

Whole Transcriptome Analysis Revealed a Stress Response to Deep Underground Environment Conditions in Chinese Hamster V79 Lung Fibroblast Cells

Background: Prior studies have shown that the proliferation of V79 lung fibroblast cells could be inhibited by low background radiation (LBR) in deep underground laboratory (DUGL). In the current study, we revealed further molecular changes by performing whole transcriptome analysis on the expression profiles of long non-coding RNA (lncRNA), messenger RNA (mRNA), circular RNA (circRNA) and microRNA (miRNA) in V79 cells cultured for two days in a DUGL.

Methods: Whole transcriptome analysis including lncRNA, mRNAs, circ RNA and miRNA was performed in V79 cells cultured for two days in DUGL and above ground laboratory (AGL), respectively. The differentially expressed (DE) lncRNA, mRNA, circRNA, and miRNA in V79 cells were identified by the comparison between DUGL and AGL groups. Quantitative real-time polymerase chain reaction(qRT-PCR)was conducted to verify the selected RNA sequencings. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was analyzed for the DE mRNAs which enabled to predict target genes of lncRNA and host genes of circRNA.

Results: With |log₂(Fold-change)| ≥ 1.0 and p < 0.05, a total of 1257 mRNAs (353 mRNAs up-regulated, 904 mRNAs down-regulated), 866 lncRNAs (145 lncRNAs up-regulated, 721 lncRNAs down-regulated), and 474 circRNAs (247 circRNAs up-regulated, 227 circRNAs down-regulated) were significantly altered between the two groups. There was no significant difference in miRNA between the two groups. The altered RNA profiles were mainly discovered in lncRNAs, mRNAs and circRNAs. DE RNAs were involved in many pathways including ECM-RI, PI3K-Akt signaling, RNA transport and the cell cycle under the LBR stress of the deep underground environment.

Conclusion: Taken together, these results suggest that the LBR in the DUGL could induce transcriptional repression, thus reducing metabolic process and reprogramming the overall gene expression profile in V79 cells.

First transcriptome profiling of D. melanogaster after development in a deep underground low radiation background laboratory

Natural background radiation is a permanent multicomponent factor. It has an influence on biological organisms, but effects of its deprivation still remain unclear. The aim of our work was to study for the first time responses of D. melanogaster to conditions of the Deep Underground Low-Background Laboratory DULB-4900 (BNO, INR, RAS, Russia) at the transcriptome level by RNA-seq profiling. Overall 77 transcripts demonstrated differential abundance between flies exposed to low and natural background radiation. Enriched biological process functional categories were established for all genes with differential expression. The results showed down-regulation of primary metabolic processes and up-regulation of both the immune system process and the response to stimuli. The comparative analysis of our data and publicly available transcriptome data on D. melanogaster exposed to low and high doses of ionizing radiation did not reveal common DEGs in them. We hypothesize that the observed changes in gene expression can be explained by the influence of the underground conditions in DULB-4900, in particular, by the lack of stimuli. Thus, our study challenges the validity of the LNT model for the region of background radiation doses below a certain level (~16.4 nGy h-1) and the presence of a dose threshold for D. melanogaster.

Proteomic Characterization of Proliferation Inhibition of Well-Differentiated Laryngeal Squamous Cell Carcinoma Cells Under Below-Background Radiation in a Deep Underground Environment

Background: There has been a considerable concern about cancer induction in response to radiation exposure. However, only a limited number of studies have focused on the biological effects of below-background radiation (BBR) in deep underground environments. To improve our understanding of the effects of BBR on cancer, we studied its biological impact on well-differentiated laryngeal squamous cell carcinoma cells (FD-LSC-1) in a deep underground laboratory (DUGL). Methods: The growth curve, morphological, and quantitative proteomic experiments were performed on FD-LSC-1 cells cultured in the DUGL and above-ground laboratory (AGL). Results: The proliferation of FD-LSC-1 cells from the DUGL group was delayed compared to that of cells from the AGL group. Transmission electron microscopy scans of the cells from the DUGL group indicated the presence of hypertrophic endoplasmic reticulum (ER) and a higher number of ER. At a cutoff of absolute fold change ≥ 1.2 and p < 0.05, 807 differentially abundant proteins (DAPs; 536 upregulated proteins and 271 downregulated proteins in the cells cultured in the DUGL) were detected. KEGG pathway analysis of these DAPs revealed that seven pathways were enriched. These included ribosome (p < 0.0001), spliceosome (p = 0.0001), oxidative phosphorylation (p = 0.0001), protein export (p = 0.0001), thermogenesis (p = 0.0003), protein processing in the endoplasmic reticulum (p = 0.0108), and non-alcoholic fatty liver disease (p = 0.0421). Conclusion: The BBR environment inhibited the proliferation of FD-LSC-1 cells. Additionally, it induced changes in protein expression associated with the ribosome, gene spliceosome, RNA transport, and energy metabolism among others. The changes in protein expression might form the molecular basis for proliferation inhibition and enhanced survivability of cells adapting to BBR exposure in a deep underground environment. RPL26, RPS27, ZMAT2, PRPF40A, SNRPD2, SLU7, SRSF5, SRSF3, SNRPF, WFS1, STT3B, CANX, ERP29, HSPA5, COX6B1, UQCRH, and ATP6V1G1 were the core proteins associated with the BBR stress response in cells.