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

WormSpace μ-TAS enabling automated on-chip multi-strain culturing and multi-function imaging of Caenorhabditis elegans at the single-worm level on the China Space Station

As a model organism for space biology experiments, Caenorhabditis elegans (C. elegans) has low demand for life support and strong resistance to unfavorable environments, making experimentation with C. elegans relatively easy and cost-effective. Previously, C. elegans has been flown in several spaceflight investigations, but there is still an urgent need for analytical platforms enabling on-orbit automated monitoring of multiple phenotypes of worms, such as growth and development, movement, changes of biomarkers, etc. To solve this problem, we presented a fully integrated microfluidic system (WormSpace μ-TAS) with an arrayed microfluidic chip (WormChip-4.8.1) and a replaceable microfluidic module (WormChip cartridge), which was compatible with the experimental facility on the China Space Station (CSS). By adopting technologies of programmed fluid control based on liquid medium CeMM as well as multi-function imaging with a camera mounted on a three-dimensional (3D) transportation stage, automated and long-term experimentation can be performed for on-chip multi-strain culturing and bright-field and fluorescence imaging of C. elegans at the single-worm level. The presented WormSpace μ-TAS enabled its successful application on the CSS, achieving flight launch of the sample unit (WormChip cartridge) at low temperature (controlled by a passive thermal case at 12 °C), automated 30-day cultivation of 4 strains of C. elegans, on-orbit monitoring of multiple phenotypes (growth and development, movement, and changes of fluorescent protein expression) at the single worm-level, on-chip fixation of animals at the end of the experiment and returning the fixed samples to earth. In summary, this study presented a verified microfluidic system and experimental protocols for automated on-chip multi-strain culturing and multi-function imaging of C. elegans at the single-worm level on the CSS. The WormSpace μ-TAS will provide a novel experimental platform for the study of biological effects of space radiation and microgravity, and for the development of protective drugs.

Transcriptome reveals the roles and potential mechanisms of lncRNAs in the regulation of albendazole resistance in Haemonchus contortus

BACKGROUND

Haemonchus contortus (H. contortus) is the most common parasitic nematode in ruminants and is prevalent worldwide. H. contortus resistance to albendazole (ABZ) hinders the efficacy of anthelmintic drugs, but little is known about the molecular mechanisms that regulate this of drug resistance. Recent research has demonstrated that long noncoding RNAs (lncRNAs) can exert significant influence as pivotal regulators of the emergence of drug resistance.

RESULTS

In this study, transcriptome sequencing was conducted on both albendazole-sensitive (ABZ-sensitive) and albendazole-resistant (ABZ-resistant) H. contortus strains, with three biological replicates for each group. The analysis of lncRNA in the transcriptomic data revealed that there were 276 differentially expressed lncRNA (DElncRNA) between strains with ABZ-sensitive and ABZ-resistant according to the criteria of |log2Foldchange|≥ 1 and FDR < 0.05. Notably, MSTRG.12969.2 and MSTRG.9827.1 exhibited the most significant upregulation and downregulation, respectively, in the resistant strains. The potential roles of the DElncRNAs included catalytic activity, stimulus response, regulation of drug metabolism, and modulation of the immune response. Moreover, we investigated the interactions between DElncRNAs and other RNAs, specifically MSTRG.12741.1, MSTRG.11848.1, MSTRG.5895.1, and MSTRG.14070.1, involved in regulating drug stimulation through cis/trans/antisense/lncRNA‒miRNA-mRNA interaction networks. This regulation leads to a decrease (or increase) in the expression of relevant genes, consequently enhancing the resistance of H. contortus to albendazole. Furthermore, through comprehensive analysis of competitive endogenous RNAs (ceRNAs) involved in drug resistance-related pathways, such as the mTOR signalling pathway and ABC transporter signalling pathway, the relevance of the MSTRG.2499.1-novel-m0062-3p-HCON_00099610 interaction was identified to mainly involve the regulation of catalytic activity, metabolism, ubiquitination and transcriptional regulation of gene promoters. Additionally, quantitative real-time polymerase chain reaction (qRT-PCR) validation indicated that the transcription profiles of six DElncRNAs and six DEmRNAs were consistent with those obtained by RNA-seq.

