Tacrolimus alleviates pulmonary fibrosis progression through inhibiting the activation and interaction of ILC2 and monocytes.

Idiopathic pulmonary fibrosis (IPF) is a heterogeneous group of lung diseases with different etiologies and characterized by progressive fibrosis. This disease usually causes pulmonary structural remodeling and decreased pulmonary function. The median survival of IPF patients is 2-5 years. Predominantly accumulation of type II innate immune cells accelerates fibrosis progression by secreting multiple pro-fibrotic cytokines. Group 2 innate lymphoid cells (ILC2) and monocytes/macrophages play key roles in innate immunity and aggravate the formation of pro-fibrotic environment. As a potent immunosuppressant, tacrolimus has shown efficacy in alleviating the progression of pulmonary fibrosis. In this study, we found that tacrolimus is capable of suppressing ILC2 activation, monocyte differentiation and the interaction of these two cells. This effect further reduced activation of monocyte-derived macrophages (Mo-M), thus resulting in a decline of myofibroblast activation and collagen deposition. The combination of tacrolimus and nintedanib was more effective than either drug alone. This study will reveal the specific process of tacrolimus alleviating pulmonary fibrosis by regulating type II immunity, and explore the potential feasibility of tacrolimus combined with nintedanib in the treatment of pulmonary fibrosis. This project will provide new ideas for clinical optimization of anti-pulmonary fibrosis drug strategies.

IL20Rb aggravates pulmonary fibrosis through enhancing bone marrow derived profibrotic macrophage activation.

Idiopathic pulmonary fibrosis (IPF) is one of the most fatal chronic interstitial lung diseases with unknown pathogenesis, current treatments cannot truly reverse the progression of the disease. Pulmonary macrophages, especially bone marrow derived pro-fibrotic macrophages, secrete multiple kinds of profibrotic mediators (SPP1, CD206, CD163, IL-10, CCL18…), thus further promote myofibroblast activation and fibrosis procession. IL20Rb is a cell-surface receptor that belongs to IL-20 family. The role of IL20Rb in macrophage activation and pulmonary fibrosis remains unclear. In this study, we established a bleomycin-induced pulmonary fibrosis model, used IL4/13-inducing THP1 cells to induce profibrotic macrophage (M2-like phenotype) polarization models. We found that IL20Rb is upregulated in the progression of pulmonary fibrosis, and its absence can alleviate the progression of pulmonary fibrosis. In addition, we demonstrated that IL20Rb promote the activation of bone marrow derived profibrotic macrophages by regulating the Jak2/Stat3 and Pi3k/Akt signaling pathways. In terms of therapeutic strategy, we used IL20Rb neutralizing antibodies for animal administration, which was found to alleviate the progression of IPF. Our results suggest that IL20Rb plays a profibrotic role by promoting profibrotic macrophage polarization, and IL20Rb may become a potential therapeutic target for IPF. Neutralizing antibodies against IL20Rb may become a potential drug for the clinical treatment of IPF.

Favipiravir ameliorates bleomycin-induced pulmonary fibrosis by reprogramming M1/M2 macrophage polarization.

Corona Virus Disease 2019 (COVID-19) is an infectious disease that seriously endangers human life and health. The pathological anatomy results of patients who died of the COVID-19 showed that there was an excessive inflammatory response in the lungs. It is also known that most of the COVID-19 infected patients will cause different degrees of lung damage after infection, and may have pulmonary fibrosis remaining after cure. Macrophages are a type of immune cell population with pluripotency and plasticity. In the early and late stages of infection, the dynamic changes of the balance and function of M1/M2 alveolar macrophages have a significant impact on the inflammatory response of the lungs. In the early stage of pulmonary fibrosis inflammation, the increase in the proportion of M1 type is beneficial to clear pathogenic microorganisms and promote the progress of inflammation; in the later stage of fibrosis, the increase in the number of M2 type macrophages can inhibit the inflammatory response and promote the degradation of fibrosis. As a potential treatment drug for new coronavirus pneumonia, favipiravir is in the process of continuously carried out relevant clinical trials. This study aims to discuss whether the antiviral drug favipiravir can suppress inflammation and immune response by regulating the M1/M2 type of macrophages, thereby alleviating fibrosis. We established a bleomycin-induced pulmonary fibrosis model, using IL-4/13 and LPS/IFN-γ cell stimulating factor to induce macrophage M1 and M2 polarization models, respectively. Our study shows that favipiravir exerts anti-fibrotic effects mainly by reprogramming M1/M2 macrophages polarization, that is, enhancing the expression of anti-fibrotic M1 type, reducing the expression of M2 type pro-fibrotic factors and reprogramming it to anti-fibrotic phenotype. Aspects of pharmacological mechanisms, favipiravir inhibits the activation of JAK2-STAT6 and JAK2-PI3K-AKT signaling by targeting JAK2 protein, thereby inhibiting pro-fibrotic M2 macrophages polarization and M2-induced myofibroblast activation. In summary, favipiravir can reduce the progression of pulmonary fibrosis, we hope to provide a certain reference for the treatment of pulmonary fibrosis.

