Background Idiopathic pulmonary fibrosis (IPF) is a fatal, progressive interstitial lung disease characterized by abnormal fibroblast activation and excessive extracellular matrix deposition. Traditional epigenetic and omics studies are costly and technically complex; therefore, the ability to retrospectively predict and deduce complex post-translational modification (PTM) landscapes based on the abundance of small-molecule substrates has become a frontier in epimetabolomics. Methods In this study, high-resolution non-targeted metabolomics (LC-MS/MS) analysis was performed on lung tissue samples from 9 IPF patients and 3 healthy controls (HC). Global metabolomic profiles were evaluated using multivariate statistical analysis (PCA and OPLS-DA), and differentially expressed metabolites were screened based on VIP > 1 and P < 0.05. Subsequently, pathway mapping was performed using the KEGG and HMDB databases, and a “substrate-multi-modification” prediction model was constructed, covering lactylation, methylation, acetylation, glycosylation, succinylation, and phosphorylation modifications. Results A total of 2,325 metabolites were detected in lung tissue. Multivariate analysis indicated significant separation of metabolic profiles between the IPF group and the HC group (OPLS-DA, Q²=0.523). The 345 significantly differentially expressed metabolites (266 upregulated, 79 downregulated) exhibited a strong enrichment of modified substrates. Lactate (FC = 13.43) and lactate phosphate (FC = 11.47), products of glycolysis, were dramatically upregulated, predicting high levels of lysine lactylation (Kla) in the tissue; Arginine (FC = 19.94) and trimethyllysine (FC = 5.21) surged, predicting active arginine/lysine methylation (Kme/Rme); Increases in N-acetylmannosamine (FC = 6.08) and N-acetylglucosamine 1-phosphate (FC = 4.67) predicted a remodeling of O-GlcNAc glycosylation and acetylation (Kac); Enrichments of 2,2-dimethylsuccinic acid (FC = 5.31) and fructose-6-phosphate (FC = 15.64) corresponded to substrate overload for succinylation and multi-site phosphorylation (Pho), respectively. Conclusion The reversal of the characteristic small-molecule expression profile in IPF lung tissue essentially constitutes a “building block library” for downstream multidimensional protein post-translational modifications (PTMs). Predicting the PTM landscape by reverse engineering metabolite abundances not only significantly reduces the cost of multi-omics exploration but also provides a novel molecular window for deciphering the multi-phenotypic regulation of fibrosis.

Lung cancer is the leading cause of cancer-related mor-tality globally,including small-cell lung cancer and non-small-cell lung cancer.As the most prevalent histological subtype of non-small-cell lung cancer,lung adenocarci-noma(LUAD)accounts for approximately 40％of all lung cancer cases.

Background Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of many malignant tumors. However, ICI-induced hyper-immune activation causes cardiotoxicity. Traditional treatments such as glucocorticoids and immunosuppressants have limited effectiveness and may even accelerate tumor growth. This study aimed to identify approaches that effectively reduce cardiotoxicity and simultaneously preserve or enhance the antitumor immunity of ICI therapy.Methods ICI injection in melanoma-bearing C57BL/6J female mice was used to simulate cardiotoxicity in patients with tumor undergoing immune therapy. MCC950 was used to block nod-like receptor protein 3 (NLRP3) inflammasome activity. Echocardiography, immunofluorescence, flow cytometry, and reverse transcription quantitative polymerase chain reaction were used to assess cardiac function, immune cell populations, and inflammatory factor levels. Bulk and single-cell RNA sequencing was used to detect the changes in cardiac transcriptome and immunological network.Results NLRP3 inhibition reduced inflammatory response and improved cardiac function. Notably, NLRP3 inhibition also resulted in a pronounced suppression of tumor growth. Single-cell RNA sequencing elucidated that MCC950 treatment reduced the cardiac infiltration of pathogenic macrophages, cytotoxic T cells, activated T cells, and their production of inflammatory cytokines, while enhancing the presence of reparative macrophages and naive T cells. In addition, MCC950 attenuated cardiotoxicity induced by dual programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) immunotherapy and promoted tumor regression, and showed efficacy in treating established cardiotoxicity.Conclusions Our findings provide a promising clinical approach for preventing and treating cardiotoxicity induced by ICIs, dissociating the antitumor efficacy of ICI-based therapies from their cardiotoxic side effects.

