Mining potential biomarkers associated with space flight in Caenorhabditis elegans experienced Shenzhou-8 mission with multiple feature selection techniques

Integrated analysis of miRNAome and transcriptome reveals that microgravity induces the alterations of critical functional gene modules via the regulation of miRNAs in short-term space-flown C. elegans

Microgravity, as a unique hazardous factor encountered in space, can induce a series of harmful effects on living organisms. The impact of microgravity on the pivotal functional gene modules stemming from gene enrichment analysis via the regulation of miRNAs is not fully illustrated. To explore the microgravity-induced alterations in critical functional gene modules via the regulation of miRNAs, in the present study, we proposed a novel bioinformatics algorithm for the integrated analysis of miRNAome and transcriptome from short-term space-flown C. elegans. The samples of C. elegans were exposed to two space conditions, namely spaceflight (SF) and spaceflight control (SC) onboard the International Space Station for 4 days. Additionally, the samples of ground control (GC) were included for comparative analysis. Using the present algorithm, we constructed regulatory networks of functional gene modules annotated from differentially expressed genes (DEGs) and their associated regulatory differentially expressed miRNAs (DEmiRNAs). The results showed that functional gene modules of molting cycle, defense response, fatty acid metabolism, lysosome, and longevity regulating pathway were facilitated by 25 down-regulated DEmiRNAs (e.g., cel-miR-792, cel-miR-65, cel-miR-70, cel-lsy-6, cel-miR-796, etc.) in the SC vs. GC groups, whereas these modules were inhibited by 13 up-regulated DEmiRNAs (e.g., cel-miR-74, cel-miR-229, cel-miR-70, cel-miR-249, cel-miR-85, etc.) in the SF vs. GC groups. These findings indicated that microgravity could significantly alter gene expression patterns and their associated functional gene modules in short-term space-flown C. elegans. Additionally, we identified 34 miRNAs as post-transcriptional regulators that modulated these functional gene modules under microgravity conditions. Through the experimental verification, our results demonstrated that microgravity could induce the down-regulation of five critical functional gene modules (i.e., molting cycle, defense response, fatty acid metabolism, lysosome, and longevity regulating pathways) via the regulation of miRNAs in short-term space-flown C. elegans.

Construction of dose prediction model and identification of sensitive genes for space radiation based on single-sample networks under spaceflight conditions

PURPOSE

To identify sensitive genes for space radiation, we integrated the transcriptomic samples of spaceflight mice from GeneLab and predicted the radiation doses absorbed by individuals in space.

METHODS AND MATERIALS

A single-sample network (SSN) for each individual sample was constructed. Then, using machine learning and genetic algorithms, we built the regression models to predict the absorbed dose equivalent based on the topological structure of SSNs. Moreover, we analyzed the SSNs from each tissue and compared the similarities and differences among them.

RESULTS

Our model exhibited excellent performance with the following metrics: R 2 = 0.980 , MSE = 6.74 e - 04 , and the Pearson correlation coefficient of 0.990 (p value <.0001) between predicted and actual values. We identified 20 key genes, the majority of which had been proven to be associated with radiation. However, we uniquely established them as space radiation sensitive genes for the first time. Through further analysis of the SSNs, we discovered that the different tissues exhibited distinct mechanisms in response to space stressors.

CONCLUSIONS

The topology structures of SSNs effectively predicted radiation doses under spaceflight conditions, and the SSNs revealed the gene regulatory patterns within the organisms under space stressors.

Integrating evolutionarily conserved mechanism of response to radiation for exploring novel Caenorhabditis elegans radiation-responsive genes for estimation of radiation dose associated with spaceflight