Deciphering recursive polyploidization in Lamiales and reconstructing their chromosome evolutionary trajectories.

Lamiales is an order of core eudicots with abundant diversity, and many Lamiales plants have important medicinal and ornamental values. Here, we comparatively reanalyzed 11 Lamiales species with well-assembled genome sequences and found evidence that Lamiales plants, in addition to a hexaploidization or whole-genome triplication (WGT) shared by core eudicots, experienced further polyploidization events, establishing new groups in the order. Notably, we identified a whole-genome duplication (WGD) occurred just before the split of Scrophulariaceae from the other Lamiales families, such as Acanthaceae, Bignoniaceae, and Lamiaceae, suggesting its likely being the causal reason for the establishment and fast divergence of these families. We also found that a WGT occurred ∼68 to 78 million years ago (Mya), near the split of Oleaceae from the other Lamiales families, implying that it may have caused their fast divergence and the establishment of the Oleaceae family. Then, by exploring and distinguishing intra- and intergenomic chromosomal homology due to recursive polyploidization and speciation, respectively, we inferred that the Lamiales ancestral cell karyotype had 11 proto-chromosomes. We reconstructed the evolutionary trajectories from these proto-chromosomes to form the extant chromosomes in each Lamiales plant under study. We must note that most of the inferred 11 proto-chromosomes, duplicated during a WGD thereafter, have been well preserved in jacaranda (Jacaranda mimosifolia) genome, showing the credibility of the present inference implementing a telomere-centric chromosome repatterning model. These efforts are important to understand genome repatterning after recursive polyploidization, especially shedding light on the origin of new plant groups and angiosperm cell karyotype evolution.

Effects of vacuum microwave combined with freeze-drying on the physicochemical properties, phenolic compounds, and antioxidant capacity of pear fruit slices.

The effects of freeze-drying (FD), vacuum microwave drying after freeze-drying (FD-VMD), and freeze-drying after vacuum microwave drying (VMD-FD) on the physicochemical properties, phenolic compounds, and antioxidant capacity of pear fruit slices were investigated. The results showed that FD samples had the highest crispness value (116.30 N·sec) and the lowest volume shrinkage ratio value (5.48%). Compared to FD, the VMD-FD and FD-VMD methods could save drying time without affecting the color of dried samples. FD-VMD samples had the lowest rehydration capacity and maintained a homogeneous porous structure, while the VMD-FD samples had obvious collapse. Compared to VMD-FD samples, FD-VMD samples had higher contents of ascorbic acid (20.91 mg/100 g), total phenolic (7.62 mg/g), total anthocyanin (0.21 mg/g), and gallic acid (1.21 µg/g). Moreover, FD-VMD samples showed the highest antioxidant capacity as evaluated by the 2,2-diphenyl-1-(2,4,6-trinitrophenyl) hydrazyl scavenging activity, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) scavenging capacity, and H2 O2 content. Compared with FD and VMD-FD, FD-VMD was most effective in maintaining better quality and shortening drying time of pear fruit slices. These findings suggested that FD-VMD might be a promising drying technique in the fruits and vegetable processing industries.

GNAEMDA: Microbe-Drug Associations Prediction on Graph Normalized Convolutional Network.