CONCLUSIONS

The results of the present study allowed us to better understand the changes in the lncRNA expression profile of ABZ-resistant H. contortus. In total, these results suggest that the lncRNAs MSTRG.963.1, MSTRG.12741.1, MSTRG.11848.1 and MSTRG.2499.1 play important roles in the development of ABZ resistance and can serve as promising biomarkers for further study.

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.

Multi-Omic Profiling, Structural Characterization, and Potent Inhibitor Screening of Evasion-Related Proteins of a Parasitic Nematode, Haemonchus contortus, Surviving Vaccine Treatment

The emergence of drug-resistant parasitic nematodes in both humans and livestock calls for development of alternative and cost-effective control strategies. Barbervax^® is the only registered vaccine for the economically important ruminant strongylid Haemonchus contortus. In this study, we compared the microbiome, genome-wide diversity, and transcriptome of H. contortus adult male populations that survived vaccination with an experimental vaccine after inoculation in sheep. Our genome-wide SNP analysis revealed 16 putative candidate vaccine evasion genes. However, we did not identify any evidence for changes in microbial community profiling based on the 16S rRNA gene sequencing results of the vaccine-surviving parasite populations. A total of fifty-eight genes were identified as significantly differentially expressed, with six genes being long non-coding (lnc) RNAs and none being putative candidate SNP-associated genes. The genes that highly upregulated in surviving parasites from vaccinated animals were associated with GO terms belonging to predominantly molecular functions and a few biological processes that may have facilitated evasion or potentially lessened the effect of the vaccine. These included five targets: astacin (ASTL), carbonate dehydratase (CA2), phospholipase A2 (PLA2), glutamine synthetase (GLUL), and fatty acid-binding protein (FABP3). Our tertiary structure predictions and modelling analyses were used to perform in silico searches of all published and commercially available inhibitor molecules or substrate analogs with potential broad-spectrum efficacy against nematodes of human and veterinary importance.

A review of transgenerational and multigenerational toxicology in the in vivo model animal Caenorhabditis elegans

A large number of pollutants existing in the environment can last for a long time, and their potential toxic effects can transfer from parents to their offspring. Thus, it is necessary to investigate the toxicity of environmental pollutants across multigenerations and the underlying mechanisms in organisms. Due to its short life cycle and sensitivity to environmental exposures, Caenorhabditis elegans is an important animal model for toxicity assessment of environmental pollutants across multigenerations. In this review, we introduced the transgenerational and multigenerational toxicity caused by various environmental pollutants in C. elegans. Moreover, we discussed the underlying mechanisms for the observed transgenerational and multigenerational toxicity of environmental contaminants in C. elegans.

Nanoplastics: Focus on the role of microRNAs and long non-coding RNAs

When plastic objects in our surroundings are degraded, they may produce particles ranging in size from 1 to 100 nm therefore called nanoplastics. The environmental chemicals including nanoplastics may be able to affect biological processes in the nuclear level like altering DNA methylation and regulating microRNAs (miRNAs) as well as long non-coding RNAs (lncRNAs) expression and therefore are implicated in chronic human diseases like neoplasms. The regulatory role of miRNAs and lncRNAs in gene expression is appreciated. In vitro as well as in vivo experiments have shown that environmental elements including nanoplastics are able to dysregulate miRNAs and lncRNAs expression with possible genetic consequences that increase the risk of cancer development. In the current article, we review the biological effects of miRNAs and lncRNAs alterations following nanoplastics exposure.

