The effect of N6-methyladenosine (m6A) factors on the development of acute respiratory distress syndrome in the mouse model

FTO Deficiency Alleviates LPS-induced Acute Lung Injury by TXNIP/NLRP3-mediated Alveolar Epithelial Cell Pyroptosis

N6-methyladenosine (m6A) plays a role in various diseases, but it has rarely been reported in acute lung injury (ALI). The FTO (fat mass and obesity-associated) protein can regulate mRNA metabolism by removing m6A residues. The aim of this study was to examine the role and mechanism of the m6A demethylase FTO in LPS-induced ALI. Lung epithelial FTO-knockout mice and FTO-knockdown/overexpression human alveolar epithelial (A549) cell lines were constructed to evaluate the effects of FTO on ALI. Bioinformatics analysis and a series of in vivo and in vitro assays were used to examine the mechanism of FTO regulation. Rescue assays were conducted to examine whether the impact of FTO on ALI depended on the TXNIP/NLRP3 pathway. In LPS-induced ALI, RNA m6A modification amounts were upregulated, and FTO expression was downregulated. In vivo, lung epithelial FTO knockout alleviated alveolar structure disorder, tissue edema, and pulmonary inflammation and improved the survival of ALI mice. In vitro, FTO knockdown reduced A549 cell damage and death induced by LPS, whereas FTO overexpression exacerbated cell damage and death. Mechanistically, bioinformatics analysis revealed that TXNIP was a downstream target of FTO. FTO deficiency mitigated pyroptosis in LPS-induced ALI via the TXNIP/NLRP3 pathway. Rescue assays confirmed that the impact of FTO on the TXNIP/NLRP3 pathway was significantly reversed by the TXNIP inhibitor SRI-37330. Deficiency of FTO alleviates LPS-induced ALI via TXNIP/NLRP3 pathway-mediated alveolar epithelial cell pyroptosis, which might be a novel therapeutic strategy for combating ALI.

RNA modifications in pulmonary diseases

Threatening public health, pulmonary disease (PD) encompasses diverse lung injuries like chronic obstructive PD, pulmonary fibrosis, asthma, pulmonary infections due to pathogen invasion, and fatal lung cancer. The crucial involvement of RNA epigenetic modifications in PD pathogenesis is underscored by robust evidence. These modifications not only shape cell fates but also finely modulate the expression of genes linked to disease progression, suggesting their utility as biomarkers and targets for therapeutic strategies. The critical RNA modifications implicated in PDs are summarized in this review, including N6-methylation of adenosine, N1-methylation of adenosine, 5-methylcytosine, pseudouridine (5-ribosyl uracil), 7-methylguanosine, and adenosine to inosine editing, along with relevant regulatory mechanisms. By shedding light on the pathology of PDs, these summaries could spur the identification of new biomarkers and therapeutic strategies, ultimately paving the way for early PD diagnosis and treatment innovation.

Recruitment of PVT1 Enhances YTHDC1-Mediated m6A Modification of IL-33 in Hyperoxia-Induced Lung Injury During Bronchopulmonary Dysplasia

Bronchopulmonary dysplasia (BPD) is a chronic lung disease that specifically affects preterm infants. Oxygen therapy administered to treat BPD can lead to hyperoxia-induced lung injury, characterized by apoptosis of lung alveolar epithelial cells. Our epitranscriptomic microarray analysis of normal mice lungs and hyperoxia-stimulated mice lungs revealed elevated RNA expression levels of IL-33, as well as increased m6A RNA methylation levels of IL-33 and PVT1 in the hyperoxia-stimulated lungs. This study aimed to investigate the role of the PVT1/IL-33 axis in BPD. A mouse model of BPD was established through hyperoxia induction, and lung histological changes were assessed by hematoxylin-eosin staining. Parameters such as radial alveolar count and mean chord length were measured to assess lung function. Mouse and human lung alveolar epithelial cells (MLE12 and A549, respectively) were stimulated with hyperoxia to create an in vitro BPD model. Cell apoptosis was detected using Western blotting and flow cytometry analysis. Our results demonstrated that silencing PVT1 suppressed apoptosis in MLE12 and A549 cells and improved lung function in hyperoxia-stimulated lungs. Additionally, IL-33 reversed the effects of PVT1 both in vivo and in vitro. Through online bioinformatics analysis and RNA-binding protein immunoprecipitation assays, YTHDC1 was identified as a RNA-binding protein (RBP) for both PVT1 and IL-33. We found that PVT1 positively regulated IL-33 expression by recruiting YTHDC1 to mediate m6A modification of IL-33. In conclusion, silencing PVT1 demonstrated beneficial effects in alleviating BPD by facilitating YTHDC1-mediated m6A modification of IL-33. Inhibition of the PVT1/IL-33 axis to suppress apoptosis in lung alveolar epithelial cells may hold promise as a therapeutic approach for managing hyperoxia-induced lung injury in BPD.