The importance of microbe-drug associations (MDA) prediction is evidenced in research. Since traditional wet-lab experiments are both time-consuming and costly, computational methods are widely adopted. However, existing research has yet to consider the cold-start scenarios that commonly seen in real-world clinical research and practices where data of confirmed microbe-drug associations are highly sparse. Therefore, we aim to contribute by developing two novel computational approaches, the GNAEMDA (Graph Normalized Auto-Encoder to predict Microbe-Drug Associations), and a variational extension of the GNAEMDA (called VGNAEMDA), to provide effective and efficient solutions for well-annotated cases and cold-start scenarios. Multi-modal attribute graphs are constructed by collecting multiple features of microbes and drugs, and then input into a graph normalized convolutional network, where a l2-normalization is introduced to avoid the norm-towards-zero tendency of isolated nodes in embedding space. Then the reconstructed graph output by the network is used to infer undiscovered MDA. The difference between the proposed two models lays in the way to generate the latent variables in network. To verify the effectiveness of the two proposed models, we conduct a series of experiments on three benchmark datasets in comparison with six state-of-the-art methods. The comparison results indicate that both GNAEMDA and VGNAEMDA have strong prediction performances in all cases, especially in identifying associations for new microbes or drugs. In addition, we conduct case studies on two drugs and two microbes and find that more than 75% of the predicted associations have been reported in PubMed. The comprehensive experimental results validate the reliability of our models in accurately inferring potential MDA.

Postharvest melatonin treatment enhanced antioxidant activity and promoted GABA biosynthesis in yellow-flesh peach.

The effects of postharvest melatonin treatment on antioxidant activity and γ-aminobutyric acid (GABA) biosynthesis in yellow-flesh peach fruit stored at 4 °C and 90% RH for 28 d were explored. Results showed that melatonin treatment was effective in maintaining firmness, total soluble solids content and color in peach fruit. Melatonin treatment significantly reduced H2O2 and MDA contents, enhanced high level of non-enzymatic antioxidant system (ABTS∙+ scavenging capacity), and increased the activity or content of antioxidant enzymes including CAT, POD, SOD and APX. Melatonin treatment increased the contents of total soluble protein and glutamate, while reducing total free amino acid content. Moreover, melatonin treatment up-regulated the expression of GABA biosynthesis genes (PpGAD1 and PpGAD4) and suppressed the expression of GABA degradation gene (PpGABA-T), resulting in the accumulation of endogenous GABA. These findings indicated that melatonin treatment exerted positive effects on improving antioxidant activity and promoting GABA biosynthesis in yellow-flesh peach fruit.

Machine learning-based prediction of candidate gene biomarkers correlated with immune infiltration in patients with idiopathic pulmonary fibrosis.

Objective: This study aimed to identify candidate gene biomarkers associated with immune infiltration in idiopathic pulmonary fibrosis (IPF) based on machine learning algorithms. Methods: Microarray datasets of IPF were extracted from the Gene Expression Omnibus (GEO) database to screen for differentially expressed genes (DEGs). The DEGs were subjected to enrichment analysis, and two machine learning algorithms were used to identify candidate genes associated with IPF. These genes were verified in a validation cohort from the GEO database. Receiver operating characteristic (ROC) curves were plotted to assess the predictive value of the IPF-associated genes. The cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm was used to evaluate the proportion of immune cells in IPF and normal tissues. Additionally, the correlation between the expression of IPF-associated genes and the infiltration levels of immune cells was examined. Results: A total of 302 upregulated and 192 downregulated genes were identified. Functional annotation, pathway enrichment, Disease Ontology and gene set enrichment analyses revealed that the DEGs were related to the extracellular matrix and immune responses. COL3A1, CDH3, CEBPD, and GPIHBP1 were identified as candidate biomarkers using machine learning algorithms, and their predictive value was verified in a validation cohort. Additionally, ROC analysis revealed that the four genes had high predictive accuracy. The infiltration levels of plasma cells, M0 macrophages and resting dendritic cells were higher and those of resting natural killer (NK) cells, M1 macrophages and eosinophils were lower in the lung tissues of patients with IPF than in those of healthy individuals. The expression of the abovementioned genes was correlated with the infiltration levels of plasma cells, M0 macrophages and eosinophils. Conclusion: COL3A1, CDH3, CEBPD, and GPIHBP1 are candidate biomarkers of IPF. Plasma cells, M0 macrophages and eosinophils may be involved in the development of IPF and may serve as immunotherapeutic targets in IPF.

Predicting miRNA-Disease Associations via Node-Level Attention Graph Auto-Encoder.

