CircRNA, lncRNA, and mRNA profiles of umbilical cord blood exosomes from preterm newborns showing bronchopulmonary dysplasia

In Vitro and Vivo Experiments Revealing Astragalin Inhibited Lung Adenocarcinoma Development via LINC00582/miR-140-3P/PDPK1

This study aimed to explore the mechanism of the development of lung adenocarcinoma (LUAD) treated by astragalin. Transcriptome sequencing was performed to obtain the gene profile of LUAD treated by astragalin. Combining with bioinformatics analysis including differential gene screening, function enrichment analysis (gene ontology and KEGG), and ceRNA construction, we obtained the novel mechanism of lncRNA mediated miRNA/mRNA axis. Then, the cell experiments were performed to examine the role of lncRNA in cell proliferation, migration and invasion, and apoptosis for LUAD treated with astragalin. Moreover, the tumor formation in nude mice was carried out to detect the ceRNA mechanism in LUAD treated by astragalin in vivo. The lncRNA mediated ceRNA network was obtained, that is, LINC00852 LINC00582/miR-140-3p/PDPK1 played an important role in LUAD treated by astragalin. Function experiments indicated that si-LINC00852 inhibited LUAD cell proliferation, migration and invasion, and promoted cell apoptosis via miR-140-3p/PDPK1 (p < 0.05, p < 0.01). The animal experiments further confirmed that si-LINC00852 inhibited tumor growth through miR-140-3p/PDPK1 in vivo. Conversely, this study provides comprehensive insights into the diagnostic and therapeutic implications of LINC00582 in LUAD, LINC00582 mediated miR-140-3p/PDPK1 axis was the novel drug target of astragalin for treating LUAD.

Circ-ECH1 May Compete With miR-708-5p to Regulate Ntrk2 in Bronchopulmonary Dysplasia

Bronchopulmonary dysplasia (BPD) affects patients' quality of life. Circular RNAs participated in BPD. However, circ-ECH1's role in BPD has not been reported yet. This study aimed to explore the role and mechanism of circ-ECH1 in BPD. Hyperoxia-treated type II alveolar epithelial cells (L2 cells) were used as the in vitro BPD model. CCK-8, flow cytometry, and reactive oxygen species (ROS) were used to evaluate cell viability. Fluorescence in situ hybridization confirmed the subcellular localization. Circ-ECH1 overexpression (or inhibited) and miR-708-5p mimics were used to investigate the roles of circ-ECH1 and miR-708-5p in BPD. Quantitative reverse-transcription polymerase reaction (qRT-PCR) detected the expressions of circ-ECH1, miR-708-5p, and neurotrophic receptor tyrosine kinase 2 (Ntrk2). Ntrk2 expression was evaluated by Western blot analysis. Changes in lung tissues were evaluated by hematoxylin and eosin staining. Pulmonary fibrosis was examined by Mason staining. TUNEL staining was performed to evaluate cell apoptosis in lung tissues. RNA sequencing was performed in the lung tissues of BPD rats. The binding between circ-ECH1 and miR-708-5p was confirmed through dual luciferase activity. Hyperoxia reduced cell viability and increased cell apoptosis and ROS accumulation. In addition, hyperoxia decreased the expression levels of circ-ECH1, which is mainly located in the cytoplasm. Circ-ECH1 overexpression increased cell viability but reduced cell apoptosis and ROS accumulation. On the contrary, interference with circ-ECH1 further promoted cell apoptosis and reduced cell activity. Furthermore, circ-ECH1 overexpression reduced the incidence of pulmonary fibrosis and lung cell apoptosis. RNA sequencing, followed by qRT-PCR, confirmed that the expressions of Ntrk2 and miR-708-5p were affected by circ-ECH1. miR-708-5p mimics reversed the role of circ-ECH1 in the BPD. Mechanistically, circ-ECH1 may bind with miR-708-5p to regulate Ntrk2 expression. Circ-ECH1 may compet with miR-708-5p to regulate Ntrk2 expression in BPD. The findings provided a new target for BPD treatment.

