AIM: To investigate the effect of acute (daily) inhalation of nanoparticles (NPs) on the transcriptomic profile of male nanocomposite research workers with a history of long-term exposure (years). MATERIALS & METHODS: Whole genome mRNA and miRNA expression changes were analyzed from blood samples collected before and after machining or welding. Exposure in the work environment was assessed using stationary and personal monitoring. RESULTS: Following PM0.1 exposure, a significant decrease in the expression of DDIT4 and FKBP5, genes involved in the stress response, was detected in exposed workers. In the Machining group, the DDIT4 expression correlated with the exposure dose. Increased levels of miR30-d-5p and miR-3613-5p (both involved in carcinogenesis) in welders were associated with the NP exposure dose, highlighting their potential suitability as inhalation exposure markers. CONCLUSION: The results from this pilot transcriptomic analysis (mRNA and miRNA) indicate that exposure to NPs contributes to immune system deregulation and alters the pathways related to cancer. Therefore, the use of protective equipment, as well as obtaining more data by additional research, is highly recommended.
This is a follow-up study to our previous research that examined the acute effects of occupational inhalation exposure to nanoparticles (NPs) in females without a previous exposure history. This time, we reexamined the impacts of acute exposure in a group of 18 male workers, including welders and nanocomposite machinists with a long-term previous exposure history at the transcriptomic level. Whole genome transcriptomics studies the complete set of RNA molecules, or transcripts, produced in a cell or organism at a specific time. The analysis allows us to understand which genes are active/inactive, how they are regulated, and how they contribute to various biological processes or diseases. We looked at changes in mRNA and miRNA (types of RNA) from blood samples taken before and after workers were exposed to dust and fumes during machining and welding. We also monitored the exposure doses. The results suggest that inhaled NPs may present an occupational hazard to human health. The transcriptomic analysis shows that exposure to welding fumes and nanocomposite dust from machining affects the immune system and alters cancer-related pathways. Our research helps to understand NP exposure effects and may contribute to minimizing the negative health consequences of their inhalation.
- Klíčová slova
- Occupational exposure, machining, nanoparticles, transcriptome changes, welding,
- MeSH
- dospělí MeSH
- inhalační expozice škodlivé účinky analýza MeSH
- lidé středního věku MeSH
- lidé MeSH
- messenger RNA genetika krev MeSH
- mikro RNA genetika krev MeSH
- nanočástice * škodlivé účinky MeSH
- pracovní expozice * škodlivé účinky analýza MeSH
- stanovení celkové genové exprese MeSH
- transkriptom * účinky léků MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- messenger RNA MeSH
- mikro RNA MeSH
BACKGROUND: Current experimental data on RNA interactions remain limited, particularly for non-coding RNAs, many of which have only recently been discovered and operate within complex regulatory networks. Researchers often rely on in-silico interaction detection algorithms, such as TargetScan, which are based on biochemical sequence alignment. However, these algorithms have limited performance. RNA-seq expression data can provide valuable insights into regulatory networks, especially for understudied interactions such as circRNA-miRNA-mRNA. By integrating RNA-seq data with prior interaction networks obtained experimentally or through in-silico predictions, researchers can discover novel interactions, validate existing ones, and improve interaction prediction accuracy. RESULTS: This paper introduces Pi-GMIFS, an extension of the generalized monotone incremental forward stagewise (GMIFS) regression algorithm that incorporates prior knowledge. The algorithm first estimates prior response values through a prior-only regression, interpolates between these prior values and the original data, and then applies the GMIFS method. Our experimental results on circRNA-miRNA-mRNA regulatory interaction networks demonstrate that Pi-GMIFS consistently enhances precision and recall in RNA interaction prediction by leveraging implicit information from bulk RNA-seq expression data, outperforming the initial prior knowledge. CONCLUSION: Pi-GMIFS is a robust algorithm for inferring acyclic interaction networks when the variable ordering is known. Its effectiveness was confirmed through extensive experimental validation. We proved that RNA-seq data of a representative size help infer previously unknown interactions available in TarBase v9 and improve the quality of circRNA disease annotation.