Previous studies have confirmed microRNA (miRNA), small single-stranded non-coding RNA, participates in various biological processes and plays vital roles in many complex human diseases. Therefore, developing an efficient method to infer potential miRNA disease associations could greatly help understand operational mechanisms for diseases at the molecular level. However, during these early stages for miRNA disease prediction, traditional biological experiments are laborious and expensive. Therefore, this study proposes a novel method called AGAEMD (node-level Attention Graph Auto-Encoder to predict potential MiRNA Disease associations). We first create a heterogeneous matrix incorporating miRNA similarity, disease similarity, and known miRNA-disease associations. Then these matrixes are input into a node-level attention encoder-decoder network which utilizes low dimensional dense embeddings to represent nodes and calculate association scores. To verify the effectiveness of the proposed method, we conduct a series of experiments on two benchmark datasets (the Human MicroRNA Disease Database v2.0 and v3.2) and report the averages over 10 runs in comparison with several state-of-the-art methods. Experimental results have demonstrated the excellent performance of AGAEMD in comparison with other methods. Three important diseases (Colon Neoplasms, Lung Neoplasms, Lupus Vulgaris) were applied in case studies. The results comfirm the reliable predictive performance of AGAEMD.

The Effectiveness and Safety of Huangqi Xixin Decoction for Cough Variant Asthma: A Systematic Review and Meta-Analysis.

Objective: A comprehensive and systematic review is needed to evaluate the safety and effectiveness of Huangqi Xixin decoction (HQXXD) for cough variant asthma (CVA). In this systematic review, we comprehensively interrogate the safety and effectiveness of HQXXD for CVA. Methods: An overall search for studies in main English and Chinese electronic databases from their inception to June 30, 2022, was performed. Randomized controlled trials (RCTs) involving HQXXD for CVA were included. According to Cochrane Reviewer's Handbook, the risk of bias related to the included studies was evaluated. A meta-analysis using RevMan 5.4 software from the Cochrane Collaboration was used to integrate the outcomes of the included RCTs. Results: A systematic review and meta-analysis were conducted using the seven eligible RCTs that had been retrieved. The included RCT-related risk of bias was evaluated. According to the findings of the meta-analysis, the HQXXD group had significantly higher total effective rates of clinical efficacy and airway responsiveness, and a significantly lower recurrence rate in comparison with the conventional Western medicine treatment group. Conclusion: In the treatment of CVA patients, HQXXD is safe and effective, which benefits clinical efficacy and airway responsiveness, reduces the recurrence rate, and has no adverse effects.

A novel defined cuproptosis-related gene signature for predicting the prognosis of lung adenocarcinoma.

Lung adenocarcinoma (LUAD) has become the most prevalent histologic subset of primary lung cancer, and effective innovative prognostic models are needed to enhance the feasibility of targeted therapies for the disease. Programmed cell death (PCD) performs an integral function in the origin and treatment of cancer. Some PCD-related effective signatures for predicting prognosis in LUAD patients could provide potential therapeutic options in LUAD. A copper-dependent cell death referred to as cuproptosis is distinct from known PCD. However, whether cuproptosis is associated with LUAD patients' prognoses and the potential roles of cuproptosis-related genes involved is still unknown. For the prediction of LUAD prognosis, we developed a unique cuproptosis-associated gene signature. In The Cancer Genome Atlas (TCGA) cohort, the score derived from the risk signature on the basis of six cuproptosis-related genes was found to independently serve as a risk factor for anticipating lung cancer-related death. The differentially expressed genes between the high- and low-risk groups were linked to the cilium-related function. LUAD patients' prognoses may now be predicted by a unique gene signature identified in this work. This discovery also provides a substantial foundation for future research into the links between cuproptosis-associated genes and cilium-related function in LUAD patients.

Pickering emulsion hydrogel based on alginate-gellan gum with carboxymethyl chitosan as a pH-responsive controlled release delivery system.

Pickering emulsion hydrogels (PEHs) were developed as a pH-responsive, controlled-release delivery system to address the limitations of Pickering emulsions in some harsh processing or gastrointestinal conditions. Specifically, the PEHs were fabricated based on alginate and various concentrations of gellan gum (GG) with carboxymethyl chitosan (CMCS) matrix. The encapsulation efficiency (EE), Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD) results proved the successful encapsulation. Furthermore, the hydrogels remained stable in the presence of destabilizing ions (Na+ or phosphate ions) and high osmotic pressure mediums. The texture profile analysis (TPA) characteristics and Young's modulus of the 0.8 % GG (w/v) PEHs were superior to the others. The PEHs prevented the emulsions from being released at pH 2.0, while the emulsions were entirely released at pH 7.4 in vitro, with the rate of release controlled by CMCS and the degree by GG concentration. This work facilitates the delivery of Pickering emulsions with excellent stability and pH-responsive controlled release for hydrophobic actives in food applications.