Implication of m6A Methylation Regulators in the Immune Microenvironment of Bronchopulmonary Dysplasia

N6-methyladenosine (m6A) regulates gene expression and governs many important biological processes. However, the function of m6A in the development of bronchopulmonary dysplasia (BPD) remains poorly characterized. Thus, the purpose of this investigation was to evaluate the effects of m6A RNA methylation regulators on the development of BPD. BPD-related transcriptome data were downloaded from the GEO database. Differentially expressed m6A methylation regulators between BPD and control group were identified. Consensus clustering was conducted for the classification of BPD and association between clusters and BPD phenotypes were explored. Analysis of differentially expressed genes (DEGs) and immune-related DEGs was performed. The GSEA, GO and KEGG analyses were used to interpret the functional enrichments. The composition of immune cell subtypes in BPD subsets was predicted by CIBERSORT analysis. Compared with the control group, expression of most m6A regulators showed significant alteration, especially for IGF2BP1/2/3. BPD was classified into 2 subsets, and cluster 1 was correlated with severe BPD. Furthermore, the results of functional enrichment analyses showed a disturbed immune-related signaling pathway. Based on CIBERSORT analysis, we found that the proportion of immune cell subsets changed between cluster 1 and cluster 2. Our study revealed the implication of m6A methylation regulators in the development of BPD, which might provide a novel insight for the diagnosis and treatment of BPD.

β-defensin 2 protects against Escherichia coli-induced acute urinary tract infection by downregulating β-catenin

β-defensin 2 (BD2) is a small cationic peptide that exerts a critical role in host defense against bacterial infections. Here, we aimed to investigate the role of BD2 in protecting against acute urinary tract infection (AUTI) caused by Escherichia coli (UPEC). Here, LPS-induced human urinary bladder epithelial cell (HCV-29) model and UPEC-induced mice model were used for assessing AUTI. Visceral organ lesions of mice following treatment was assessed by HE staining. Cell viability was determined by CCK-8 assay. Permeability in HCV-29 cells was analyzed in Transwell assay. Expression of inflammatory factors (IL-1β, IL-6, and TNF-α) was measured by ELISA assay. The levels of BD2, β-catenin and tight-junction proteins (ZO-1, Occludin, and Claudin-1) were detected by RT-qPCR, western blotting, immunofluorescence or immunohistochemistry. Our results showed that BD2 was lowly expressed and β-catenin showed the reverse trend in response to bacterial infection in vitro and in vivo. BD2 overexpression alleviated the decreased cell viability, increased cell permeability, upregulation of inflammatory factors, downregulation of tight-junction protein and high β-catenin expression in LPS-induced HCV-29 cells, which may contribute to the negative regulation of β-catenin expression. Furthermore, BD2 overexpression attenuated the bacterial infection of tissues, high levels of inflammatory factors and β-catenin, and low levels of tight-junction proteins in mice stimulated with UPEC. This study showed that BD2 played a crucial role in protecting against AUTI caused by gram-negative bacteria through suppressing β-catenin expression. Targeting BD2 may provide a potential therapeutic approach for the prevention and treatment of AUTI.

N6-methyladenosine modification: Regulatory mechanisms and therapeutic potential in sepsis

Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection and is characterized by multiple biological and clinical features. N6-methyladenosine (m6A) modification is the most common type of RNA modifications in eukaryotes and plays an important regulatory role in various biological processes. Recently, m6A modification has been found to be involved in the regulation of immune responses in sepsis. In addition, several studies have shown that m6A modification is involved in sepsis-induced multiple organ dysfunctions, including cardiovascular dysfunction, acute lung injury (ALI), acute kidney injury (AKI) and etc. Considering the complex pathogenesis of sepsis and the lack of specific therapeutic drugs, m6A modification may be the important bond in the pathophysiological process of sepsis and even therapeutic targets. This review systematically highlights the recent advances regarding the roles of m6A modification in sepsis and sheds light on their use as treatment targets for sepsis.

METTL16 in human diseases: What should we do next?