Regulatory T cells (Tregs), characterized by the expression of Forkhead Box P3 (FOXP3), constitute a distinct subset of T cells crucial for immune regulation. Tregs can exert direct and indirect control over immune homeostasis by releasing inhibitory factors or differentiating into Th-like Treg (Th-Treg), thereby actively contributing to the prevention and treatment of autoimmune diseases. The epigenetic regulation of FOXP3, encompassing DNA methylation, histone modifications, and post-translational modifications, governs the development and optimal suppressive function of Tregs. In addition, Tregs can also possess the ability to maintain homeostasis in diverse microenvironments through non-suppressive mechanisms. In this review, we primarily focus on elucidating the epigenetic regulation of Tregs as well as their multifaceted roles within diverse physiological contexts while looking forward to potential strategies involving augmentation or suppression of Tregs activity for disease management, particularly in light of the ongoing global COVID-19 pandemic.

Background 8-Oxoguanine DNA glycosylase (OGG1), a well-known DNA repair enzyme, has been demonstrated to promote lung fibrosis, while the specific regulatory mechanism of OGG1 during pulmonary fibrosis remains unclarified.Methods A bleomycin (BLM)-induced mouse pulmonary fibrosis model was established, and TH5487 (the small molecule OGG1 inhibitor) and Mitochondrial division inhibitor 1 (Mdivi-1) were used for administration. Histopathological injury of the lung tissues was assessed. The profibrotic factors and oxidative stress-related factors were examined using the commercial kits. Western blot was used to examine protein expression and immunofluorescence analysis was conducted to assess macrophages polarization and autophagy. The conditional medium from M2 macrophages was harvested and added to HFL-1 cells for culture to simulate the immune microenvironment around fibroblasts during pulmonary fibrosis. Subsequently, the loss- and gain-of function experiments were conducted to further confirm the molecular mechanism of OGG1/PINK1.Results In BLM-induced pulmonary fibrosis, OGG1 was upregulated while PINK1/Parkin was downregulated. Macrophages were activated and polarized to M2 phenotype. TH5487 administration effectively mitigated pulmonary fibrosis, M2 macrophage polarization, oxidative stress and mitochondrial dysfunction while promoted PINK1/Parkin-mediated mitophagy in lung tissues of BLM-induced mice, which was partly hindered by Mdivi-1. PINK1 overexpression restricted M2 macrophages-induced oxidative stress, mitochondrial dysfunction and mitophagy inactivation in lung fibroblast cells, and OGG1 knockdown could promote PINK1/Parkin expression and alleviate M2 macrophages-induced mitochondrial dysfunction in HFL-1 cells.Conclusion OGG1 inhibition protects against pulmonary fibrosis, which is partly via activating PINK1/Parkin-mediated mitophagy and retarding M2 macrophage polarization, providing a therapeutic target for pulmonary fibrosis.

Objective: To explore and construct a 3D bone remodeling research model displaying stability, repeatability, and precise simulation of the physiological and biochemical environment in vivo.Methods: In this study, 3D bioprinting was used to construct a bone reconstruction model. Sodium alginate (SA), hydroxyapatite (HA) and gelatin (Gel) were mixed into hydrogel as scaffold material. The osteoblast precursor cells MC3T3-E1 and osteoclast precursor cells RAW264.7 were used as seed cells, which may or may not be separated by polycarbonate membrane. The cytokines osteoprotegerin (OPG) and receptor activator of NF-κB ligand (RANKL) were used to induce cell differentiation. The function of scaffolds in the process of bone remodeling was analyzed by detecting the related markers of osteoblasts (alkaline phosphatase, ALP) and osteoclasts (tartrate resistant acid phosphatase, TRAP).Results: The scaffold showed good biocompatibility and low toxicity. The surface morphology aided cell adhesion and growth. The scaffold had optimum degradability, water absorption capacity and porosity, which are in line with the conditions of biological experiments. The effect of induced differentiation of cells was the best when cultured alone. After direct contact between the two types of cells at 2D or 3D level, the induced differentiation of cells was inhibited to varying degrees, although they still showed osteogenesis and osteoclast. After the cells were induced by indirect contact culture, the effect of induced differentiation improved when compared with direct contact culture, although it was still not as good as that of single culture. On the whole, the effect of inducing differentiation at 3D level was the same as that at 2D level, and its relative gene expression and enzyme activity were higher than that in the control group. Hence the scaffold used in this study could induce osteogenesis as well as osteoclast, thereby rendering it more effective in inducing new bone formation.Conclusion: This method can be used to construct the model of 3D bone remodeling mechanism.