During space exploration, space radiation is widely recognized as an inescapable perilous stressor, owing to its capacity to induce genomic DNA damage and escalate the likelihood of detrimental health outcomes. Rapid and reliable estimation of space radiation dose holds paramount significance in accurately assessing the health risks associated with spaceflight. However, the identification of space radiation-responsive genes, with their potential to serve as early indicators for diagnosing radiation dose associated with spaceflight, continues to pose a significant challenge. In this study, based on the evolutionarily conserved mechanism of radiation response, an in silico analysis method of homologous comparison was performed to identify the Caenorhabditis elegans orthologues of human radiation-responsive genes with possible roles in the major processes of response to radiation, and thereby to explore the potential C. elegans radiation-responsive genes for evaluating the levels of space radiation exposure. The results showed that there were 60 known C. elegans radiation-responsive genes and 211 C. elegans orthologues of human radiation-responsive genes implicated in the major processes of response to radiation. Through an investigation of all available transcriptomic datasets obtained from space-flown C. elegans, it was observed that the expression levels of the majority of these putative C. elegans radiation-responsive genes identified in this study were notably changed across various spaceflight conditions. Furthermore, this study indicated that within the identified genes, 19 known C. elegans radiation-responsive genes and 40 newly identified C. elegans orthologues of human radiation-responsive genes exhibited a remarkable positive correlation with the duration of spaceflight. Moreover, a noteworthy presence of substantial multi-collinearity among the majority of these identified genes was observed. This observation lends support to the possibility of treating each identified gene as an independent indicator of radiation dose in space. Ultimately, a subset of 15 potential radiation-responsive genes was identified, presenting the most promising indicators for estimation of radiation dose associated with spaceflight in C. elegans.

Spaceflight Induces Strength Decline in Caenorhabditis elegans

Background: Understanding and countering the well-established negative health consequences of spaceflight remains a primary challenge preventing safe deep space exploration. Targeted/personalized therapeutics are at the forefront of space medicine strategies, and cross-species molecular signatures now define the 'typical' spaceflight response. However, a lack of direct genotype-phenotype associations currently limits the robustness and, therefore, the therapeutic utility of putative mechanisms underpinning pathological changes in flight. Methods: We employed the worm Caenorhabditis elegans as a validated model of space biology, combined with 'NemaFlex-S' microfluidic devices for assessing animal strength production as one of the most reproducible physiological responses to spaceflight. Wild-type and dys-1 (BZ33) strains (a Duchenne muscular dystrophy (DMD) model for comparing predisposed muscle weak animals) were cultured on the International Space Station in chemically defined media before loading second-generation gravid adults into NemaFlex-S devices to assess individual animal strength. These same cultures were then frozen on orbit before returning to Earth for next-generation sequencing transcriptomic analysis. Results: Neuromuscular strength was lower in flight versus ground controls (16.6% decline, p < 0.05), with dys-1 significantly more (23% less strength, p < 0.01) affected than wild types. The transcriptional gene ontology signatures characterizing both strains of weaker animals in flight strongly corroborate previous results across species, enriched for upregulated stress response pathways and downregulated mitochondrial and cytoskeletal processes. Functional gene cluster analysis extended this to implicate decreased neuronal function, including abnormal calcium handling and acetylcholine signaling, in space-induced strength declines under the predicted control of UNC-89 and DAF-19 transcription factors. Finally, gene modules specifically altered in dys-1 animals in flight again cluster to neuronal/neuromuscular pathways, suggesting strength loss in DMD comprises a strong neuronal component that predisposes these animals to exacerbated strength loss in space. Conclusions: Highly reproducible gene signatures are strongly associated with space-induced neuromuscular strength loss across species and neuronal changes in calcium/acetylcholine signaling require further study. These results promote targeted medical efforts towards and provide an in vivo model for safely sending animals and people into deep space in the near future.

Caenorhabditis elegans in microgravity: An omics perspective

The application of omics to study Caenorhabditis elegans (C. elegans) in the context of spaceflight is increasing, illuminating the wide-ranging biological impacts of spaceflight on physiology. In this review, we highlight the application of omics, including transcriptomics, genomics, proteomics, multi-omics, and integrated omics in the study of spaceflown C. elegans, and discuss the impact, use, and future direction of this branch of research. We highlight the variety of molecular alterations that occur in response to spaceflight, most notably changes in metabolic and neuromuscular gene regulation. These transcriptional features are reproducible and evident across many spaceflown species (e.g., mice and astronauts), supporting the use of C. elegans as a model organism to study spaceflight physiology with translational capital. Integrating tissue-specific, spatial, and multi-omics approaches, which quantitatively link molecular responses to phenotypic adaptations, will facilitate the identification of candidate regulatory molecules for therapeutic intervention and thus represents the next frontiers in C. elegans space omics research.