Recent progress in neonatal hyperoxic lung injury

With the progress in neonatal intensive care, there has been an increase in the survival rates of premature infants. However, this has also led to an increased incidence of neonatal hyperoxia lung injury and bronchopulmonary dysplasia (BPD), whose pathogenesis is believed to be influenced by various prenatal and postnatal factors, although the exact mechanisms remain unclear. Recent studies suggest that multiple mechanisms might be involved in neonatal hyperoxic lung injury and BPD, with sex also possibly playing an important role, and numerous drugs have been proposed and shown promise for improving the treatment outcomes of hyperoxic lung injury. Therefore, this paper aims to analyze and summarize sex differences in neonatal hyperoxic lung injury, potential pathogenesis and treatment progress to provide new ideas for basic and clinical research in this field.

Epigenetic modifications in the development of bronchopulmonary dysplasia: a review

While perinatal medicine advancements have bolstered survival outcomes for premature infants, bronchopulmonary dysplasia (BPD) continues to threaten their long-term health. Gene-environment interactions, mediated by epigenetic modifications such as DNA methylation, histone modification, and non-coding RNA regulation, take center stage in BPD pathogenesis. Recent discoveries link methylation variations across biological pathways with BPD. Also, the potential reversibility of histone modifications fuels new treatment avenues. The review also highlights the promise of utilizing mesenchymal stem cells and their exosomes as BPD therapies, given their ability to modulate non-coding RNA, opening novel research and intervention possibilities. IMPACT: The complexity and universality of epigenetic modifications in the occurrence and development of bronchopulmonary dysplasia were thoroughly discussed. Both molecular and cellular mechanisms contribute to the diverse nature of epigenetic changes, suggesting the need for deeper biochemical techniques to explore these molecular alterations. The utilization of innovative cell-specific drug delivery methods like exosomes and extracellular vesicles holds promise in achieving precise epigenetic regulation.

Hsa_circ_0001359 in Serum Exosomes: A Promising Marker to Predict Bronchopulmonary Dysplasia in Premature Infants

Objective

This prospective study is to explore the role of specific circRNAs in predicting the development of bronchopulmonary dysplasia (BPD).

Methods

From July 1, 2021 to December 1, 2021, peripheral blood samples were collected from 62 premature infants with gestational age (GA) ≤32 weeks on the 7th, 14th, and 28th day after birth. Then, on the 28th day, the included infants were divided into the BPD group and the non-BPD group according to the definition of BPD. Serum exosomal circRNAs from peripheral blood were identified, sequenced, and compared between the BPD and non-BPD groups at different time points. Specific differentially expressed circRNAs were further verified from another 42 enrolled premature infants (GA ≤32 weeks). The classical lung biological markers in serum were also measured simultaneously.

Results

Hsa_circ_0001359 in serum exosomes showed continuous differential expression between the BPD group and the non-BPD group on the 7th, 14th, and 28th day. Compared with that, classical lung biological markers like IL-6, IL-33, KL-6, and ET-1 did not exhibit continuous differences. Moreover, the expression of hsa_circ_0001359 on day 7 had a higher predictive value in predicting BPD (area under curve:0.853, 95% CI:0.738-0.968; adjusted odds ratio:6.033, 95% CI:2.373-13.326). The calibration curve further showed the mean absolute error = 0.033, mean squared error = 0.00231, and quantile of absolute error = 0.058.

Conclusion

Hsa_circ_0001359 in serum exosomes is a promising marker for predicting BPD in preterm infants with gestational age ≤32 weeks.