Supplementary Figure S2 shows SUR1 regulated the growth of NSCLCs, and the expression levels of phosphorylated p70S6K and KLF4.

Supplementary Table S1 shows the clinicopathological characteristics of non-small cell lung carcinoma patients in Fig. 1C.

Supplementary Table S2 shows the gene ontology biological process analysis of glibenclamide regulated genes.

Supplementary Figure S3 shows glibenclamide downregulated cyclin D1 expression and p70S6K signaling pathway in NSCLCs.

Background: Platinum-based chemotherapy is the main treatment for advanced lung squamous cell carcinoma (LUSC). Eventually, patients with LUSC develop resistance to cisplatin, which affects the prognosis. Hence, the researchers sought to find a lncRNA in LUSC that affects resistance to cisplatin. Methods: The lncRNA microarray assay was used to screen the differential expression of lncRNA. qPCR was used to detect lncRNA DSCAS (DSCAS) expression in tissues and cell lines. Lentiviral transfection was used to regulate the expression of DSCAS. CCK-8, colony formation, wound healing, transwell, and flow cytometry assays were used to assess the biological behaviors and sensitivity to cisplatin of LUSC cell. RNA-RNA interaction was tested using the dual luciferase reporting assay, RNA-IP, and RNA-RNA pull-down assay. The downstream pathway of DSCAS was verified by qPCR and Western blotting assays. Results: DSCAS was highly expressed in LUSC tissues and cells, and its expression levels were higher in cisplatin-insensitive tissues than in cisplatin-sensitive tissues. Elevation of DSCAS promoted cell proliferation, migration and invasion as well as increased cisplatin resistance of lung cancer cells, while demotion of DSCAS inhibited cell proliferation, migration and invasion as well as decreased the cisplatin resistance of lung cancer cells. DSCAS bound to miR-646-3p to regulate the expression of Bcl-2 and Survivin, which affected the cell apoptosis and sensitivity to cisplatin in LUSC cells. Conclusions: DSCAS regulates biological behavior and cisplatin sensitivity in LUSC cells by competitively binding to miR-646-3p to mediate the expression of Survivin and Bcl-2, known as apoptosis-related proteins.

Supplementary Figure S8 shows photos and histological sections of xenografts and livers.

Supplementary Figure S4 shows KATP channels openers inhibited the growth of NSCLCs.

Supplementary Figure S6 shows knockdown of KLF4 expression promoted cell growth, EMT, and migration.

Supplementary Figure S1 shows the expression and survival correlation of Kir6.1 and Kir6.2 in NSCLC.

Background: Transcriptome dysregulation caused by epigenetic mechanisms plays a crucial role in the heterogeneous progression of lung adenocarcinoma (LUAD). In order to address different responses to the same treatment among distinct patients due to heterogeneity of LUAD, a new classification that can stratify patients in prognosis urgently demands to be constructed.Methods: LUAD patients were enrolled from seven independent datasets. LUAD molecular subtypes based on DNA methylation-correlated (METcor) and microRNA-correlated (MIRcor) genes were identified by iClusterBayes method. The nearest template prediction (NTP) algorithm was used to identify LUAD subtypes in six independent datasets by signature genes for the subsequent validation. The clinical outcomes, multi-omics landscape, potential mechanisms, immune features, and treatment options of the LUAD subtypes were further explored.Findings: Based on METcor and MIRcor gene expression profiles, the four subtypes were well characterized and showed distinct clinical and molecular features: (i) Cluster 1: high metabolic activity, low immune infiltration, and intermediate prognosis; (ii) Cluster 2: marked proliferation, highly unstable genome, and intermediate prognosis; (iii) Cluster 3: high immune infiltration, marked proliferation, high metastasis features, low mutation burden, immune-excluded phenotype, sensitive to CTLA4 and MAGE-A3 inhibitor treatment and poor prognosis, and (iv) Cluster 4: high immune infiltration, low proliferation, immune-inflamed phenotype, sensitive to PD-1 inhibitor treatment and best prognosis.Interpretation: This study establishes a molecular classification of gene expression profiles based on epigenetic regulation with stratified prognosis, multi-omics landscape, potential mechanisms, and treatment options.Funding Information: Not applicable.Declaration of Interests: The authors have no conflicts of interest to disclose.Ethics Approval Statement: Public data used in this work can be acquired from the UCSC Xena website (https://xena.ucsc.edu/), TCGA database (http://cancergenome.nih.gov/), cBioPortal (https://www.cbioportal.org/) and Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/).