Microgravity alters the expressions of DNA repair genes and their regulatory miRNAs in space-flown Caenorhabditis elegans

During spaceflight, multiple unique hazardous factors, particularly microgravity and space radiation, can induce different types of DNA damage, which pose a constant threat to genomic integrity and stability of living organisms. Although organisms have evolved different kinds of conserved DNA repair pathways to eliminate this DNA damage on Earth, the impact of space microgravity on the expressions of these DNA repair genes and their regulatory miRNAs has not been fully explored. In this study, we integrated all existing datasets, including both transcriptional and miRNA microarrays in wild-type (WT) Caenorhabditis elegans that were exposed to the treatments of spaceflight (SF), spaceflight control with a 1g centrifugal device (SC), and ground control (GC) in three space experiments with the periods of 4, 8 and 16.5 days. The results of principal component analysis showed the gene expression patterns for five major DNA repair pathways (i.e., non-homologous end joining (NHEJ), homologous recombination (HR), mismatch repair (MMR), nucleotide excision repair (NER), and base excision repair (BER)) were well separated and clustered between SF/GC and SC/GC treatments after three spaceflights. In the 16.5-days space experiment, we also selected the datasets of dys-1 mutant and ced-1 mutant of C. elegans, which respectively presented microgravity-insensitivity and radiosensitivity. Compared to the WT C. elegans flown in the 16.5-days spaceflight, the separation distances between SF and SC samples were significantly reduced in the dys-1 mutant, while greatly enhanced in the ced-1 mutant for five DNA repair pathways. By comparing the results of differential expression analysis in SF/GC versus SC/GC samples, we found the DNA repair genes annotated in the pathways of BER and NER were prominently down-regulated under microgravity during both the 4- and 8-days spaceflights. While, under microgravity, the genes annotated in MMR were dominatingly up-regulated during the 4-days spaceflight, and those annotated in HR were mainly up-regulated during the 8-days spaceflight. And, most of the DNA repair genes annotated in the pathways of BER, NER, MMR, and HR were up-regulated under microgravity during the 16.5-days spaceflight. Using miRNA-mRNA integrated analysis, we determined the regulatory networks of differentially expressed DNA repair genes and their regulatory miRNAs in WT C. elegans after three spaceflights. Compared to GC conditions, the differentially expressed miRNAs were analyzed under SF and SC treatments of three spaceflights, and some altered miRNAs that responded to SF and SC could regulate the expressions of corresponding DNA repair genes annotated in different DNA repair pathways. In summary, these findings indicate that microgravity can significantly alter the expression patterns of DNA repair genes and their regulatory miRNAs in space-flown C. elegans. The alterations of the expressions of DNA repair genes and the dominating DNA repair pathways under microgravity are possibly related to the spaceflight period. In addition, the key miRNAs are identified as the post-transcriptional regulators to regulate the expressions of various DNA repair genes under microgravity. These altered miRNAs that responded to microgravity can be implicated in regulating diverse DNA repair processes in space-flown C. elegans.

Intestinal long non-coding RNAs in response to simulated microgravity stress in Caenorhabditis elegans

Long non-coding RNAs (lncRNAs) are important in regulating the response to environmental stresses in organisms. In this study, we used Caenorhabditis elegans as an animal model to determine the functions of intestinal lncRNAs in regulating response to simulated microgravity stress. Among the intestinal lncRNAs, linc-2, linc-46, linc-61, and linc-78 were increased by simulated microgravity treatment, and linc-13, linc-14, linc-50, and linc-125 were decreased by simulated microgravity treatment. Among these 8 intestinal lncRNAs, RNAi knockdown of linc-2 or linc-61 induced a susceptibility to toxicity of simulated microgravity, whereas RNAi knockdown of linc-13, linc-14, or linc-50 induced a resistance to toxicity of simulated microgravity. In simulated microgravity treated nematodes, linc-50 potentially binds to three transcriptional factors (DAF-16, SKN-1, and HLH-30). RNAi knockdown of daf-16, skn-1, or hlh-30 could suppress resistance of linc-50(RNAi) nematodes to the toxicity of simulated microgravity. Therefore, our results provide an important basis for intestinal lncRNAs, such as the linc-50, in regulating the response to simulated microgravity in nematodes.

Notch receptor GLP-1 regulates toxicity of simulated microgravity stress by activating germline-intestine communication of insulin signaling in C. elegans

We here investigated molecular basis of notch receptor GLP-1 in controlling simulated microgravity stress in Caenorhabditis elegans. glp-1 expression was decreased by simulated microgravity. Meanwhile, glp-1 mutation caused resistance to toxicity of simulated microgravity. GLP-1 acted in germline cells to control toxicity of simulated microgravity. In germline cells, RNAi knockdown of glp-1 increased daf-16 expression. RNAi knockdown of daf-16 suppressed resistance to toxicity of simulated microgravity in glp-1 mutant. In simulated microgravity treated worms, germline RNAi knockdown of glp-1 decreased expressions of daf-28, ins-39, and ins-8 encoding insulin peptides, and resistance to simulated microgravity toxicity could be detected in daf-28(RNAi), ins-39(RNAi), and ins-8(RNAi) worms. In simulated microgravity treated worms, RNAi knockdown of daf-28, ins-39, or ins-8 in germline cells further increased expression and nucleus localization of transcriptional factor DAF-16 in intestinal cells. Therefore, the GLP-1-activated germline-intestine communication of insulin signaling is required for control of simulated microgravity toxicity in C. elegans.