Elevated Expression of Growth Differentiation Factor-15 Is Associated With Acute Exacerbation of Idiopathic Pulmonary Fibrosis.

Backgrounds: Growth differentiation factor 15 (GDF-15) is a highly divergent member of the TGF-ß superfamily and has been implicated in various biological functions. However, the expression of GDF-15 in patients with acute exacerbation of idiopathic pulmonary fibrosis (AE-IPF) is unclear. Method: The study included 47 AE-IPF patients, 61 stable IPF (S-IPF) subjects, and 31 healthy controls (HCs). Serum GDF-15 levels and their expression in the lung were measured. The correlation between serum GDF-15 and other clinical parameters and the risk factors for AE occurrence and the survival of IPF patients were analyzed. Results: Serum GDF-15 levels were significantly elevated in AE-IPF patients (1279.22 ± 540.02 pg/ml) as compared with HCs (891.30 ± 479.90 pg/ml) or S-IPF subjects (107.82 ± 14.21 pg/ml) (both p < 0.001). The protein and mRNA expressions of GDF-15 in the lung of AE-IPF patients were significantly increased as compared with S-IPF cases (p = 0.007 and p = 0.026, respectively). The serum GDF-15 level was correlated with the clinical variables of inflammation, metabolism, and disease severity in IPF subjects (all p < 0.05). The GDF-15 serum concentration was significantly higher in decedents than in survivors (p = 0.005). A serum GDF-15 level above 989.3 pg/ml was a risk factor for AE occurrence (p = 0.04), and the level above 1,075.76 pg/ml was an independent predictor for survival in IPF cases (p = 0.007). Conclusions: The GDF-15 level was significantly elevated in subjects with AE-IPF. GDF-15 could be a promising biomarker for AE occurrence and survival in IPF patients.

Danggui Buxue Decoction Ameliorates Idiopathic Pulmonary Fibrosis through MicroRNA and Messenger RNA Regulatory Network.

OBJECTIVE: To develop a putative microRNA (miRNA) and messenger RNA (mRNA) regulatory network of Danggui Buxue decoction's (DGBXD) amelioration of idiopathic pulmonary fibrosis (IPF). METHODS: The Gene Expression Omnibus (GEO) database was used to identify differentially expressed miRNAs (DE-miRNAs) and differentially expressed mRNAs (DE-mRNAs). Using miRNet, the predicted target genes of identified DE-miRNAs were estimated, and then the target genes of DE-miRNAs in IPF were comprehensively examined. The Enrichr database was used to conduct functional enrichment and pathway enrichment. Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was employed to obtain the target genes of DGBXD as well as active compounds. A putative miRNA-mRNA regulatory network of DGBXD acting on IPF was developed by intersecting the target genes of DGBXD with the DE-miRNA target genes in IPF. A bleomycin-induced mouse model was established and used to perform histopathology as well as real-time quantitative polymerase chain reaction (qRT-PCR) analyses of some miRNA-mRNA pairs. RESULTS: Fourteen upmodulated DE-miRNAs and six downmodulated DE-miRNAs were screened. The downstream target genes of upmodulated and downmodulated DE-miRNAs were predicted. Subsequently, 1160 upmodulated DE-mRNAs and 1427 downmodulated DE-mRNAs were identified. Then, target genes of DE-miRNAs comprising 49 downmodulated and 53 upmodulated target genes were further screened to perform functional enrichment and pathway enrichment analyses. Subsequently, 196 target genes of DGBXD were obtained from TCMSP, with six downregulated target genes and six upregulated target genes of DGBXD acting on IPF being identified. A promising miRNA-mRNA regulatory network of DGBXD acting on IPF was developed in this study. Moreover, mir-493 together with its target gene Olr1 and mir-338 together with Hif1a were further validated by qRT-PCR. CONCLUSION: This study proposed detailed possible processes of miRNA-mRNA modulatory axis in IPF and constructed a prospective IPF-related miRNA-mRNA modulatory network with the aim of alleviating IPF with DGBXD.