Bioinformatics in Neonatal/Pediatric Medicine-A Literature Review

Bioinformatics is a scientific field that uses computer technology to gather, store, analyze, and share biological data and information. DNA sequences of genes or entire genomes, protein amino acid sequences, nucleic acid, and protein-nucleic acid complex structures are examples of traditional bioinformatics data. Moreover, proteomics, the distribution of proteins in cells, interactomics, the patterns of interactions between proteins and nucleic acids, and metabolomics, the types and patterns of small-molecule transformations by the biochemical pathways in cells, are further data streams. Currently, the objectives of bioinformatics are integrative, focusing on how various data combinations might be utilized to comprehend organisms and diseases. Bioinformatic techniques have become popular as novel instruments for examining the fundamental mechanisms behind neonatal diseases. In the first few weeks of newborn life, these methods can be utilized in conjunction with clinical data to identify the most vulnerable neonates and to gain a better understanding of certain mortalities, including respiratory distress, bronchopulmonary dysplasia, sepsis, or inborn errors of metabolism. In the current study, we performed a literature review to summarize the current application of bioinformatics in neonatal medicine. Our aim was to provide evidence that could supply novel insights into the underlying mechanism of neonatal pathophysiology and could be used as an early diagnostic tool in neonatal care.

Human milk exosome-derived circDNAJB6 improves bronchopulmonary dysplasia model by promoting DNAJB6 gene transcription

To verify the protective effect of circDNAJB6 on Bronchopulmonary dysplasia (BPD) cell and animal models and to explore the possible mechanism of its protective effect. The function of circDNAJB6 was investigated at the cell and animal levels. Nuclear and Cytoplasmic RNA extraction kits and fluorescence in situ hybridization (FISH) were used to explore the distribution of circDNAJB6 in cells, and the potential mechanism of circDNAJB6 was verified by q-PCR, luciferase assays and rescue experiments.CircDNAJB6 is abundant in breast milk exosomes. Overexpression of circDNAJB6 can ameliorate damage in BPD models caused by hyperoxia exposure in vivo and in vitro. Mechanistically, circDNAJB6 can target the downstream DNAJB6 gene and promote the transcription of DNAJB6, exertive a protective effect on the experimental BPD model. Our results showed that circDNAJB6 alleviated damage and inhibited the proliferation of alveolar epithelial cells in the BPD model by promoting transcription of parent gene DNAJB6. Human milk exosome-derived circDNAJB6 provides new directions for preventing and treating BPD.

Genetic analysis of potential biomarkers and therapeutic targets associated with ferroptosis from bronchopulmonary dysplasia

Ferroptosis is a recently identified form of cell death that is distinct from the conventional modes such as necrosis, apoptosis, and autophagy. Its role in bronchopulmonary dysplasia (BPD) remains inadequately understood. To address this gap, we obtained BPD-related RNA-seq data and ferroptosis-related genes (FRGs) from the GEO database and FerrDb, respectively. A total of 171 BPD-related differentially expressed ferroptosis-related genes (DE-FRGs) linked to the regulation of autophagy and immune response were identified. Least absolute shrinkage and selection operator and SVM-RFE algorithms identified 23 and 14 genes, respectively, as marker genes. The intersection of these 2 sets yielded 9 genes (ALOX12B, NR1D1, LGMN, IFNA21, MEG3, AKR1C1, CA9, ABCC5, and GALNT14) with acceptable diagnostic capacity. The results of the functional enrichment analysis indicated that these identified marker genes may be involved in the pathogenesis of BPD through the regulation of immune response, cell cycle, and BPD-related pathways. Additionally, we identified 29 drugs that target 5 of the marker genes, which could have potential therapeutic implications. The ceRNA network we constructed revealed a complex regulatory network based on the marker genes, further highlighting their potential roles in BPD. Our findings offer diagnostic potential and insight into the mechanism underlying BPD. Further research is needed to assess its clinical utility.

