NFATc3 and VIP in Idiopathic Pulmonary Fibrosis and Chronic Obstructive Pulmonary Disease

Integration of scRNA-seq data by disentangled representation learning with condition domain adaptation

BACKGROUND

The integration of single-cell RNA sequencing data from multiple experimental batches and diverse biological conditions holds significant importance in the study of cellular heterogeneity.

RESULTS

To expedite the exploration of systematic disparities under various biological contexts, we propose a scRNA-seq integration method called scDisco, which involves a domain-adaptive decoupling representation learning strategy for the integration of dissimilar single-cell RNA data. It constructs a condition-specific domain-adaptive network founded on variational autoencoders. scDisco not only effectively reduces batch effects but also successfully disentangles biological effects and condition-specific effects, and further augmenting condition-specific representations through the utilization of condition-specific Domain-Specific Batch Normalization layers. This enhancement enables the identification of genes specific to particular conditions. The effectiveness and robustness of scDisco as an integration method were analyzed using both simulated and real datasets, and the results demonstrate that scDisco can yield high-quality visualizations and quantitative outcomes. Furthermore, scDisco has been validated using real datasets, affirming its proficiency in cell clustering quality, retaining batch-specific cell types and identifying condition-specific genes.

CONCLUSION

scDisco is an effective integration method based on variational autoencoders, which improves analytical tasks of reducing batch effects, cell clustering, retaining batch-specific cell types and identifying condition-specific genes.

The role of vasoactive intestinal peptide in pulmonary diseases

Vasoactive intestinal peptide (VIP) is an abundant neurotransmitter in the lungs and other organs. Its discovery dates back to 1970. And VIP gains attention again due to the potential application in COVID-19 after a research wave in the 1980s and 1990s. The diverse biological impacts of VIP extend beyond its usage in COVID-19 treatment, encompassing its involvement in various pulmonary and systemic disorders. This review centers on the function of VIP in various lung diseases, such as pulmonary arterial hypertension, chronic obstructive pulmonary disease, asthma, cystic fibrosis, acute lung injury/acute respiratory distress syndrome, pulmonary fibrosis, and lung tumors. This review also outlines two main limitations of VIP as a potential medication and gathers information on extended-release formulations and VIP analogues.

NFATc3 Promotes Pulmonary Inflammation and Fibrosis by Regulating Production of CCL2 and CXCL2 in Macrophages

Idiopathic pulmonary fibrosis (IPF) is a progressive and highly lethal inflammatory interstitial lung disease characterized by aberrant extracellular matrix deposition. Macrophage activation by cytokines released from repetitively injured alveolar epithelial cells regulates the inflammatory response, tissue remodeling, and fibrosis throughout various phases of IPF. Our previous studies demonstrate that nuclear factor of activated T cells cytoplasmic member 3 (NFATc3) regulates a wide array of macrophage genes during acute lung injury pathogenesis. However, the role of NFATc3 in IPF pathophysiology has not been previously reported. In the current study, we demonstrate that expression of NFATc3 is elevated in lung tissues and pulmonary macrophages in mice subjected to bleomycin (BLM)-induced pulmonary fibrosis and IPF patients. Remarkably, NFATc3 deficiency (NFATc3+/-) was protective in bleomycin (BLM)-induced lung injury and fibrosis. Adoptive transfer of NFATc3+/+ macrophages to NFATc3+/- mice restored susceptibility to BLM-induced pulmonary fibrosis. Furthermore, in vitro treatment with IL-33 or conditioned medium from BLM-treated epithelial cells increased production of CCL2 and CXCL2 in macrophages from NFATc3+/+ but not NFATc3+/- mice. CXCL2 promoter-pGL3 Luciferase reporter vector showed accentuated reporter activity when co-transfected with the NFATc3 expression vector. More importantly, exogenous administration of recombinant CXCL2 into NFATc3+/- mice increased fibrotic markers and exacerbated IPF phenotype in BLM treated mice. Collectively, our data demonstrate, for the first time, that NFATc3 regulates pulmonary fibrosis by regulating CCL2 and CXCL2 gene expression in macrophages.

lncRNA NEAT1 promotes hypoxia-induced inflammation and fibrosis of alveolar epithelial cells via targeting miR-29a/NFATc3 axis