Polystyrene nanoparticles cause dynamic alteration in mitochondrial unfolded protein response from parents to the offspring in C. elegans

The mitochondrial unfolded protein response (mt UPR) is important for organisms against the toxicity from toxicants and stresses. Polystyrene nanoparticle (PS-NP), one of the emerging pollutants, has aroused increasing concern for its toxicity in the offspring. Nevertheless, the molecular basis for this transgenerational toxicity remains largely unclear. In this study, the role of mt UPR in the induction of transgenerational toxicity was determined in Caenorhabditis elegans (C. elegans) after parental exposure to PS-NP. After exposure to PS-NP (1-100 μg/L), the suppression in mt UPR showed the concentration-dependent in nematodes from P0 generation (P0-G) to F2-G. Moreover, the decreased expression of genes required for controlling mt UPR (atfs-1, dve-1, and ubl-5 genes) were observed from P0-G to F2-G after exposure to PS-NP (1 μg/L). The adverse effects on locomotion and reproductive capacity were more severe over generations in nematodes with RNAi of these three genes, indicating that these genes were involved in controlling transgenerational toxicity. After parental PS-NP exposure (1 μg/L), the mt UPR was significantly inhibited by RNAi of atfs-1, dve-1, and ubl-5, indicating the association between the transgenerational PS-NP toxicity and mt UPR suppression. Additionally, during the transgenerational process, RNAi of atfs-1, dve-1, and ubl-5 enhanced the PS-NP toxicity by suppressing mt UPR, while RNAi of daf-2 encoding an insulin receptor inhibited the PS-NP toxicity by increasing mt UPR. Therefore, our data highlighted the role of inhibition in mt UPR in mediating the transgenerational nanoplastic toxicity in nematodes.

Induction of transgenerational toxicity is associated with the activated germline insulin signals in nematodes exposed to nanoplastic at predicted environmental concentrations

Exposure to nanoplastics can induce toxicity on organisms at both parental generation (P0-G) and the offspring. However, the underlying mechanism remains unknown. Using Caenorhabditis elegans as a model organism, exposure to 20-nm polystyrene nanoparticle (PS-NP) (1-100 μg/L) upregulated the expressions of insulin ligands (INS-39, INS-3, and DAF-28), and this increase could be further detected in the offspring after PS-NP exposure. Germline ins-39, ins-3, and daf-28 RNAi induced resistance to transgenerational toxicity of PS-NP, indicating that increase in expression of these three insulin ligands mediated induction of transgenerational toxicity. These three insulin ligands transgenerationally activated function of insulin receptor DAF-2 to control transgenerational toxicity of PS-NP. Exposure to 1-100 μg/L PS-NP further upregulated DAF-2, AGE-1, and AKT-1 expressions and downregulated DAF-16 expression. During transgenerational toxicity control, DAF-16/AKT-1/AGE-1 was identified as downstream signaling cascade of DAF-2. Moreover, transcriptional factor DAF-16 activated two downstream targets of HSP-6 (a mitochondrial UPR marker) and SOD-3 (a mitochondrial SOD) to modulate transgenerational toxicity of PS-NP. Our findings indicate a crucial link between activation of insulin signaling and induction of transgenerational toxicity of nanoplastics at low concentrations in organisms.

Multi-walled carbon nanotubes induce transgenerational toxicity associated with activation of germline long non-coding RNA linc-7 in C.elegans

With the increase in application, multi-walled carbon nanotubes (MWCNTs) are potentially bioavailable to environmental organisms. However, the potential transgenerational effect of MWCNTs and underlying mechanisms remains still unclear. Here, we examined transgenerational MWCNT toxicity and the underlying mechanism mediated by germline long non-coding RNAs (lncRNAs) in Caenorhabditis elegans. Exposure to 0.1-10 μg/L MWCNT caused transgenerational toxicity reflected by endpoints of brood size and locomotion behavior. Meanwhile, among germline lncRNAs, expression of 5 lncRNAs were dysregulated by MWCNT exposure. Among these 5 dysregulated lncRNAs, only germline RNAi of linc-7 affected MWCNT toxicity. Increase in germline linc-7 expression was observed transgenerationally, and transgenerational MWCNT toxicity was prevented in linc-7(RNAi) nematodes. Moreover, germline linc-7 controlled transgenerational MWCNT toxicity by activating downstream DAF-12, a transcriptional factor. Therefore, our data indicated the association between induction of transgenerational MWCNT toxicity and increase in germline linc-7 expression in organisms.

