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1. Transcriptomic Evidence That Switching from Tobacco to Electronic Cigarettes Does Not Reverse Damage to the Respiratory Epithelium

   https://doi.org/10.3390/toxics10070370  

   Pozuelos, Giovanna L.; Kagda, Meenakshi; Rubin, Matine A.; Goniewicz, Maciej L.; Girke, Thomas; Talbot, Prue (July 2022, Toxics)

   The health benefits of switching from tobacco to electronic cigarettes (ECs) are neither confirmed nor well characterized. To address this problem, we used RNA-seq analysis to compare the nasal epithelium transcriptome from the following groups (n = 3 for each group): (1) former smokers who completely switched to second generation ECs for at least 6 months, (2) current tobacco cigarette smokers (CS), and (3) non-smokers (NS). Group three included one former cigarette smoker. The nasal epithelial biopsies from the EC users vs. NS had a higher number of differentially expressed genes (DEGs) than biopsies from the CS vs. NS and CS vs. EC sets (1817 DEGs total for the EC vs. NS, 407 DEGs for the CS vs. NS, and 116 DEGs for the CS vs. EC comparison). In the EC vs. NS comparison, enriched gene ontology terms for the downregulated DEGs included cilium assembly and organization, whereas gene ontologies for upregulated DEGs included immune response, keratinization, and NADPH oxidase. Similarly, ontologies for cilium movement were enriched in the downregulated DEGs for the CS vs. NS group. Reactome pathway analysis gave similar results and also identified keratinization and cornified envelope in the upregulated DEGs in the EC vs. NS comparison. In the CS vs. NS comparison, the enriched Reactome pathways for upregulated DEGs included biological oxidations and several metabolic processes. Regulator effects identified for the EC vs. NS comparison were inflammatory response, cell movement of phagocytes and degranulation of phagocytes. Disease Ontology Sematic Enrichment analysis identified lung disease, mouth disease, periodontal disease and pulmonary fibrosis in the EC vs. NS comparison. Squamous metaplasia associated markers, keratin 10, keratin 13 and involucrin, were increased in the EC vs. NS comparison. Our transcriptomic analysis showed that gene expression profiles associated with EC use are not equivalent to those from non-smokers. EC use may interfere with airway epithelium recovery by promoting increased oxidative stress, inhibition of ciliogenesis, and maintaining an inflammatory response. These transcriptomic alterations may contribute to the progression of diseases with chronic EC use. 

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2. In planta transcriptomics reveals conflicts between pattern-triggered immunity and the AlgU sigma factor regulon

   https://doi.org/10.1371/journal.pone.0274009  

   Wang, Haibi; Smith, Amy; Lovelace, Amelia; Kvitko, Brian H. (September 2022, PLOS ONE)

   Lai, Erh-Min (Ed.)

   In previous work, we determined the transcriptomic impacts of flg22 pre-induced Pattern Triggered Immunity (PTI) in Arabidopsis thaliana on the pathogen Pseudomonas syringae pv. tomato DC3000 ( Pto ). During PTI exposure we observed expression patterns in Pto reminiscent of those previously observed in a Pto algU mutant. AlgU is a conserved extracytoplasmic function sigma factor which has been observed to regulate over 950 genes in Pto in growth media. We sought to identify the AlgU regulon when the bacteria are inside the plant host and which PTI-regulated genes overlapped with AlgU-regulated genes. In this study, we analyzed transcriptomic data from RNA-sequencing to identify the AlgU regulon (while in the host) and its relationship with PTI. Our results showed that the upregulation of 224 genes while inside the plant host require AlgU, while another 154 genes are downregulated dependent on AlgU in Arabidopsis during early infection. Both stress response and virulence-associated genes were upregulated in a manner dependent on AlgU, while the flagellar motility genes are downregulated in a manner dependent on AlgU. Under the pre-induced PTI condition, more than half of these AlgU-regulated genes have lost induction/suppression in contrast to mock treated plants, and almost all function groups regulated by AlgU were affected by PTI. 