The objective of the present study was to explore the function and mechanism of long noncoding RNA (lncRNA) nuclear paraspeckle assembly transcript 1 (NEAT1) in pulmonary fibrosis (PF) progression. HPAEpic cells and A549 cells were exposed to hypoxic conditions to establish an in vitro model. Cell apoptosis was detected by TUNEL assay, and inflammatory cytokine levels were detected by ELISA. Gene and protein expression levels were identified by qRT-PCR and Western blot assays, respectively. The interaction among NEAT1, miR-29a, and NFATc3 was identified by dual-luciferase reporter and RNA pull-down assays. In hypoxia-treated cells, hypoxia markers (HIF-1α and HIF-2α), cytokines (TNF-α, IL-1β, and IL-6) and fibrotic markers (α-SMA, collagen I and collagen III) were significantly enhanced. Consistently, the expression levels of NEAT1 and NFATc3 were increased, but miR-29a was decreased in hypoxia-stimulated cells. Knockdown of NEAT1 significantly decreased cell apoptosis and the releases of TNF-α, IL-1β, and IL-6 as well as reduced the levels of α-SMA, collagen I, and collagen III. Moreover, NEAT1 positively regulated NFATc3 expression by directly targeting miR-29a. Functional experiments showed that the anti-apoptotic, anti-inflammatory, and anti-fibrotic effects mediated by NETA1 silencing were impeded by miR-29a inhibition or NFATc3 overexpression in hypoxia-stimulated HPAEpic and A549 cells. Collectively, these data demonstrated that NEAT1 knockdown inhibited hypoxia-induced cell apoptosis, inflammation, and fibrosis by targeting the miR-29a/NFATc3 axis in PF, suggesting that NEAT1 might be a potential therapeutic target for relieving PF progression.

Neuroimmune Interaction: A Widespread Mutual Regulation and the Weapons for Barrier Organs

Since the embryo, the nervous system and immune system have been interacting to regulate each other’s development and working together to resist harmful stimuli. However, oversensitive neural response and uncontrolled immune attack are major causes of various diseases, especially in barrier organs, while neural-immune interaction makes it worse. As the first defense line, the barrier organs give a guarantee to maintain homeostasis in external environment. And the dense nerve innervation and abundant immune cell population in barrier organs facilitate the neuroimmune interaction, which is the physiological basis of multiple neuroimmune-related diseases. Neuroimmune-related diseases often have complex mechanisms and require a combination of drugs, posing challenges in finding etiology and treatment. Therefore, it is of great significance to illustrate the specific mechanism and exact way of neuro-immune interaction. In this review, we first described the mutual regulation of the two principal systems and then focused on neuro-immune interaction in the barrier organs, including intestinal tract, lungs and skin, to clarify the mechanisms and provide ideas for clinical etiology exploration and treatment.

eNAMPT Is a Novel Damage-associated Molecular Pattern Protein That Contributes to the Severity of Radiation-induced Lung Fibrosis

The paucity of therapeutic strategies to reduce the severity of radiation-induced lung fibrosis (RILF), a life-threatening complication of intended or accidental ionizing radiation exposure, is a serious unmet need. We evaluated the contribution of eNAMPT (extracellular nicotinamide phosphoribosyltransferase), a damage-associated molecular pattern (DAMP) protein and TLR4 (Toll-like receptor 4) ligand, to the severity of whole-thorax lung irradiation (WTLI)-induced RILF. Wild-type (WT) and Nampt+/- heterozygous C57BL6 mice and nonhuman primates (NHPs, Macaca mulatta) were exposed to a single WTLI dose (9.8 or 10.7 Gy for NHPs, 20 Gy for mice). WT mice received IgG1 (control) or an eNAMPT-neutralizing polyclonal or monoclonal antibody (mAb) intraperitoneally 4 hours after WTLI and weekly thereafter. At 8-12 weeks after WTLI, NAMPT expression was assessed by immunohistochemistry, biochemistry, and plasma biomarker studies. RILF severity was determined by BAL protein/cells, hematoxylin and eosin, and trichrome blue staining and soluble collagen assays. RNA sequencing and bioinformatic analyses identified differentially expressed lung tissue genes/pathways. NAMPT lung tissue expression was increased in both WTLI-exposed WT mice and NHPs. Nampt+/- mice and eNAMPT polyclonal antibody/mAb-treated mice exhibited significantly attenuated WTLI-mediated lung fibrosis with reduced: 1) NAMPT and trichrome blue staining; 2) dysregulated lung tissue expression of smooth muscle actin, p-SMAD2/p-SMAD1/5/9, TGF-β, TSP1 (thrombospondin-1), NOX4, IL-1β, and NRF2; 3) plasma eNAMPT and IL-1β concentrations; and 4) soluble collagen. Multiple WTLI-induced dysregulated differentially expressed lung tissue genes/pathways with known tissue fibrosis involvement were each rectified in mice receiving eNAMPT mAbs.The eNAMPT/TLR4 inflammatory network is essentially involved in radiation pathobiology, with eNAMPT neutralization an effective therapeutic strategy to reduce RILF severity.

