Proteomic and transcriptomic analysis of lung tissue in OVA-challenged mice

The impact of inflammation and acute phase activation in cancer cachexia

The development of cachexia in the setting of cancer or other chronic diseases is a significant detriment for patients. Cachexia is associated with a decreased ability to tolerate therapies, reduction in ambulation, reduced quality of life, and increased mortality. Cachexia appears intricately linked to the activation of the acute phase response and is a drain on metabolic resources. Work has begun to focus on the important inflammatory factors associated with the acute phase response and their role in the immune activation of cachexia. Furthermore, data supporting the liver, lung, skeletal muscle, and tumor as all playing a role in activation of the acute phase are emerging. Although the acute phase is increasingly being recognized as being involved in cachexia, work in understanding underlying mechanisms of cachexia associated with the acute phase response remains an active area of investigation and still lack a holistic understanding and a clear causal link. Studies to date are largely correlative in nature, nonetheless suggesting the possibility for a role for various acute phase reactants. Herein, we examine the current literature regarding the acute phase response proteins, the evidence these proteins play in the promotion and exacerbation of cachexia, and current evidence of a therapeutic potential for patients.

Identification of Molecular Markers Related to Immune Infiltration in Patients with Severe Asthma: A Comprehensive Bioinformatics Analysis Based on the Human Bronchial Epithelial Transcriptome

Background. Severe asthma (SA), a heterogeneous inflammatory disease characterized by immune cell infiltration, is particularly difficult to treat and manage. The airway epithelium is an important tissue in regulating innate and adaptive immunity, and targeting airway epithelial cell may contribute to improving the efficacy of asthma therapy. Methods. Bioinformatics methods were utilized to identify the hub genes and signaling pathways involved in SA. Experiments were performed to determine whether these hub genes and signaling pathways were affected by the differences in immune cell infiltration. Results. The weighted gene coexpression network analysis identified 14 coexpression modules, among which the blue and salmon modules exhibited the strongest associations with SA. The blue module was mainly enriched in actomyosin structure organization and was associated with regulating stem cell pluripotency signaling pathways. The salmon module was mainly involved in cornification, skin development, and glycosphingolipid biosynthesis-lacto and neolacto series. The protein-protein interaction network and module analysis identified 11 hub genes in the key modules. The CIBERSORTx algorithm revealed statistically significant differences in CD8+ T cells ( $P=0.013$ ), T follicular helper cells ( $P=0.002$ ), resting mast cells ( $P=0.004$ ), and neutrophils ( $P=0.002$ ) between patients with SA and mild-moderate asthma patients. Pearson’s correlation analysis identified 11 genes that were significantly associated with a variety of immune cells. We further predicted the utility of some potential drugs and validated our results in external datasets. Conclusion. Our results may help provide a better understanding of the relationship between the airway epithelial transcriptome and clinical data of SA. And this study will help to guide the development of SA-targeted molecular therapy.

Single-Cell RNA-Seq Analysis Reveals Lung Epithelial Cell Type-Specific Responses to HDM and Regulation by Tet1

Tet1 protects against house dust mite (HDM)-induced lung inflammation in mice and alters the lung methylome and transcriptome. In order to explore the role of Tet1 in individual lung epithelial cell types in HDM-induced inflammation, we established a model of HDM-induced lung inflammation in Tet1 knockout and littermate wild-type mice, then studied EpCAM+ lung epithelial cells using single-cell RNA-seq analysis. We identified eight EpCAM+ lung epithelial cell types, among which AT2 cells were the most abundant. HDM challenge altered the relative abundance of epithelial cell types and resulted in cell type-specific transcriptomic changes. Bulk and cell type-specific analysis also showed that loss of Tet1 led to the altered expression of genes linked to augmented HDM-induced lung inflammation, including alarms, detoxification enzymes, oxidative stress response genes, and tissue repair genes. The transcriptomic regulation was accompanied by alterations in TF activities. Trajectory analysis supports that HDM may enhance the differentiation of AP and BAS cells into AT2 cells, independent of Tet1. Collectively, our data showed that lung epithelial cells had common and unique transcriptomic signatures of allergic lung inflammation. Tet1 deletion altered transcriptomic networks in various lung epithelial cells, which may promote allergen-induced lung inflammation.