- Klíčová slova
- Bayesian network, Circular RNA, Functional annotation, Penalized regression, Structure inference,
- MeSH
- algoritmy MeSH
- genové regulační sítě MeSH
- kruhová RNA * genetika metabolismus MeSH
- lidé MeSH
- lineární modely MeSH
- messenger RNA * genetika metabolismus MeSH
- mikro RNA * genetika metabolismus MeSH
- sekvenční analýza RNA metody MeSH
- sekvenování transkriptomu * metody MeSH
- výpočetní biologie metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- kruhová RNA * MeSH
- messenger RNA * MeSH
- mikro RNA * MeSH
The aim of the study was to analyze the variables that modify the levels of oxidative DNA damage and lipid peroxidation in non-smoking mothers and their newborns from environmentally distinct localities of the Czech Republic: Ceske Budejovice (CB, an agricultural region) and Karvina (an industrial region). Personal, socio-economic and medical data, concentrations of particulate matter of aerodynamic diameter < 2.5 µm (PM2.5) and benzo[a]pyrene (B[a]P) in the ambient air, the activities of antioxidant mechanisms (superoxide dismutase, catalase, glutathione peroxidase) and antioxidant capacity), the levels of pro-inflammatory cytokines, the concentrations of persistent organic pollutants (POPs) in blood plasma/cord blood plasma and urinary levels of polycyclic aromatic hydrocarbons metabolites (OH-PAHs) were investigated as parameters potentially affecting the markers of DNA oxidation (8-oxo-7,8-dihydro-2'-deoxyguanosine, 8-oxodG) and lipid peroxidation (15-F2t-isoprostane, 15-F2t-IsoP). Significantly higher levels of POPs were detected in the plasma of mothers/newborns from CB (p < 0.001), while increased external levels of B[a]P and PM2.5, confirmed by analyzing urinary OH-PAHs, were found in Karvina subjects (p < 0.001). In mothers, multivariate analysis showed no significant difference in oxidative stress markers (15-F2t-IsoP, 8-oxodG) between the two localities. The analysis further revealed that neither in CB nor, unexpectedly, in Karvina, did PAH exposure affect maternal lipid peroxidation. Significant associations between OH-PAHs and 15-F2t-IsoP or 8-oxodG were observed only in newborns. In addition, multivariate analyses revealed a borderline significant association between locality and 8-oxodG in the urine of all newborns (p = 0.05). In conclusion, not only the maternal exposure of PAHs but also some POPs can negatively affect oxidative stress status in the early-life of newborns.
- Klíčová slova
- antioxidant response and inflammatory cytokines, environmental pollution, lipid peroxidation, maternal exposure to newborn, oxidative DNA damage,
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Myelodysplastic neoplasms (MDS) are heterogeneous hematopoietic disorders characterized by ineffective hematopoiesis and genome instability. Mobilization of transposable elements (TEs) is an important source of genome instability leading to oncogenesis, whereas small PIWI-interacting RNAs (piRNAs) act as cellular suppressors of TEs. However, the roles of TEs and piRNAs in MDS remain unclear. METHODS: In this study, we examined TE and piRNA expression through parallel RNA and small RNA sequencing of CD34+ hematopoietic stem cells from MDS patients. RESULTS: Comparative analysis of TE and piRNA expression between MDS and control samples revealed several significantly dysregulated molecules. However, significant differences were observed between lower-risk MDS (LR-MDS) and higher-risk MDS (HR-MDS) samples. In HR-MDS, we found an inverse correlation between decreased TE levels and increased piRNA expression and these TE and piRNA levels were significantly associated with patient outcomes. Importantly, the upregulation of PIWIL2, which encodes a key factor in the piRNA pathway, independently predicted poor prognosis in MDS patients, underscoring its potential as a valuable disease marker. Furthermore, pathway analysis of RNA sequencing data revealed that dysregulation of the TE‒piRNA axis is linked to the suppression of processes related to energy metabolism, the cell cycle, and the immune response, suggesting that these disruptions significantly affect cellular activity. CONCLUSIONS: Our findings demonstrate the parallel dysregulation of TEs and piRNAs in HR-MDS patients, highlighting their potential role in MDS progression and indicating that the PIWIL2 level is a promising molecular marker for prognosis.