METTL16 is a class-I methyltransferase that is responsible for depositing a vertebrate-conserved S-adenosylmethionine site. Since 2017, there has been a growing body of research focused on METTL16, particularly in the field of structural studies. However, the role of METTL16 in cell biogenesis and human diseases has not been extensively studied, with limited understanding of its function in disease pathology. Recent studies have highlighted the complex and sometimes contradictory role that METTL16 plays in various diseases. In this work, we aim to provide a comprehensive summary of the current research on METTL16 in human diseases.

Inhibition of METTL3 alleviated LPS-induced alveolar epithelial cell apoptosis and acute lung injury via restoring neprilysin expression

AIMS

To investigate the role and mechanisms of methyltransferase-like 3 (METTL3) in the pathogenesis of lipopolysaccharide (LPS)-induced acute lung injury (ALI).

MAIN METHODS

LPS intratracheally instillation was applied in alveolar epithelial cell METTL3 conditional knockout (METTL3-CKO) mice and their wild-type littermates. In addition, METTL3 inhibitor STM2457 was used. LPS treatment on mouse lung epithelial 12 (MLE-12) cell was applied to establish an in vitro model of LPS-induced ALI. H&E staining, lung wet-to-dry ratio, and total broncho-alveolar lavage fluid (BALF) concentrations were used to evaluate lung injury. Overall, the m6A level was determined with the m6A RNA Methylation Quantification Kit and dot blot assay. Expression of METTL3 and neprilysin were measured with immunohistochemistry, immunofluorescence, immunofluorescence-fluorescence in situ hybridization, and western blot. Apoptosis was detected with TUNEL, western blot, and flow cytometry. The interaction of METTL3 and neprilysin was determined with RIP-qPCR and MeRIP.

KEY FINDINGS

METTL3 expression and apoptosis were increased in alveolar epithelial cells of mice treated with LPS, and METTL3-CKO or METTL3 inhibitor STM2457 could alleviate apoptosis and LPS-induced ALI. In MLE-12 cells, LPS-Induced METTL3 expression and apoptosis. Knockdown of METTL3 alleviated, while overexpression of METTL3 exacerbated LPS-induced apoptosis. LPS treatment reduced neprilysin expression, the intervention of neprilysin expression negatively regulated apoptosis without affecting METTL3 expression, and mitigated the promoting effect of METTL3 on LPS-induced apoptosis. Additionally, METTL3 could bind to the mRNA of neprilysin, and reduce its expression.

SIGNIFICANCE

Our findings revealed that inhibition of METTL3 could exert anti-apoptosis and ALI-protective effects via restoring neprilysin expression.

N6-methyladenosine methylation regulator RBM15 promotes the progression of diabetic nephropathy by regulating cell proliferation, inflammation, oxidative stress, and pyroptosis through activating the AGE-RAGE pathway

BACKGROUND

Diabetic nephropathy (DN) is a major cause of end-stage renal disease throughout the world, and m6A modification plays a critical role in the progression of DN. We aimed to find m6A-related genes and their regulatory mechanisms in DN.

METHODS

The expression levels of four important m6A-related genes (METTL16, RBM15, IGF2BP1, and ALKBH5) were detected by quantitative real-time PCR (RT-qPCR). RBM15 was chosen and its function was explored. The downstream pathway of RBM15 was screened by transcriptome sequencing. The levels of AGE, inflammation, and oxidative stress were determined with enzyme-linked immunosorbent assay, and the expression of AGE-RAGE pathway-related proteins were detected by Western blot (WB). Cell proliferation was assessed by Cell counting Kit-8 (CCK-8). The levels of pyroptosis-related proteins were evaluated by RT-qPCR or WB.

RESULTS

METTL16 and RBM15 were up regulated in the mouse model of DN, in which RBM15 was more significant. Silencing RBM15 recovered cell proliferation, reduced the levels of inflammation factors, and inhibited cell pyroptosis in high glucose-induced HK-2 cells. Transcriptome sequencing suggested that the AGE-RAGE pathway might be downstream of RBM15. RBM15 knockdown reduced AGE level and the expression of AGE-RAGE pathway-related proteins. After silencing RBM15, we found that activating the AGE-RAGE pathway inhibited cell proliferation, increased the levels of inflammation factors, promoted oxidative stress, and induced cell pyroptosis in HK-2 cell model of DN.

CONCLUSION

The m6A-related gene RBM15 inhibited cell proliferation, promoted inflammation, oxidative stress, and cell pyroptosis, thereby facilitating the progression of DN through the activation of the AGE-RAGE pathway.