Long noncoding RNAs (LncRNAs) is a class of RNA molecules that are more than 200bp but cannot be translated into proteins. More and more studies have proved that lncRNA plays a crucial role in various biological functions and disease processes, including virus infection. It's worth noting that studies have also shown that lncRNAs play an essential role in the pathogenesis of human immunodeficiency virus 1 (HIV-1), one of the lethal virus that can destroy immune system. Although lncRNA-mediated gene regulation involves a variety of mechanisms, such as transcription regulation, translation regulation, protein modification, and the formation of RNA-protein complexes, in this review, we primarily focus on the role of lncRNAs in HIV-1 transcription regulation, which is one of the most important mechanisms that control the activation and development of HIV-1. This review also briefly summarizes the latest research progress of lncRNAs related to HIV-1 infection and its potential application in HIV-1 therapy. Although there are antiretroviral drugs that interfere with the function of HIV-1 virus-encoded proteins, this treatment for the HIV-1 virus is limited by its ability to produce drug resistance. Hence, a further understanding of HIV-1 transcription regulation by lncRNAs might help develop non-traditional antiviral therapy strategies.

Breast cancer is the most prevalent cancer among women, and it is characterized by a high rate of tumor development and heterogeneity. Breast cancer stem cells (CSCs) may well contribute to these pathological properties, but the mechanisms underlying their self-renewal and maintenance are still elusive. Here, we found that the long noncoding RNA HOTAIR is highly expressed in breast CSCs. HOTAIR is required for breast CSC self-renewal and tumor propagation. Mechanistically, we demonstrate that HOTAIR recruits the PRC2 protein complex to the promoter of IκBα to inhibit its expression, leading to activation of the NF-κB signaling pathway. The activated NF-κB signaling promotes downstream c-Myc and Cyclin D1 expression. Furthermore, our analysis of clinical samples from the GEPIA database indicated that the IκBα level, as well as the survival rate of patients, with high HOTAIR expression was significantly lower than that of patients with relatively low HOTAIR expression. Our data suggest that HOTAIR-mediated NF-κB signaling primes breast CSC self-renewal and tumor propagation. In sum, we have identified HOTAIR-based NF-κB signaling regulatory circuit that promotes tumorigenic activity in breast CSCs, further indicating that HOTAIR could be a promising target for clinical treatment of breast cancers.

ObjectiveTo investigate the effects of miRNA-145-5p on the tumor development and progression of prostate cancer (Pca) bone metastasis.MethodsLevels of miRNA-145-5p were assessed by real-time quantitative PCR in PC3 (bone metastatic Pca cells), 22RV1 (non-metastatic Pca cells), RWPE-1 (non-cancerous prostate epithelial cells) and Pca tissues collected from patients with and without bone metastases. The impact of miRNA-145-5p on cell proliferation was tested by CCK8 assay, colony formation assay and flow cytometric cell cycle analysis. Effects on invasion and migration of PC3 cells were determined by Transwell and wound healing assays. Western blotting, enzyme-linked immunosorbent assay, and flow cytometry apoptosis analyses were also performed to assess roles in metastasis.ResultsLevels of miRNA-145-5p were decreased in Pca bone metastases and miRNA-145-5p inhibited cell proliferation, migration and invasion. miRNA-145-5p inhibited the expression of basic fibroblast growth factor (bFGF), insulin-like growth factor (IGF) and transforming growth factor-β (TGF-β) in PC3 cells. miR-145-5p increased the expression of the epithelial marker E-cadherin and reduced the expression of matrix metalloproteinase 2 and 9 (MMP-2 and MMP-9). It was found that miRNA-145-5p mediated the epithelial-mesenchymal transition (EMT) and induced apoptosis.ConclusionsmiRNA-145-5p negatively regulated the EMT, inhibited Pca bone metastasis and promoted apoptosis in Pca bone metastasis. Mimicry of miRNA-145-5p action raises the possibility of a novel target for treating Pca with bone metastases.