Circular RNAs and Their Role in Male Infertility: A Systematic Review

Male infertility is a global health problem that is on the rise. Today, many noncoding RNAs (ncRNAs) are associated with male infertility. Circular RNAs (circRNAs) have recently drawn attention, but a comprehensive understanding of the role of circRNAs in male infertility is limited. This systematic review investigates the differential expression of circRNAs in male infertility or circRNAs that could serve as candidate biomarkers. The PRISMA guidelines were used to search PubMed and Web of Science on 11 January 2023. Inclusion criteria were human participants, experimental studies aiming to associate circRNAs with male infertility reporting differentially expressed circRNAs, and the English language. A total of 156 articles were found, and after the screening and eligibility stages, 13 studies were included in the final sample. Many circRNAs are deregulated in male infertility, and their interactions with miRNAs play an important role in affecting cellular processes and pathways. CircRNAs could also be used as biomarkers to screen patients before sperm retrieval. However, most studies focus on the role of circRNAs in azoospermia, and there is a knowledge gap regarding other subtypes of male infertility. Future research is needed to explore the exact mechanism of action of circRNAs and investigate their use as biomarkers.

Identification and Experimental Validation of LINC00582 Associated with B Cell Immune and Development of Pulpitis: Bioinformatics and In Vitro Analysis

BACKGROUND

Pulpitis is a common oral disease. Increasing evidence has demonstrated that long non-coding RNAs (lncRNAs) can regulate the immune response in pulpitis. This study focused on finding the key immune-related lncRNAs that regulate the development of pulpitis.

METHODS

Differentially expressed lncRNAs were analyzed. Enrichment analysis was performed to explore the function of differentially expressed genes. Immune cell infiltration was evaluated with Immune Cell Abundance Identifier. Cell Counting Kit-8 (CCK-8) and lactate dehydrogenase release assays were conducted to measure the viability of human dental pulp cells (HDPCs) and BALL-1 cells. Transwell assay was processed to prove migration and invasion of BALL-1 cells.

RESULTS

Our results revealed that 17 lncRNAs were significantly upregulated. Pulpitis-related genes were mainly enriched in inflammatory relative signal pathways. The abundance of various immune cells was significantly abnormal in pulpitis tissues, among which the expression of eight lncRNAs was significantly correlated with the expression of B cell marker protein CD79B. As the most relevant lncRNA for B cells, LINC00582 could regulate the proliferation, migration, invasion, and CD79B expression of BALL-1 cells.

CONCLUSIONS

Our study identified eight B cell immune-related lncRNAs. Meanwhile, LINC00582 has a positive effect on B cell immunity in the development of pulpitis.

Circular RNAs in the Origin of Developmental Lung Disease: Promising Diagnostic and Therapeutic Biomarkers

Circular RNA (circRNA) is a newly discovered noncoding RNA that regulates gene transcription, binds to RNA-related proteins, and encodes protein microRNAs (miRNAs). The development of molecular biomarkers such as circRNAs holds great promise in the diagnosis and prognosis of clinical disorders. Importantly, circRNA-mediated maternal-fetus risk factors including environmental (high altitude), maternal (preeclampsia, smoking, and chorioamnionitis), placental, and fetal (preterm birth and low birth weight) factors are the early origins and likely to contribute to the occurrence and progression of developmental and pediatric cardiopulmonary disorders. Although studies of circRNAs in normal cardiopulmonary development and developmental diseases have just begun, some studies have revealed their expression patterns. Here, we provide an overview of circRNAs’ biogenesis and biological functions. Furthermore, this review aims to emphasize the importance of circRNAs in maternal-fetus risk factors. Likewise, the potential biomarker and therapeutic target of circRNAs in developmental and pediatric lung diseases are explored.

Circular RNAs expression profiles and bioinformatics analysis in bronchopulmonary dysplasia

BACKGROUND

Bronchopulmonary dysplasia (BPD) has long been considered the most challenging chronic lung disease for neonatologists and researchers due to its complex pathological mechanisms and difficulty in prediction. Growing evidence indicates that BPD is associated with the dysregulation of circular RNAs (circRNAs). Therefore, we aimed to explore the expression profiles of circRNAs and investigate the underlying molecular network associated with BPD.

