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      Robust differential gene expression patterns in the prefrontal cortex of male mice exposed to an occupationally relevant dose of laboratory-generated wildfire smoke

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          Abstract

          Wildfires have become common global phenomena concurrent with warmer and drier climates and are now major contributors to ambient air pollution worldwide. Exposure to wildfire smoke has been classically associated with adverse cardiopulmonary health outcomes, especially in vulnerable populations. Recent work has expanded our understanding of wildfire smoke toxicology to include effects on the central nervous system and reproductive function; however, the neurotoxic profile of this toxicant remains ill-explored in an occupational context. Here, we sought to address this by using RNA sequencing to examine transcriptomic signatures in the prefrontal cortex of male mice modeling career wildland firefighter smoke exposure. We report robust changes in gene expression profiles between smoke-exposed samples and filtered air controls, evidenced by 2,862 differentially expressed genes (51.2% increased). We further characterized the functional relevance of these genes highlighting enriched pathways related to synaptic transmission, neuroplasticity, blood–brain barrier integrity, and neurotransmitter metabolism. Additionally, we identified possible contributors to these alterations through protein–protein interaction network mapping, which revealed a central node at ß-catenin and secondary hubs centered around mitochondrial oxidases, the Wnt signaling pathway, and gene expression machinery. The data reported here will serve as the foundation for future experiments aiming to characterize the phenotypic effects and mechanistic underpinnings of occupational wildfire smoke neurotoxicology.

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          REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

          Outcomes of high-throughput biological experiments are typically interpreted by statistical testing for enriched gene functional categories defined by the Gene Ontology (GO). The resulting lists of GO terms may be large and highly redundant, and thus difficult to interpret. REVIGO is a Web server that summarizes long, unintelligible lists of GO terms by finding a representative subset of the terms using a simple clustering algorithm that relies on semantic similarity measures. Furthermore, REVIGO visualizes this non-redundant GO term set in multiple ways to assist in interpretation: multidimensional scaling and graph-based visualizations accurately render the subdivisions and the semantic relationships in the data, while treemaps and tag clouds are also offered as alternative views. REVIGO is freely available at http://revigo.irb.hr/.
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            iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

            Background RNA-seq is widely used for transcriptomic profiling, but the bioinformatics analysis of resultant data can be time-consuming and challenging, especially for biologists. We aim to streamline the bioinformatic analyses of gene-level data by developing a user-friendly, interactive web application for exploratory data analysis, differential expression, and pathway analysis. Results iDEP (integrated Differential Expression and Pathway analysis) seamlessly connects 63 R/Bioconductor packages, 2 web services, and comprehensive annotation and pathway databases for 220 plant and animal species. The workflow can be reproduced by downloading customized R code and related pathway files. As an example, we analyzed an RNA-Seq dataset of lung fibroblasts with Hoxa1 knockdown and revealed the possible roles of SP1 and E2F1 and their target genes, including microRNAs, in blocking G1/S transition. In another example, our analysis shows that in mouse B cells without functional p53, ionizing radiation activates the MYC pathway and its downstream genes involved in cell proliferation, ribosome biogenesis, and non-coding RNA metabolism. In wildtype B cells, radiation induces p53-mediated apoptosis and DNA repair while suppressing the target genes of MYC and E2F1, and leads to growth and cell cycle arrest. iDEP helps unveil the multifaceted functions of p53 and the possible involvement of several microRNAs such as miR-92a, miR-504, and miR-30a. In both examples, we validated known molecular pathways and generated novel, testable hypotheses. Conclusions Combining comprehensive analytic functionalities with massive annotation databases, iDEP (http://ge-lab.org/idep/) enables biologists to easily translate transcriptomic and proteomic data into actionable insights. Electronic supplementary material The online version of this article (10.1186/s12859-018-2486-6) contains supplementary material, which is available to authorized users.
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              Critical Review of Health Impacts of Wildfire Smoke Exposure

              Background: Wildfire activity is predicted to increase in many parts of the world due to changes in temperature and precipitation patterns from global climate change. Wildfire smoke contains numerous hazardous air pollutants and many studies have documented population health effects from this exposure. Objectives: We aimed to assess the evidence of health effects from exposure to wildfire smoke and to identify susceptible populations. Methods: We reviewed the scientific literature for studies of wildfire smoke exposure on mortality and on respiratory, cardiovascular, mental, and perinatal health. Within those reviewed papers deemed to have minimal risk of bias, we assessed the coherence and consistency of findings. Discussion: Consistent evidence documents associations between wildfire smoke exposure and general respiratory health effects, specifically exacerbations of asthma and chronic obstructive pulmonary disease. Growing evidence suggests associations with increased risk of respiratory infections and all-cause mortality. Evidence for cardiovascular effects is mixed, but a few recent studies have reported associations for specific cardiovascular end points. Insufficient research exists to identify specific population subgroups that are more susceptible to wildfire smoke exposure. Conclusions: Consistent evidence from a large number of studies indicates that wildfire smoke exposure is associated with respiratory morbidity with growing evidence supporting an association with all-cause mortality. More research is needed to clarify which causes of mortality may be associated with wildfire smoke, whether cardiovascular outcomes are associated with wildfire smoke, and if certain populations are more susceptible. Citation: Reid CE, Brauer M, Johnston FH, Jerrett M, Balmes JR, Elliott CT. 2016. Critical review of health impacts of wildfire smoke exposure. Environ Health Perspect 124:1334–1343; http://dx.doi.org/10.1289/ehp.1409277
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                Author and article information

                Contributors
                Journal
                Toxicol Sci
                Toxicol Sci
                toxsci
                Toxicological Sciences
                Oxford University Press
                1096-6080
                1096-0929
                October 2024
                06 August 2024
                06 August 2024
                : 201
                : 2
                : 300-310
                Affiliations
                Department of Environmental and Radiological Health Sciences, Colorado State University , Fort Collins, CO 80523, United States
                Department of Bioengineering, Northeastern University , Boston, MA 02120, United States
                Department of Health and Exercise Science, Colorado State University , Fort Collins, CO 80523, United States
                Department of Bioengineering, Northeastern University , Boston, MA 02120, United States
                Department of Bioengineering, Northeastern University , Boston, MA 02120, United States
                Department of Bioengineering, Northeastern University , Boston, MA 02120, United States
                Department of Environmental and Radiological Health Sciences, Colorado State University , Fort Collins, CO 80523, United States
                Author notes
                Corresponding author: Department of Environmental and Radiological Health Sciences, Colorado State University, 350 W Lake St, Fort Collins, CO 80538, United States. E-mail: luke.montrose@ 123456colostate.edu
                Author information
                https://orcid.org/0000-0001-9669-0680
                Article
                kfae097
                10.1093/toxsci/kfae097
                11424885
                39107885
                2bdf2c24-9b54-4dcb-964b-0ef21bf82323
                © The Author(s) 2024. Published by Oxford University Press on behalf of the Society of Toxicology.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 10 August 2024
                Page count
                Pages: 12
                Funding
                Funded by: NIH, DOI 10.13039/100000002;
                Funded by: NIGMS, DOI 10.13039/100000057;
                Award ID: P20GM103408
                Funded by: Boise State COBRE program in Matrix Biology;
                Funded by: NIH, DOI 10.13039/100000002;
                Award ID: P20GM109095
                Categories
                Neurotoxicology
                AcademicSubjects/MED00305
                AcademicSubjects/SCI01040

                Pharmacology & Pharmaceutical medicine
                wildfire smoke,wildland firefighter,occupational health,transcriptomics

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