Long-term exposure to polystyrene nanoparticles causes transgenerational toxicity by affecting the function and expression of MEV-1 and DAF-2 signals in Caenorhabditis elegans

In this study, we determined the roles of oxidative stress and related signals in mediating transgenerational toxicity of 30 nm polystyrene nanoparticles (PS-NPs) in Caenorhabditis elegans. Using brood size and locomotion behavior as endpoints, exposure to 1-100 μg/L PS-NPs caused transgenerational toxicity. Meanwhile, the activation of reactive oxygen species (ROS) was also observed transgenerationally after exposure to 1-100 μg/L PS-NPs. After exposure to 1 μg/L PS-NPs, the transgenerational toxicity was monitored until F2 generation (F2-G) and recovered at F3-G. At the F1-G of 1 μg/L PS-NPs-exposed nematodes, RNAi knockdown of daf-2 with function to inhibit oxidative stress suppressed the transgenerational toxicity and increased the mitochondrial SOD-3 expression. In contrast, at F3-G of 1 μg/L PS-NPs-exposed nematodes, RNAi knockdown of mev-1 with function to induce oxidative stress promoted locomotion and brood size, and suppressed the SOD-3 expression. Moreover, we observed the dynamic expressions of mev-1, daf-2, and sod-2 transgenerationally after exposure to 1 μg/L PS-NPs at P0-G, which further suggested the involvement of MEV-1, DAF-2, and SOD-3 in affecting induction of transgenerational PS-NP toxicity. Therefore, we provided the evidence to suggest the roles of oxidative stress activation and related molecular signals in mediating induction of transgenerational PS-NP toxicity. Our data highlights the crucial function of oxidative stress-related signals during induction of transgenerational PS-NP toxicity.

Neuronal Gα subunits required for the control of response to polystyrene nanoparticles in the range of μg/L in C. elegans

The aim of this study was to identify Gα proteins mediating function of neuronal G protein-coupled receptors (GPCRs) in controlling the response to polystyrene nanoparticles (PS-NPs). Caenorhabditis elegans was used as an animal model, and both gene expression and functional analysis were performed to identify the Gα proteins in controlling PS-NPs toxicity. In nematodes, exposure to PS-NPs (1-100 μg/L) significantly altered transcriptional expressions of some neuronal Gα genes, including gpa-5, gpa-10, gpa-11, gpa-15 gsa-1, egl-30, and goa-1. Among these 7 Gα genes, only neuronal RNAi knockdown of gsa-1, gpa-10, and goa-1 affected toxicity of PS-NPs in inducing ROS production and in decreasing locomotion behavior. Some neuronal GPCRs (such as GTR-1, DCAR-1, DOP-2, NPR-8, NPR-12, NPR-9, and DAF-37) functioned upstream of GOA-1, some neuronal GPCRs (such as DCAR-1, DOP-2, NPR-9, NPR-8, and DAF-37) functioned upstream of GSA-1, and some neuronal GPCRs (such as DOP-2, NPR-8, DAF-37, and DCAR-1) functioned upstream of GPA-10 to regulate the toxicity of PS-NPs. Moreover, GOA-1 acted upstream of MPK-1/ERK MAPK, JNK-1/JNK MAPK, DBL-1/TGF-β, and DAF-7/ TGF-β, GSA-1 functioned upstream of MPK-1/ERK MAPK, JNK-1/JNK MAPK, and DBL-1/TGF-β, and GPA-10 functioned upstream of GLB-1/Globin and DBL-1/TGF-β to control the PS-NPs toxicity. Therefore, neuronal Gα proteins of GOA-1, GSA-1, and GPA-10 functioned to transduce signals of multiple GPCRs to different downstream signaling pathways during the control of PS-NPs toxicity in nematodes. Our results provide clues for understanding the important function of GPCRs-Gα signaling cascade in the neurons in controlling response to nanoplastics in organisms.