Effects of Edible Insect Tenebrio molitor Larva Fermentation Extract as a Substitute Protein on Hepatosteatogenesis and Proteomic Changes in Obese Mice Induced by High-Fat Diet

Mealworms (Tenebrio molitor larva) are an edible insect and a protein-rich food; however, research on mealworms as a substitute protein is insufficient. In this study, mealworm fermentation extract (TMP) was assessed as a replacement for soy protein (SP) in a control diet (CON) or a high-fat diet (HFD) of mice for 12 weeks. TMP substitution reduced body weight, body weight gain, body fat mass (perirenal and mesenteric), fat size, glucose intolerance, and insulin resistance compared to the HFD-SP group. TMP alleviated hepatic steatosis (lipid contents and lipid droplets) in high-fat-fed mice and down-regulated the PPARγ, CD36, and DGAT2 gene levels. Proteomic analysis showed that a HFD for 12 weeks up-regulated 20 proteins and down-regulated 17 proteins in mice fed SP. On the other hand, TMP reversed the protein profiles. TMP significantly down-regulated KHK, GLO1, ATP5H, SOD, and DDAH1 and up-regulated DLD, Mup1, CPS1, Ces3b, PDI, and HYOU1 compared to the HFD-SP group. These proteins are involved in the glucose, lipid, and amino acid metabolism, as well as in oxidative stress and endoplasmic reticulum stress. Thus, substituting SP for TMP helped improve HFD-induced obesity, steatosis, and insulin resistance in mice. These results suggest that TMP is a potential substitute for commonly used protein sources.

The application of proteomics in the diagnosis and treatment of bronchial asthma

Bronchial asthma is a common chronic inflammatory disease of the airways. Although its pathogenic mechanism remains unknown, it is influenced by both genetic and environmental factors. The emergence and application of proteomic technologies can help to facilitate analysis of the changes in transcription factors, inflammatory mediators, chemokines, cytokines, and cell apoptosis-and proliferation-related proteins in the pathological processes of asthma. Proteomic technologies can unearth prospects and theoretical bases for improved understanding of the biological mechanism of asthma and effective identification of diagnostic and therapeutic targets.

Transcriptional Profiles of Murine Bone Marrow-Derived Dendritic Cells in Response to Peste des Petits Ruminants Virus

Background: Peste des petits ruminants virus (PPRV) is the causative agent of PPR, which can cause an acute, highly contagious and fatal disease of sheep and goats, resulting in significant economic losses for commercial animal husbandry due to its high mortality and morbidity. As professional antigen-presenting cells, dendritic cells (DCs) play a unique role in innate immunity. This study aimed to gain a deeper understanding of the transcriptional response of bone marrow-derived dendritic cells (BMDCs) stimulated with PPRV. Results: Transcriptional profiling was performed using RNA sequencing. Herein, we reported that compared to untreatedBMDCs, 4492 differentially expressed genes (DEGs) were identified following PPRV stimulation, out of these DEGs 2311 were upregulated and 2181 were downregulated, respectively. A total of three gene ontology (GO) term clusters of biological process, cell component and molecular function were significantly enriched in 963 GO terms in the PPRV-stimulated BMDCs. These GO clusters were related to inflammatory response, cell division and vacuole, anchoring junction, positive regulation of cellular component and nucleoside binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of DEGs were enriched in a chemokine signaling pathway, protein processing in endoplasmic reticulum, cell cycle and mTOR signaling pathway. Additionally, identified DEGs of BMDCs were further validated by qRT-PCR and the results were in accordance with the change of the genes. This study suggested the effects of PPRV stimulation on the maturation and function of BMDCs. Conclusion: We found that the dramatic BMDCs transcriptome changes triggered were predominantly related to an inflammatory response and chemokine signaling pathway.