METHODS

Peripheral blood was collected from very-low-birth-weight (VLBW) infants at 5-8 days of life to extract PBMCs. Microarray analysis and qRT-PCR tests were performed to determine the differentially expressed circRNAs (DEcircRNAs) between BPD and non-BPD VLBW infants. Simultaneous analysis of GSE32472 was conducted to obtain differentially expressed mRNAs (DEmRNA) from BPD infants. The miRNAs were predicted by DEcircRNAs and DEmRNAs of upregulated, respectively, and then screened for overlapping ones. GO and KEGG analysis was performed following construction of the competing endogenous RNA regulatory network (ceRNA) for further investigation.

RESULTS

A total of 65 circRNAs (52 upregulated and 13 downregulated) were identified as DEcircRNAs between the two groups (FC >2.0 and p.adj <0.05). As a result, the ceRNA network was constructed based on three upregulated DEcircRNAs validated by qRT-PCR (hsa_circ_0007054, hsa_circ_0057950, and hsa_circ_0120151). Bioinformatics analysis indicated these DEcircRNAs participated in response to stimulus, IL-1 receptor activation, neutrophil activation, and metabolic pathways.

CONCLUSIONS

In VLBW infants with a high risk for developing BPD, the circRNA expression profiles in PBMCs were significantly altered in the early post-birth period, suggesting immune dysregulation caused by infection and inflammatory response already existed.

Pathogenesis of Bronchopulmonary Dysplasia: Role of Oxidative Stress from 'Omics' Studies

Bronchopulmonary dysplasia (BPD) remains the most common respiratory complication of prematurity as younger and smaller infants are surviving beyond the immediate neonatal period. The recognition that oxidative stress (OS) plays a key role in BPD pathogenesis has been widely accepted since at least the 1980s. In this article, we examine the interplay between OS and genetic regulation and review 'omics' data related to OS in BPD. Data from animal models (largely models of hyperoxic lung injury) and from human studies are presented. Epigenetic and transcriptomic analyses have demonstrated several genes related to OS to be differentially expressed in murine models that mimic BPD as well as in premature infants at risk of BPD development and infants with established lung disease. Alterations in the genetic regulation of antioxidant enzymes is a common theme in these studies. Data from metabolomics and proteomics have also demonstrated the potential involvement of OS-related pathways in BPD. A limitation of many studies includes the difficulty of obtaining timely and appropriate samples from human patients. Additional 'omics' studies could further our understanding of the role of OS in BPD pathogenesis, which may prove beneficial for prevention and timely diagnosis, and aid in the development of targeted therapies.

Circ007071 Inhibits Unsaturated Fatty Acid Synthesis by Interacting with miR-103-5p to Enhance PPARγ Expression in the Dairy Goat Mammary Gland

Understanding more precisely the mechanisms controlling the metabolism of fatty acid in the mammary gland of dairy goats is essential for future improvements in milk quality. Particularly since recent data have underscored a key role for circular RNAs (circRNAs) in the mammary gland function, high-throughput sequencing technology was used to identify expression levels of circRNAs in the mammary tissue of dairy goats during early and peak lactation in the present study. Compared with early lactation, results demonstrated that the expression level of circ007071 during peak lactation was 12.02-fold up-regulated. Subsequent studies in goat mammary epithelial cells (GMECs) revealed that circ007071 stimulated the synthesis of triglycerides (TAG) and cholesterol, as well as increased the content of saturated fatty acids (C16:0 and C18:0). More importantly, using a double luciferase reporting system allowed us to detect the circ007071 sequence at a binding site of miR-103-5p, indicating that it targeted this miRNA. Overexpression of circ007071 significantly decreased the abundance of miR-103-5p and led to inhibition of TAG synthesis. In contrast, the abundance of peroxisome proliferator-activated receptor γ (PPARγ), a target gene of miR-103-5p, was reinforced with the overexpression of circ007071. Thus, we conclude that one key function of circ007071 in the regulation of milk fat synthesis is to attenuate the inhibitory effect of miR-103-5p on PPARγ via direct interactions with miRNA. As a result, the process of TAG and saturated fatty acid is able to proceed.