- Klíčová slova
- Bioinformatics, Biomarkers, Myelodysplastic neoplasms, Next-generation sequencing, Transposable elements, piRNA,
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Presensitized patients with circulating donor-specific antibodies (DSAs) before transplantation are at risk for antibody-mediated rejection (AMR). Peritransplant desensitization mitigates but does not eliminate the alloimmune response. We examined the possibility that subthreshold AMR activity undetected by histology could be operating in some early biopsies. METHODS: Transcriptome of kidney allograft biopsies performed within the first month in presensitized patients (DSA+) who had received desensitization and did not develop active/probable AMR by histology (R-) was compared with biopsies showing active/probable AMR (R+/DSA+). As negative controls, biopsies without rejection by histology in patients without DSA at transplantation were used (R-/DSA-). RNA sequencing from biopsies selected from the biobank was used in cohort 1 (n = 32) and microarray, including the molecular microscope (Molecular Microscope Diagnostic System [MMDx]) algorithm, in recent cohort 2 (n = 30). RESULTS: The transcriptome of R-/DSA+ was similar to R+/DSA+ as these groups differed in 14 transcripts only. Contrarily, large differences were found between both DSA+ groups and negative controls. Fast gene set enrichment analyses showed upregulation of the immune system in both DSA+ groups (gene ontology terms: adaptive immune response, humoral immune response, antigen receptor-mediated signaling, and B-cell receptor signaling or complement activation) when compared with negative controls. MMDx assessment in cohort 2 classified 50% of R-/DSA+ samples as AMR and found no differences in AMR molecular scores between R+ and R- DSA+ groups. In imlifidase desensitization, MMDx series showed a gradual increase in AMR scores over time. CONCLUSIONS: Presensitized kidney transplant recipients exhibited frequent molecular calls of AMR in biopsy-based transcript diagnostics despite desensitization therapy and negative histology.
- Publikační typ
- časopisecké články MeSH
Aim: Today, there is a lack of research studies concerning human acute exposure to nanoparticles (NPs). Our investigation aimed to simulate real-world acute inhalation exposure to NPs released during work with dental nanocomposites in a dental office or technician laboratory. Methods: Blood samples from female volunteers were processed before and after inhalation exposure. Transcriptomic mRNA and miRNA expression changes were analyzed. Results: We detected large interindividual variability, 90 significantly deregulated mRNAs, and 4 miRNAs when samples of participants before and after dental nanocomposite grinding were compared. Conclusion: The results suggest that inhaled dental NPs may present an occupational hazard to human health, as indicated by the changes in the processes related to oxidative stress, synthesis of eicosanoids, and cell division.
What is this article about? We searched for a possible impact of acute inhalation exposure to nanoparticles (NPs) released during the grinding of dental nanocomposites used for teeth reconstruction. The exposure design utilized in our study simulated the acute exposure of the dental staff to the NPs. Our research fills the gaps in knowledge in the field of acute human inhalation exposure to dental nanocomposites.What were the results? Results indicate that the impact of exposure to NPs is dependent on the style of working as well as on the interindividual biological variability among study subjects. Changes in expression levels of genes associated with an increase of oxidative stress, synthesis of eicosanoids (signaling molecules related to e.g., immune responses), and cell division were detected.What do the results of the study mean? All the observed changes may contribute to the pathogenesis of neurodegenerative disorders, carcinogenesis, or problems during pregnancy. Occupational exposure to inhaled NPs, including those generated in dental practice can pose a significant health risk, and protective measures when working with these materials should be considered. More research is needed to compare our results with chronic (long-term) exposure to similar materials to show the hazards related to their inhalation.