New evidence and insight for abnormalities in early embryonic development after short-term spaceflight onboard the Chinese SJ-10 satellite

During space travel, radiation and microgravity are recognized to be major hazardous factors in the overall health and well-being of astronauts. Although some efforts have been made to elucidate the effects of short-term space travel on the reproductive health of astronauts and multiple  other species in a variety of in vitro and in vivo studies, it is still unclear whether space travel can cause abnormal embryonic development or if it poses any reproductive risks. Recently, Lei et al. (2020) investigated the effects of short-term spaceflight onboard the Chinese SJ-10 satellite on murine preimplantation embryonic development. In the article, the authors claimed that the developmental abnormalities after short-term spaceflight onboard the SJ-10 satellite were attributed to space radiation and that these alterations in space was equivalent to those induced by a 2 mGy dose of gamma-rays in a ground-based facility. In this commentary, we discuss the possible space environmental factors and associated mechanisms that contribute to abnormalities in early embryonic development, and the potential health risks to mammals after short-term space travel. This commentary provides new evidence and a fresh perspective on whether and how short-term space travel poses potential reproductive risks in mammals.

microRNAs involved in the control of toxicity on locomotion behavior induced by simulated microgravity stress in Caenorhabditis elegans

microRNAs (miRNAs) post-transcriptionally regulate the expression of targeted genes. We here systematically identify miRNAs in response to simulated microgravity based on both expressions and functional analysis in Caenorhabditis elegans. After simulated microgravity treatment, we observed that 19 miRNAs (16 down-regulated and 3 up-regulated) were dysregulated. Among these dysregulated miRNAs, let-7, mir-54, mir-67, mir-85, mir-252, mir-354, mir-789, mir-2208, and mir-5592 were required for the toxicity induction of simulated microgravity in suppressing locomotion behavior. In nematodes, alteration in expressions of let-7, mir-67, mir-85, mir-252, mir-354, mir-789, mir-2208, and mir-5592 mediated a protective response to simulated microgravity, whereas alteration in mir-54 expression mediated the toxicity induction of simulated microgravity. Moreover, among these candidate miRNAs, let-7 regulated the toxicity of simulated microgravity by targeting and suppressing SKN-1/Nrf protein. In the intestine, a signaling cascade of SKN-1/Nrf-GST-4/GST-5/GST-7 required for the control of oxidative stress was identified to act downstream of let-7 to regulate the toxicity of simulated microgravity. Our data demonstrated the crucial function of miRNAs in regulating the toxicity of simulated microgravity stress in organisms. Moreover, our results further provided an important molecular basis for epigenetic control of toxicity of simulated microgravity.

Identification of potential radiation-responsive biomarkers based on human orthologous genes with possible roles in DNA repair pathways by comparison between Arabidopsis thaliana and homo sapiens

Rapid and reliable ionization radiation (IR) exposure estimation has become increasingly important in environment due to the urgent requirement of medical evaluation and treatment in the event of nuclear accident emergency. Human DNA repair genes can be identified as important candidate biomarkers to assess IR exposure, while how to find the enough sensitive and specific biomarkers in the DNA repair networks is still challenged and not fully determined. The conserved features of DNA repair pathways may facilitate interdisciplinary studies that cross the traditional boundaries between animal and plant biology, with the aim of identifying undiscovered human DNA repair genes for potential radiation-responsive biomarkers. In this work, an in silico method of homologous comparison was performed to identify the human orthologues of A. thaliana DNA repair genes, and thereby to explore the sensitive and specific human radiation-responsive genes to evaluate the IR exposure levels. The results showed that a total of 16 putative candidate genes were involved in the human DNA repair pathways of homologous recombination (HR) and non-homologous end joining (NHEJ), and most of them were confirmed by previous experiments. Additionally, we analyzed the gene expression patterns of these 16 candidate genes in several human transcript microarray datasets with different IR treatments. The results indicated that most of the gene expression levels for these candidate genes were significantly changed under different radiation treatments. Based on these results, we integrated these putative human DNA repair genes into the DNA repair pathways to propose new insights of the HR and NHEJ pathways, which can also provide the potential targets for the development of radiation biomarkers. Notably, two putative DNA repair genes, named ERCC1 and ESCO2, were identified and were considered to be the sensitive and specific biomarkers in response to γ-ray exposures.