LncRNA THRIL, transcriptionally activated by AP-1 and stabilized by METTL14-mediated m6A modification, accelerates LPS-evoked acute injury in alveolar epithelial cells

Acute lung injury (ALI) and its extreme manifestation, acute respiratory distress syndrome (ARDS), are life-threatening diseases in intensive care units. LncRNA THRIL plays a crucial role in regulating the inflammatory response; however, the potential function of THRIL in ALI/ARDS and the associated mechanism remain unclear. In our study, we found that THRIL was upregulated in the serum of ALI/ARDS patients, and its increased expression was positively correlated with the inflammatory cytokines IL-17. In LPS-induced A549 cells, knockdown of THRIL inhibited the release of the proinflammatory cytokines TNF-α, IL-1β, IL-17, and IL-6, decreased the number of monodansylcadaverine-positive cells and LC3-II with immunofluorescence staining, decreased the expression of autophagy marker ATG7 and Beclin1, and increased expression of p62. Mechanistically, the transcription factor AP-1 bound directly to the THRIL promoter region and activated its transcription by c-Jun upon LPS exposure. Moreover, m6A modification of THRIL was increased in LPS-treated A549 cells, and METTL14 knockdown significantly abolished m6A modification and reduced stabilization of THRIL mRNA. In conclusion, our findings reveal that THRIL, transcriptionally activated by AP-1 and modified by METTL14-mediated m6A modification, induces autophagy in LPS-treated A549 cells, suggesting the potential application of THRIL for ALI/ARDS therapy.

Exploring m6A-RNA methylation as a potential therapeutic strategy for acute lung injury and acute respiratory distress syndrome

N6-methyladenosine (m6A) is the most common methylation modification in mammalian messenger RNA (mRNA) and noncoding RNAs. m6A modification plays a role in the regulation of gene expression and deregulation of m6A methylation has been implicated in many human diseases. Recent publications suggest that exploitation of this methylation process may possess utility against acute lung injury (ALI). ALI and its more severe form, acute respiratory distress syndrome (ARDS) are acute, inflammatory clinical syndromes characterized by poor oxygenation and diffuse pulmonary infiltrates. This syndrome is associated with microvascular endothelial dysfunction, subsequent pulmonary hypertension and may ultimately lead to mortality without rigorous and acute clinical intervention. Over the years, many attempts have been made to detect novel therapeutic avenues for research without much success. The urgency for the discovery of novel therapeutic agents has become more pronounced recently given the current pandemic infection of coronavirus disease 2019 (COVID-2019), still ongoing at the time that this review is being written. We review the current landscape of literature regarding ALI and ARDS etiology, pathophysiology, and therapeutics and present a potential role of m6A methylation. Additionally, we will establish the axiomatic principles of m6A methylation to provide a framework. In conclusion, METTL3, or methyltransferase-like 3, the selective RNA methyltransferase for m6A, is a hub of proinflammatory gene expression regulation in ALI, and using a modern drug discovery strategy will identify new and effective ALI drug candidates targeting METTTL3.

Modulation of gene expression by YTH domain family (YTHDF) proteins in human physiology and pathology

The advent of high throughput techniques in the past decade has significantly advanced the field of epitranscriptomics. The internal chemical modification of the target RNA at a specific site is a basic feature of epitranscriptomics and is critical for its structural stability and functional property. More than 170 modifications at the transcriptomic level have been reported so far, among which m6A methylation is one of the more conserved internal RNA modifications, abundantly found in eukaryotic mRNAs and frequently involved in enhancing the target messenger RNA's (mRNA) stability and translation. m6A modification of mRNAs is essential for multiple physiological processes including stem cell differentiation, nervous system development and gametogenesis. Any aberration in the m6A modification can often result in a pathological condition. The deregulation of m6A methylation has already been described in inflammation, viral infection, cardiovascular diseases and cancer. The m6A modification is reversible in nature and is carried out by specialized m6A proteins including writers (m6A methyltransferases) that add methyl groups and erasers (m6A demethylases) that remove methyl groups selectively. The fate of m6A-modified mRNA is heavily reliant on the various m6A-binding proteins ("readers") which recognize and generate a functional signal from m6A-modified mRNA. In this review, we discuss the role of a family of reader proteins, "YT521-B homology domain containing family" (YTHDF) proteins, in human physiology and pathology. In addition, we critically evaluate the potential of YTHDF proteins as therapeutic targets in human diseases.