- Klíčová slova
- acute exposure, nanocomposite, nanoparticles, stomatology, transcriptomics,
- MeSH
- dospělí MeSH
- inhalační expozice * škodlivé účinky MeSH
- lidé MeSH
- messenger RNA genetika MeSH
- mikro RNA * genetika MeSH
- nanočástice chemie MeSH
- nanokompozity * chemie MeSH
- oxidační stres účinky léků MeSH
- pracovní expozice škodlivé účinky MeSH
- transkriptom * účinky léků MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- messenger RNA MeSH
- mikro RNA * MeSH
We analyzed gene expression in THP-1 cells exposed to metal-based nanomaterials (NMs) [TiO2 (NM-100), ZnO (NM-110), SiO2 (NM-200), Ag (NM-300 K)]. A functional enrichment analysis of the significant differentially expressed genes (DEGs) identified the key modulated biological processes and pathways. DEGs were used to construct protein-protein interaction networks. NM-110 and NM-300 K induced changes in the expression of genes involved in oxidative and genotoxic stress, immune response, alterations of cell cycle, detoxification of metal ions and regulation of redox-sensitive pathways. Both NMs shared a number of highly connected protein nodes (hubs) including CXCL8, ATF3, HMOX1, and IL1B. NM-200 induced limited transcriptional changes, mostly related to the immune response; however, several hubs (CXCL8, ATF3) were identical with NM-110 and NM-300 K. No effects of NM-100 were observed. Overall, soluble nanomaterials NM-110 and NM-300 K exerted a wide variety of toxic effects, while insoluble NM-200 induced immunotoxicity; NM-100 caused no detectable changes on the gene expression level.
- Klíčová slova
- THP-1 cells, gene expression, metal-based nanoparticles, protein-protein interactions,
- MeSH
- hemoxygenasa-1 MeSH
- interleukin-8 metabolismus genetika MeSH
- kovové nanočástice toxicita MeSH
- lidé MeSH
- mapy interakcí proteinů * účinky léků MeSH
- nanostruktury toxicita MeSH
- oxid křemičitý toxicita MeSH
- oxid zinečnatý toxicita chemie MeSH
- stříbro * toxicita MeSH
- THP-1 buňky MeSH
- titan * toxicita MeSH
- transkripční faktor ATF3 genetika metabolismus MeSH
- transkriptom účinky léků MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- ATF3 protein, human MeSH Prohlížeč
- CXCL8 protein, human MeSH Prohlížeč
- hemoxygenasa-1 MeSH
- HMOX1 protein, human MeSH Prohlížeč
- interleukin-8 MeSH
- oxid křemičitý MeSH
- oxid zinečnatý MeSH
- stříbro * MeSH
- titan * MeSH
- titanium dioxide MeSH Prohlížeč
- transkripční faktor ATF3 MeSH
Mutations in the splicing factor 3b subunit 1 (SF3B1) gene are frequent in myelodysplastic neoplasms (MDS). Because the splicing process is involved in the production of circular RNAs (circRNAs), we investigated the impact of SF3B1 mutations on circRNA processing. Using RNA sequencing, we measured circRNA expression in CD34+ bone marrow MDS cells. We defined circRNAs deregulated in a heterogeneous group of MDS patients and described increased circRNA formation in higher-risk MDS. We showed that the presence of SF3B1 mutations did not affect the global production of circRNAs; however, deregulation of specific circRNAs was observed. Particularly, we demonstrated that strong upregulation of circRNAs processed from the zinc finger E-box binding homeobox 1 (ZEB1) transcription factor; this upregulation was exclusive to SF3B1-mutated patients and was not observed in those with mutations in other splicing factors or other recurrently mutated genes, or with other clinical variables. Furthermore, we focused on the most upregulated ZEB1-circRNA, hsa_circ_0000228, and, by its knockdown, we demonstrated that its expression is related to mitochondrial activity. Using microRNA analyses, we proposed miR-1248 as a direct target of hsa_circ_0000228. To conclude, we demonstrated that mutated SF3B1 leads to deregulation of ZEB1-circRNAs, potentially contributing to the defects in mitochondrial metabolism observed in SF3B1-mutated MDS.