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3. Determination of Biomarkers for Diagnosis of Lung Cancer Using Cytoscape-based GO and Pathway Analysis

   Maharjan, Mona; Tanvir, Raihanul Bari; Chowdhury, Kamal; Mondal, Ananda Mohan (July 2019, The 20th International Conference on Bioinformatics and Computational Biology)

   Lung cancer is the second most common cancer in the world. The aim of this study is to identify biomarkers for lung cancer that can aid in its diagnosis and treatment. The gene expression profiles from GEO database were analyzed by GEO2R to identify Differentially Expressed Genes (DEGs) and further analyzed using Cytoscape. The data was divided into two categories: non-treatment and treatment groups. A total of 407 DEGs (254 upregulated and 153 downregulated) and 259 DEGs (124 upregulated and 135 downregulated) were isolated for non-treatment and treatment studies respectively. The significant Gene Ontologies and pathways enriched with DEGS were identified using Cytoscape apps, BiNGO and ReactomeFIPlugIn, respectively. Hub genes based on network parameters - Degree, Closeness and Betweenness - were isolated using CytoHubba. In conclusion, DEGs identified in this study may play an important role in early diagnosis or as biomarkers of lung cancer. 

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4. Differential Defense Responses of Upland and Lowland Switchgrass Cultivars to a Cereal Aphid Pest

   https://doi.org/10.3390/ijms21217966  

   Pingault, Lise; Palmer, Nathan A.; Koch, Kyle G.; Heng-Moss, Tiffany; Bradshaw, Jeffrey D.; Seravalli, Javier; Twigg, Paul; Louis, Joe; Sarath, Gautam (November 2020, International Journal of Molecular Sciences)

   Yellow sugarcane aphid (YSA) (Sipha flava, Forbes) is a damaging pest on many grasses. Switchgrass (Panicum virgatum L.), a perennial C4 grass, has been selected as a bioenergy feedstock because of its perceived resilience to abiotic and biotic stresses. Aphid infestation on switchgrass has the potential to reduce the yields and biomass quantity. Here, the global defense response of switchgrass cultivars Summer and Kanlow to YSA feeding was analyzed by RNA-seq and metabolite analysis at 5, 10, and 15 days after infestation. Genes upregulated by infestation were more common in both cultivars compared to downregulated genes. In total, a higher number of differentially expressed genes (DEGs) were found in the YSA susceptible cultivar (Summer), and fewer DEGs were observed in the YSA resistant cultivar (Kanlow). Interestingly, no downregulated genes were found in common between each time point or between the two switchgrass cultivars. Gene co-expression analysis revealed upregulated genes in Kanlow were associated with functions such as flavonoid, oxidation-response to chemical, or wax composition. Downregulated genes for the cultivar Summer were found in co-expression modules with gene functions related to plant defense mechanisms or cell wall composition. Global analysis of defense networks of the two cultivars uncovered differential mechanisms associated with resistance or susceptibility of switchgrass in response to YSA infestation. Several gene co-expression modules and transcription factors correlated with these differential defense responses. Overall, the YSA-resistant Kanlow plants have an enhanced defense even under aphid uninfested conditions. 

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5. Genome-wide identification and characterization of Solanum tuberosum BiP genes reveal the role of the promoter architecture in BiP gene diversity

   https://doi.org/10.1038/s41598-020-68407-2  

   Herath, Venura; Gayral, Mathieu; Adhikari, Nirakar; Miller, Rita; Verchot, Jeanmarie (July 2020, Scientific Reports)

   Abstract The endoplasmic reticulum (ER) immunoglobulin binding proteins (BiPs) are molecular chaperones involved in normal protein maturation and refolding malformed proteins through the unfolded protein response (UPR). Plant BiPs belong to a multi-gene family contributing to development, immunity, and responses to environmental stresses. This study identified threeBiPhomologs in theSolanum tuberosum(potato) genome using phylogenetic, amino acid sequence, 3-D protein modeling, and gene structure analysis. These analyses revealed thatStBiP1andStBiP2grouped withAtBiP2, whereasStBiP3grouped withAtBiP3. While the protein sequences and folding structures are highly similar, theseStBiPsare distinguishable by their expression patterns in different tissues and in response to environmental stressors such as treatment with heat, chemicals, or virus elicitors of UPR. Ab initio promoter analysis revealed that potato and ArabidopsisBiP1andBiP2promoters were highly enriched with cis-regulatory elements (CREs) linked to developmental processes, whereasBiP3promoters were enriched with stress related CREs. The frequency and linear distribution of these CREs produced two phylogenetic branches that further resolve the groups identified through gene phylogeny and exon/intron phase analysis. These data reveal that the CRE architecture ofBiPpromoters potentially define their spatio-temporal expression patterns under developmental and stress related cues. 

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