Spironolactone Inhibits Cardiomyocyte Hypertrophy by Regulating the Ca2+/Calcineurin/p-NFATc3 Pathway

This study aimed to investigate the protective effect and molecular mechanism of spironolactone in isoproterenol-induced cardiomyocyte hypertrophy. In this study, primary cardiomyocytes were extracted from the heart of neonatal rats. After stable culture, they were processed with isoproterenol alone or isoproterenol (10 μM) combined with different doses (low dose of 10 μM and high dose of 50 μM), and the cellular activity was determined by MTT experiment. The volume of cells was measured with an inverted microscope and CIAS-1000 cell image analysis system. The mRNA expression levels of ANP and BNP in cells were explored by RT-qPCR. The levels of ANP and BNP proteins and NFATc3 phosphorylation in the nucleus were detected by western blot. The extracellular Ca2⁺ concentration and CaN activity were measured by colorimetry with the kit. Isoproterenol significantly enlarged the volume of cardiomyocytes (p < 0.001), upregulated mRNA and expression levels of ANP and BNP proteins (p < 0.001), increased extracellular Ca²⁺ concentration and CaN activity (p < 0.001), and upregulated NFATc3 phosphorylation in the nucleus (p < 0.001). The volume of cells treated with isoproterenol combined with different doses of spironolactone significantly decreased compared with those treated with isoproterenol alone (p < 0.001). mRNA and expression levels of ANP and BNP proteins downregulated significantly (p < 0.001). The extracellular Ca²⁺ (p < 0.01) concentration and CaN activity (p < 0.001) decreased significantly, and NFATc3 phosphorylation in the nucleus downregulated significantly (p < 0.001). There was no significant difference in cell volume (p=0.999), ANP and BNP mRNA (p=0.695), expression levels of proteins, CaN activity (0.154), and NFATc3 phosphorylation in the nucleus between the cells treated with isoproterenol combined with high-dose spironolactone and those in the control group. In conclusion, spironolactone can reverse isoproterenol-induced cardiomyocyte hypertrophy by inhibiting the Ca²⁺/CaN/NFATc3 pathway.

The Neuropeptide VIP Limits Human Osteoclastogenesis: Clinical Associations with Bone Metabolism Markers in Patients with Early Arthritis

We aimed to evaluate the direct action of VIP on crucial molecules involved in human osteoclast differentiation and function. We also investigated the relationship between VIP serum levels and bone remodeling mediators in early arthritis patients. The expression of VIP receptors and osteoclast gene markers in monocytes and in vitro differentiated osteoclasts was studied by real-time PCR. NFATc1 activity was measured using a TransAM^® kit. Osteoclastogenesis was confirmed by quantification of tartrate-resistant acid phosphatase positive multinucleated cells. OsteoAssay^® Surface Multiple Well Plate was used to evaluate bone-resorbing activity. The ring-shaped actin cytoskeleton and the VPAC1 and VPAC2 expression were analyzed by immunofluorescence. We described the presence of VIP receptors in monocytes and mature osteoclasts. Osteoclasts that formed in the presence of VIP showed a decreased expression of osteoclast differentiation gene markers and proteolytic enzymes involved in bone resorption. VIP reduced the resorption activity and decreased both β3 integrin expression and actin ring formation. Elevated serum VIP levels in early arthritis patients were associated with lower BMD loss and higher serum OPG concentration. These results demonstrate that VIP exerts an anti-osteoclastogenic action impairing both differentiation and resorption activity mainly through the negative regulation of NFATc1, evidencing its bone-protective effects in humans.