The biological function of m6A methyltransferase KIAA1429 and its role in human disease

KIAA1429 is a major m6A methyltransferase, which plays important biological and pharmacological roles in both human cancer or non-cancer diseases. KIAA1429 produce a tumorigenic role in various cancers through regulating DAPK3, ID2, GATA3, SMC1A, CDK1, SIRT1 and other targets, promoting cell proliferation, migration, invasion, metastasis and tumor growth . At the same time, KIAA1429 is also effective in non-tumor diseases, such as reproductive system and cardiovascular system diseases. The potential regulatory mechanism of KIAA1429 dependent on m6A modification is related to mRNA, lncRNA, circRNA and miRNAs. In this review, we summarized the current evidence on KIAA1429 in various human cancers or non-cancer diseases and its potential as a prognostic target.

Effects of microRNA-101-3p on predicting pediatric acute respiratory distress syndrome and its role in human alveolar epithelial cell

Pediatric acute respiratory distress syndrome (PARDS) is a severe form of respiratory failure associated with high mortality among children. The objective of this study is reported to explore the clinical function and molecular roles of microRNA-101-3p (miR-101-3p) in PARDS. The levels of miR-101-3p and mRNA levels of SRY-related high-mobility group box 9 (Sox9) were measured by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Additionally, the diagnostic role of miR-101-3p was identified by using the Receiver operating characteristic (ROC) curve. The cell proliferation and apoptosis were examined through Cell Counting Kit-8 (CCK-8) assay and flow cytometry. To detect inflammation in cells, enzyme-linked immunosorbent assays (ELISA) were performed. The target gene of miR-101-3p was confirmed through data obtained from the luciferase activity. In patients with PARDS, miR-101-3p expression was decreased. Moderate and severe PARDS patients had lower levels of miR-101-3p than mild PARDS patients. The inflammatory progression was related to the aberrant expression of miR-101-3p in all PARDS children. MiR-101-3p was highly predictive for the detection of children with PARDS. In addition, miR-101-3p might protect A549 cells from abnormal proliferation, apoptosis, and inflammation caused by lipopolysaccharide (LPS). Sox9 might be a target gene of miR-101-3p and increased mRNA expression of Sox9 in LPS-treated A549 cells was inhibited by overexpression of miR-101-3p. Ultimately, this study suggested that reduced expression of miR-101-3p plays a role in PARDS, providing a novel angle to study the disease.

Sp1 transcription factor represses transcription of phosphatase and tensin homolog to aggravate lung injury in mice with type 2 diabetes mellitus-pulmonary tuberculosis

Type 2 diabetes mellitus (T2DM) can enhance the risk of mycobacterium tuberculosis (Mtb) infection and aggravate pulmonary tuberculosis (PTB). This study intended to explore the function of phosphatase and tensin homolog (PTEN) in T2DM-PTB and the molecules involved. Mice were treated with streptozotocin to induce T2DM and then infected with Mtb. The mice with T2DM had increased weight, blood glucose level, glucose intolerance and insulin resistance, and increased susceptibility to PTB after Mtb infection. PTEN was significantly downregulated in mice with T2DM-PTB and it had specific predictive value in patients. Overexpression of PTEN improved mouse survival and reduced bacterial load, inflammatory infiltration, cell apoptosis, and fibrosis in lung tissues. Sp1 transcription factor (SP1) was predicted and identified as an upstream regulator of PTEN. SP1 suppressed PTEN transcription. Silencing of SP1 enhanced mouse survival and alleviated the lung injury, and it promoted the M1 polarization of macrophages in murine lung tissues. However, further downregulation of PTEN increased protein kinase B (Akt) phosphorylation and blocked the alleviating roles of SP1 silencing in T2DM-PTB. This study demonstrates that SP1 represses PTEN transcription to promote lung injury in mice with T2DM-PTB through Akt activation.

Personalized medicine using omics approaches in acute respiratory distress syndrome to identify biological phenotypes

In the last decade, research on acute respiratory distress syndrome (ARDS) has made considerable progress. However, ARDS remains a leading cause of mortality in the intensive care unit. ARDS presents distinct subphenotypes with different clinical and biological features. The pathophysiologic mechanisms of ARDS may contribute to the biological variability and partially explain why some pharmacologic therapies for ARDS have failed to improve patient outcomes. Therefore, identifying ARDS variability and heterogeneity might be a key strategy for finding effective treatments. Research involving studies on biomarkers and genomic, metabolomic, and proteomic technologies is increasing. These new approaches, which are dedicated to the identification and quantitative analysis of components from biological matrixes, may help differentiate between different types of damage and predict clinical outcome and risk. Omics technologies offer a new opportunity for the development of diagnostic tools and personalized therapy in ARDS. This narrative review assesses recent evidence regarding genomics, proteomics, and metabolomics in ARDS research.