- Klíčová slova
- SF3B1, ZEB1, circular RNA, myelodysplastic neoplasms, splicing,
- MeSH
- akutní myeloidní leukemie * MeSH
- fosfoproteiny genetika MeSH
- kruhová RNA genetika MeSH
- lidé MeSH
- mutace genetika MeSH
- myelodysplastické syndromy * genetika MeSH
- sestřihové faktory genetika MeSH
- transkripční faktory genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- fosfoproteiny MeSH
- kruhová RNA MeSH
- sestřihové faktory MeSH
- SF3B1 protein, human MeSH Prohlížeč
- transkripční faktory MeSH
This study evaluated how exposure to the ubiquitous air pollution component, ultrafine particles (UFPs), alters the olfactory bulb (OB) transcriptome. The study utilised a whole-body inhalation chamber to simulate real-life conditions and focused on UFPs due to their high translocation and deposition ability in OBs as well as their prevalence in ambient air. Female C57BL/6J mice were exposed to clean air or to freshly generated combustion derived UFPs for two weeks, after which OBs were dissected and mRNA transcripts were investigated using RNA sequencing analysis. For the first time, transcriptomics was applied to determine changes in mRNA expression levels occurring after subacute exposure to UFPs in the OBs. We found forty-five newly described mRNAs to be involved in air pollution-induced responses, including genes involved in odorant binding, synaptic regulation, and myelination signalling pathway, providing new gene candidates for future research. This study provides new insights for the environmental science and neuroscience fields and nominates future research directions.
- Klíčová slova
- Air pollution, Brain, Myelin protein zero (Mpz), Odorant-binding protein (OBP), Olfactory bulb, Ultrafine particles (UFP),
- MeSH
- biologické markery metabolismus MeSH
- bulbus olfactorius chemie metabolismus MeSH
- látky znečišťující vzduch * toxicita analýza MeSH
- messenger RNA metabolismus MeSH
- myši inbrední C57BL MeSH
- myši MeSH
- pevné částice toxicita analýza MeSH
- stanovení celkové genové exprese MeSH
- transkriptom MeSH
- velikost částic MeSH
- znečištění ovzduší * analýza MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- biologické markery MeSH
- látky znečišťující vzduch * MeSH
- messenger RNA MeSH
- pevné částice MeSH
Metagenomics provides a tool to assess the functional potential of environmental and host-associated microbiomes based on the analysis of environmental DNA: assembly, gene prediction and annotation. While gene prediction is straightforward for most bacterial and archaeal taxa, it has limited applicability in the majority of eukaryotic organisms, including fungi that contain introns in gene coding sequences. As a consequence, eukaryotic genes are underrepresented in metagenomics datasets and our understanding of the contribution of fungi and other eukaryotes to microbiome functioning is limited. Here, we developed a machine intelligence-based algorithm that predicts fungal introns in environmental DNA with reasonable precision and used it to improve the annotation of environmental metagenomes. Intron removal increased the number of predicted genes by up to 9.1% and improved the annotation of several others. The proportion of newly predicted genes increased with the share of eukaryotic genes in the metagenome and-within fungal taxa-increased with the number of introns per gene. Our approach provides a tool named SVMmycointron for improved metagenome annotation, especially of microbiomes with a high proportion of eukaryotes. The scripts described in the paper are made publicly available and can be readily utilized by microbiome researchers analysing metagenomics data.
- Klíčová slova
- artificial intelligence, eukaryote, fungi, gene prediction, intron, metagenomics,
- Publikační typ
- časopisecké články MeSH