Role of Atypical Chemokines and Chemokine Receptors Pathways in the Pathogenesis of COPD

Chronic obstructive pulmonary disease (COPD) represents a heightened inflammatory response in the lung generally resulting from tobacco smoking-induced recruitment and activation of inflammatory cells and/or activation of lower airway structural cells. Several mediators can modulate activation and recruitment of these cells, particularly those belonging to the chemokines (conventional and atypical) family. There is emerging evidence for complex roles of atypical chemokines and their receptors (such as high mobility group box 1 (HMGB1), antimicrobial peptides, receptor for advanced glycosylation end products (RAGE) or toll-like receptors (TLRs)) in the pathogenesis of COPD, both in the stable disease and during exacerbations. Modulators of these pathways represent potential novel therapies for COPD and many are now in preclinical development. Inhibition of only a single atypical chemokine or receptor may not block inflammatory processes because there is redundancy in this network. However, there are many animal studies that encourage studies for modulating the atypical chemokine network in COPD. Thus, few pharmaceutical companies maintain a significant interest in developing agents that target these molecules as potential antiinflammatory drugs. Antibody-based (biological) and small molecule drug (SMD)-based therapies targeting atypical chemokines and/or their receptors are mostly at the preclinical stage and their progression to clinical trials is eagerly awaited. These agents will most likely enhance our knowledge about the role of atypical chemokines in COPD pathophysiology and thereby improve COPD management.

VIP reduction in the pancreas of F508del homozygous CF mice and early signs of Cystic Fibrosis Related Diabetes (CFRD)

Vasoactive intestinal peptide (VIP), a 28-amino acid neuropeptide with potent anti-inflammatory, bronchodilatory and immunomodulatory functions, is secreted by intrinsic neurons innervating all exocrine glands, including the pancreas, in which it exerts a regulatory function in the secretion of insulin and glucagon. Cystic fibrosis-related diabetes (CFRD) is the most common co-morbidity associated with cystic fibrosis (CF), impacting approximately 50% of adult patients. We recently demonstrated a 50% reduction of VIP abundance in the lungs, duodenum and sweat glands of C57Bl/6 CF mice homozygous for the F508del-CFTR disease-causing mutation. VIP deficiency resulted from a reduction in VIPergic and cholinergic innervation, starting before signs of CF disease were observed. As VIP functions as a neuromodulator with insulinotropic effect on pancreatic beta cells, we sought to study changes in VIP in the pancreas of CF mice. Our goal was to examine VIP content and VIPergic innervation in the pancreas of 8- and 17-week-old F508del-CFTR homozygous mice and to determine whether changes in VIP levels would contribute to CFRD development. Our data showed that a decreased amount of VIP and reduced innervation are found in CF mice pancreas, and that these mice also exhibited reduced insulin secretion, up-regulation of glucagon production and high random blood glucose levels compared to same-age wild-type mice. We propose that low level of VIP, due to reduced innervation of the CF pancreas and starting at an early disease stage, contributes to changes in insulin and glucagon secretion that can lead to CFRD development.