Response of canonical Wnt/β-catenin signaling pathway in the intestine to microgravity stress in Caenorhabditis elegans

Considering the short life-cycle property, Caenorhabditis elegans is a suitable animal model to evaluate the long-term effects of microgravity stress on organisms. Canonical Wnt/β-catenin signaling is evolutionarily conserved in various organisms. We here investigated the response of canonical Wnt/β-catenin signaling pathway to microgravity stress in nematodes. We observed the noticeable response of canonical Wnt/β-catenin signaling to microgravity stress. In contrast, we did not detect the obvious response of non-canonical Wnt/β-catenin signaling to microgravity stress. The canonical β-catenin BAR-1 acted in the intestine to regulate the response to simulated microgravity. Moreover, in the intestine, we identified a signaling cascade of canonical Wnt/β-catenin signaling pathway in response to simulated microgravity, and this signaling cascade contained Frizzled receptor MIG-1, Disheveled protein DSH-2, GSK3A/GSK-3, and β-catenin transcriptional factor BAR-1. Our data suggests an important protective response of canonical Wnt/β-catenin signaling to simulated microgravity in nematodes.

Damage on functional state of intestinal barrier by microgravity stress in nematode Caenorhabditis elegans

Due to short life cycle, nematode Caenorhabditis elegans is a suitable animal model for assessing the effect of long-term simulated microgravity treatment on organisms. We here investigated the effect of simulated microgravity treatment for 24-h on development and functional state of intestinal barrier in nematodes. Simulated microgravity treatment not only caused a broadened intestinal lumen, but also enhanced intestinal permeability. Intestinal overexpression of SOD-2, a mitochondrial Mn-SOD protein, prevented the damage on functional state of intestinal barrier by simulated microgravity and induced a resistance to toxicity of simulated microgravity, suggesting the crucial role of oxidative stress in inducing the damage on functional state of intestinal barrier in simulated microgravity treated nematodes. For the molecular basis of damage on functional state of intestinal barrier, we observed significant decrease in expressions of some genes (acs-22, erm-1, and hmp-2) required for maintenance of functional state of intestinal barrier in simulated microgravity treated nematodes. Our results highlight the potential of long-term simulated microgravity treatment in inducing intestinal damage in animals.

Mitochondrial Unfolded Protein Response to Microgravity Stress in Nematode Caenorhabditis elegans

Caenorhabditis elegans is useful for assessing biological effects of spaceflight and simulated microgravity. The molecular response of organisms to simulated microgravity is still largely unclear. Mitochondrial unfolded protein response (mt UPR) mediates a protective response against toxicity from environmental exposure in nematodes. Using HSP-6 and HSP-60 as markers of mt UPR, we observed a significant activation of mt UPR in simulated microgravity exposed nematodes. The increase in HSP-6 and HSP-60 expression mediated a protective response against toxicity of simulated microgravity. In simulated microgravity treated nematodes, mitochondria-localized ATP-binding cassette protein HAF-1 and homeodomain-containing transcriptional factor DVE-1 regulated the mt UPR activation. In the intestine, a signaling cascade of HAF-1/DVE-1-HSP-6/60 was required for control of toxicity of simulated microgravity. Therefore, our data suggested the important role of mt UPR activation against the toxicity of simulated microgravity in organisms.

The Impact of Oxidative Stress on the Bone System in Response to the Space Special Environment

The space special environment mainly includes microgravity, radiation, vacuum and extreme temperature, which seriously threatens an astronaut’s health. Bone loss is one of the most significant alterations in mammalians after long-duration habitation in space. In this review, we summarize the crucial roles of major factors—namely radiation and microgravity—in space in oxidative stress generation in living organisms, and the inhibitory effect of oxidative stress on bone formation. We discussed the possible mechanisms of oxidative stress-induced skeletal involution, and listed some countermeasures that have therapeutic potentials for bone loss via oxidative stress antagonism. Future research for better understanding the oxidative stress caused by space environment and the development of countermeasures against oxidative damage accordingly may facilitate human beings to live more safely in space and explore deeper into the universe.