Size-dependent transgenerational toxicity induced by nanoplastics in nematode Caenorhabditis elegans

Nanoplastic exposure can potentially cause the severe transgenerational toxicity in organisms. However, the transgenerational nanoplastic toxicity and the underlying mechanisms are still largely unclear. Using Caenorhabditis elegans as an animal model, we here compared the transgenerational toxicity of two sizes of polystyrene nanoparticles (PS-NPs, 20 and 100 nm). The nematodes were exposed to PS-NPs at the P0 generation, and from the F1 generation the nematodes were grown under the normal condition. Exposure to 20 nm PS-NPs resulted in more severe transgenerational toxicity than exposure to 100 nm PS-NPs. At the concentration of 100 μg/L, the toxicity of 20 nm PS-NPs on locomotion and reproduction was detected at the F1-F6 generations, whereas the toxicity of 100 nm PS-NPs could only be observed at the F1-F3 generations. The difference in transgeneration toxicity between PS-NPs (20 nm) and PS-NPs (100 nm) was associated with the difference in transgenerational activation of oxidative stress. Based on observations on SOD-3::GFP, HSP-6::GFP, and HSP-4::GFP expressions, PS-NPs (20 nm) and PS-NPs (100 nm) further induced different transgenerational responses of anti-oxidation, mt UPR, and ER UPR. Our data suggested that the induction of transgenerational toxicity of PS-NPs was size dependent in nematodes. The results are helpful for our understanding the cellular mechanisms for the induction of transgenerational nanoplastic toxicity in organisms.

Biosafety assessment of Acinetobacter strains isolated from the Three Gorges Reservoir region in nematode Caenorhabditis elegans

Acinetobacter has been frequently detected in backwater areas of the Three Gorges Reservoir (TGR) region. We here employed Caenorhabditis elegans to perform biosafety assessment of Acinetobacter strains isolated from backwater area in the TGR region. Among 21 isolates and 5 reference strains of Acinetobacter, exposure to Acinetobacter strains of AC1, AC15, AC18, AC21, A. baumannii ATCC 19606T, A. junii NH88-14, and A. lwoffii DSM 2403T resulted in significant decrease in locomotion behavior and reduction in lifespan of Caenorhabditis elegans. In nematodes, exposure to Acinetobacter strains of AC1, AC15, AC18, AC21, A. baumannii, A. junii and A. lwoffii also resulted in significant reactive oxygen species (ROS) production. Moreover, exposure to Acinetobacter isolates of AC1, AC15, AC18, and AC21 led to significant increase in expressions of both SOD-3::GFP and some antimicrobial genes (lys-1, spp-12, lys-7, dod-6, spp-1, dod-22, lys-8, and/or F55G11.4) in nematodes. The Acinetobacter isolates of AC1, AC15, AC18, and AC21 had different morphological, biochemical, phylogenetical, and virulence gene properties. Our results suggested that exposure risk of some Acinetobacter strains isolated from the TGR region exists for environmental organisms and human health. In addition, C. elegans is useful to assess biosafety of Acinetobacter isolates from the environment.

Induction of protective response to polystyrene nanoparticles associated with dysregulation of intestinal long non-coding RNAs in Caenorhabditis elegans

Intestinal barrier plays a crucial function during the response to polystyrene nanoparticles (PS-NPs) in nematode Caenorhabditis elegans. Long non-coding RNAs (lncRNAs) are involved in the control of various biological processes, including stress response. We here used C. elegans to determine intestinal lncRNAs dysregulated by PS-NPs (1-100 μg/L). In intestine of PS-NPs exposed worms, we found four lncRNAs (linc-61, linc-50, linc-9, and linc-2) in response to PS-NPs and with the function in controlling PS-NPs toxicity. The alteration in expressions of these four intestinal lncRNAs reflected a protective response to PS-NPs exposure. During the response to PS-NPs, limited number of transcriptional factors functioned as the downstream targets of these four lncRNAs. linc-2 acted upstream of DAF-16, linc-9 acted upstream of NHR-77, linc-50 functioned upstream of DAF-16, and linc-61 regulated the functions of DAF-16, DVE-1, and FKH-2 to control PS-NPs toxicity. The obtained data demonstrated the important role of lncRNAs in intestinal barrier to mediate a protective response to PS-NPs exposure at low concentrations.