Endolysosomal Ca2+ signaling in cardiovascular health and disease

An increase in intracellular Ca²⁺ concentration ([Ca²⁺]_i) regulates a plethora of functions in the cardiovascular (CV) system, including contraction in cardiomyocytes and vascular smooth muscle cells (VSMCs), and angiogenesis in vascular endothelial cells and endothelial colony forming cells. The sarco/endoplasmic reticulum (SR/ER) represents the largest endogenous Ca²⁺ store, which releases Ca²⁺ through ryanodine receptors (RyRs) and/or inositol-1,4,5-trisphosphate receptors (InsP₃Rs) upon extracellular stimulation. The acidic vesicles of the endolysosomal (EL) compartment represent an additional endogenous Ca²⁺ store, which is targeted by several second messengers, including nicotinic acid adenine dinucleotide phosphate (NAADP) and phosphatidylinositol 3,5-bisphosphate [PI(3,5)P₂], and may release intraluminal Ca²⁺ through multiple Ca²⁺ permeable channels, including two-pore channels 1 and 2 (TPC1-2) and Transient Receptor Potential Mucolipin 1 (TRPML1). Herein, we discuss the emerging, pathophysiological role of EL Ca²⁺ signaling in the CV system. We describe the role of cardiac TPCs in β-adrenoceptor stimulation, arrhythmia, hypertrophy, and ischemia-reperfusion injury. We then illustrate the role of EL Ca²⁺ signaling in VSMCs, where TPCs promote vasoconstriction and contribute to pulmonary artery hypertension and atherosclerosis, whereas TRPML1 sustains vasodilation and is also involved in atherosclerosis. Subsequently, we describe the mechanisms whereby endothelial TPCs promote vasodilation, contribute to neurovascular coupling in the brain and stimulate angiogenesis and vasculogenesis. Finally, we discuss about the possibility to target TPCs, which are likely to mediate CV cell infection by the Severe Acute Respiratory Disease-Coronavirus-2, with Food and Drug Administration-approved drugs to alleviate the detrimental effects of Coronavirus Disease-19 on the CV system.

Analysis of expression differences of immune genes in non-small cell lung cancer based on TCGA and ImmPort data sets and the application of a prognostic model

Background

There has been little investigation carried out into the activity of immune-related genes in the prognosis of non-small cell lung cancer (NSCLC). Our study set out to analyze the correlation between the differential expression of immune genes and NSCLC prognosis by screening the differential expression of immune genes. Based on the immune genes identified, we aimed to construct a prognostic risk model and explore some novel molecules which have predictive potential for therapeutic effect and prognosis in lung cancer.

Methods

Immune gene transcriptome data and clinical data of NSCLC samples were extracted from TCGA database, and transcription factors in the ImmPort dataset were obtained. The data were divided into two groups: normal tissues and tumor tissues. The expression levels of immune genes were compared using the edgeR algorithm, and then differential expression analysis was performed. The survival analysis was carried out by combining differential immune genes with clinical survival time, so that the immune genes influencing the prognosis of NSCLC could be determined. A risk score was calculated based on the expression levels of the immune genes related to the prognosis of NSCLC and their corresponding coefficients to construct a prognostic risk model. This model was used to calculate patient risk scores and perform clinical correlation analysis. The selected molecules were further verified by clinical samples.

Results

By comparing NSCLC tissues with normal tissues, a total of 6,778 differentially expressed genes were found (P<0.05), of which 490 were differential immune-related genes. Survival analysis determined 28 differential immune genes to be associated with prognosis (P<0.05). We calculated the patient risk value based on the immune gene prognosis model. The survival curve was drawn according to the patient risk score and showed that the survival prognosis was significantly different for the high-risk and the low-risk groups (P<0.05). The area under the receiver operating characteristic (ROC) curve (AUC) was 0.723, which represented a relatively high true-positive rate. All of the results proved the reliability of our immune gene risk prognostic model. After drawing the risk curve, S100A16, IGKV4, S100P, ANGPTL4, SEMA4B, and LGR4 were found to be the high-risk immune genes in NSCLC. Clinical correlation analysis of survival-related differential immune genes revealed that in patients with lymph node metastasis, ANGPTL4 was positively correlated with T stage, S100a16 and SEMA4B were upregulated, and VIPR1 was downregulated. Further analysis revealed that VIPR1 was decreased in metastatic lung cancer compared to non-metastatic lung cancer. Furthermore, the real-time PCR detection of the clinical samples showed that S100A16 expression in lung cancer was increased, while VIPR1 expression in lung cancer was downregulated, which was consistent with the results of our bioinformatics analysis.

Conclusions

Based on big data from the TCGA and ImmPort databases, our study analyzed the relationship between differential expression of immune-related genes and clinical data, and constructed a prognostic model based on the immune genes identified. Two novel molecules, S100A16 and VIPR1, were verified to possibly have significant biological function in NSCLC. Our research may provide us with new insight into the immune genes by which the malignant biological behavior of NSCLC is mediated.