Dysregulated mir-76 mediated a protective response to nanopolystyrene by modulating heme homeostasis related molecular signaling in nematode Caenorhabditis elegans

The underlying mechanisms of microRNAs (miRNAs) in regulating nanoplastic toxicity are still largely unclear in organisms. In nanopolystyrene (NPS) exposed Caenorhabditis elegans, the expression of mir-76 (a neuronal miRNA) was significantly decreased, and the mir-76 mutant was resistant to the toxicity of NPS. The aim of this study was to determine the molecular basis of mir-76 in controlling NPS toxicity in nematodes. The mir-76 mutation increased expression of glb-10 encoding a globin protein in NPS (1 μg/L) exposed nematodes. Exposure to NPS (1-100 μg/L) increased the glb-10 expression, and the glb-10(RNAi) worm was susceptible to NPS toxicity in inducing reactive oxygen species (ROS) production and in decreasing locomotion behavior. Using ROS production and locomotion behavior as endpoints, mutation of glb-10 inhibited resistance of mir-76 mutant to NPS toxicity, and neuronal overexpression of mir-76 inhibited the resistance to NPS toxicity in nematodes overexpressing neuronal glb-10 containing 3' untranslated region (3'UTR). Thus, GLB-10 functioned as a target of mir-76 in the neurons to regulate the NPS toxicity. Moreover, a signaling cascade of HRG-7-HRG-5 required for the control of heme homeostasis was identified to function downstream of neuronal GLB-10 to regulate the NPS toxicity. In this signaling cascade, the neuronal HRG-7 regulated the NPS toxicity by antagonizing function of intestinal HRG-5. Furthermore, in the intestine, HRG-5 controlled NPS toxicity by inhibiting functions of hypoxia-inducible transcriptional factor HIF-1 and transcriptional factor ELT-2. Our results highlight the crucial function of heme homeostasis related signaling in regulating the NPS toxicity in organisms.

Induction of Protective Response Associated with Expressional Alterations in Neuronal G Protein-Coupled Receptors in Polystyrene Nanoparticle Exposed Caenorhabditis elegans

In this study, the association of expressional alterations in neuronal G protein-coupled receptors (GPCRs) with induction of protective response to polystyrene nanoparticles (PS-NPs) was investigated in Caenorhabditis elegans. On the basis of both phenotypic analysis and expression levels, the alterations in expressions of NPR-1, NPR-4, NPR-8, NPR-9, NPR-12, DCAR-1, GTR-1, DOP-2, SER-4, and DAF-37 in neuronal cells mediated the protective response to PS-NPs exposure. In neuronal cells, NPR-9, NPR-12, DCAR-1, and GTR-1 controlled the PS-NPs toxicity by activating or inhibiting JNK-1/JNK MAPK signaling. Neuronal NPR-8, NPR-9, DCAR-1, DOP-2, and DAF-37 controlled the PS-NPs toxicity by activating or inhibiting MPK-1/ERK MAPK signaling. Neuronal NPR-4, NPR-8, NPR-9, NPR-12, GTR-1, DOP-2, and DAF-37 controlled the PS-NPs toxicity by activating or inhibiting DBL-1/TGF-β signaling. Neuronal NPR-1, NPR-4, NPR-12, and GTR-1 controlled the PS-NPs toxicity by activating or inhibiting DAF-7/TGF-β signaling. Our data provides an important neuronal basis for induction of protective response to PS-NPs in C. elegans.