Genomics of neonatal sepsis: has-miR-150 targeting BCL11B functions in disease progression

Riddling Substitution of "hsa" to "has" in the Enigmatic MicroRNA Nomenclature

This concise review and analysis offers an initial unpacking of a previously under-recognized issue within the microRNA research and communications field regarding the inadvertent use of "has" instead of "hsa" in article titles in the microRNA nomenclature. This subtle change, often the result of grammar auto correction tools, introduces considerable ambiguity and confusion among readers and researchers in reporting of microRNA-related discoveries. The impact of this issue cannot be underestimated, as precise and consistent nomenclature is vital for science communication and computational retrieval of relevant scientific literature and to advance science and innovation. We suggest that the recognition and correction of these often inadvertent "hsa" to "has" substitution errors are timely and important so as to ensure a higher level of accuracy throughout the writing and publication process in the microRNA field in particular. Doing so will also contribute to clarity and consistency in the field of microRNA research, ultimately improving scientific veracity, communication, and progress.

Fangji Fuling Decoction Alleviates Sepsis by Blocking MAPK14/FOXO3A Signaling Pathway

OBJECTIVE

To examine the therapeutic effect of Fangji Fuling Decoction (FFD) on sepsis through network pharmacological analysis combined with in vitro and in vivo experiments.

METHODS

A sepsis mouse model was constructed through intraperitoneal injection of 20 mg/kg lipopolysaccharide (LPS). RAW264.7 cells were stimulated by 250 ng/mL LPS to establish an in vitro cell model. Network pharmacology analysis identified the key molecular pathway associated with FFD in sepsis. Through ectopic expression and depletion experiments, the effect of FFD on multiple organ damage in septic mice, as well as on cell proliferation and apoptosis in relation to the mitogen-activated protein kinase 14/Forkhead Box O 3A (MAPK14/FOXO3A) signaling pathway, was analyzed.

RESULTS

FFD reduced organ damage and inflammation in LPS-induced septic mice and suppressed LPS-induced macrophage apoptosis and inflammation in vitro (P<0.05). Network pharmacology analysis showed that FFD could regulate the MAPK14/FOXO signaling pathway during sepsis. As confirmed by in vitro cell experiments, FFD inhibited the MAPK14 signaling pathway or FOXO3A expression to relieve LPS-induced macrophage apoptosis and inflammation (P<0.05). Furthermore, FFD inhibited the MAPK14/FOXO3A signaling pathway to inhibit LPS-induced macrophage apoptosis in the lung tissue of septic mice (P<0.05).

CONCLUSION

FFD could ameliorate the LPS-induced inflammatory response in septic mice by inhibiting the MAPK14/FOXO3A signaling pathway.

Advancement in biomarker based effective diagnosis of neonatal sepsis

Neonatal sepsis is considered as alarming medical emergency and becomes the common global reason of neonatal mortality. Non-specific symptoms and limitations of conventional diagnostic methods for neonatal sepsis mandate fast and reliable method to diagnose disease for point of care application. Recently, disease specific biomarkers have gained interest for rapid diagnosis that led to the development of electrochemical biosensor with enhanced specificity, sensitivity, cost-effectiveness and user-friendliness. Other than conventional biomarker C-reactive protein to diagnose neonatal sepsis, several potential biomarkers including Procalcitonin (PCT), Serum amyloid A (SAA) and other candidates are extensively investigated. The present review provides insights on advancements and diagnostic abilities of protein and nucleotide based biomarkers with their incorporation in developing electrochemical biosensors by employing novel fabrication strategies. This review provides an overview of most promising biomarker and its capability for neonatal sepsis diagnosis to fulfil future demand to develop electrochemical biosensor for point-of-care applications.

Identification of potential diagnostic and prognostic biomarkers for sepsis based on machine learning

Background

To identify potential diagnostic and prognostic biomarkers of the early stage of sepsis.

Methods

The differentially expressed genes (DEGs) between sepsis and control transcriptomes were screened from GSE65682 and GSE134347 datasets. The candidate biomarkers were identified by the least absolute shrinkage and selection operator (LASSO) regression and support vector machine recursive feature elimination (SVM-RFE) analyses. The diagnostic and prognostic abilities of the markers were evaluated by plotting receiver operating characteristic (ROC) curves and Kaplan-Meier survival curves. Gene Set Enrichment Analysis (GSEA) and single-sample GSEA (ssGSEA) were performed to further elucidate the molecular mechanisms and immune-related processes. Finally, the potential biomarkers were validated in a septic mouse model by qRT-PCR and western blotting.

Results

Eleven DEGs were identified between the sepsis and control samples, including YOD1, GADD45A, BCL11B, IL1R2, UGCG, TLR5, S100A12, ITK, HP, CCR7 and C19orf59 (all AUC>0.9). Furthermore, the survival analysis identified YOD1, GADD45A, BCL11B and IL1R2 as the prognostic biomarkers of sepsis. According to GSEA, four DEGs were significantly associated with immune-related processes. In addition, ssGSEA demonstrated a significant difference in the enriched immune cell populations between the sepsis and control groups (all P < 0.05). Moreover, YOD1, GADD45A and IL1R2 were upregulated, and BCL11B was downregulated in the heart, liver, lungs, and kidneys of the septic mice model.

Conclusions

We identified four potential immune-releated diagnostic and prognostic gene markers for sepsis that offer new insights into its underlying mechanisms.

Notch Signaling in Acute Inflammation and Sepsis

Notch signaling, a highly conserved pathway in mammals, is crucial for differentiation and homeostasis of immune cells. Besides, this pathway is also directly involved in the transmission of immune signals. Notch signaling per se does not have a clear pro- or anti-inflammatory effect, but rather its impact is highly dependent on the immune cell type and the cellular environment, modulating several inflammatory conditions including sepsis, and therefore significantly impacts the course of disease. In this review, we will discuss the contribution of Notch signaling on the clinical picture of systemic inflammatory diseases, especially sepsis. Specifically, we will review its role during immune cell development and its contribution to the modulation of organ-specific immune responses. Finally, we will evaluate to what extent manipulation of the Notch signaling pathway could be a future therapeutic strategy.

MicroRNA as an Early Biomarker of Neonatal Sepsis

Sepsis is a major cause of lethality in neonatal intensive care units. Despite significant advances in neonatal care and growing scientific knowledge about the disease, 4 of every 10 infants born in developed countries and suffering from sepsis die or experience considerable disability, including substantial and permanent neurodevelopmental impairment. Pharmacological treatment strategies for neonatal sepsis remain limited and mainly based upon early initiation of antibiotics and supportive treatment. In this context, numerous clinical and serum-based markers have been evaluated for diagnosing sepsis and evaluating its severity and etiology. MicroRNAs (miRNAs) do not encode for proteins but regulate gene expression by inhibiting the translation or transcription of their target mRNAs. Recently, it was demonstrated in adult patients that miRNAs are released into the circulation and that the spectrum of circulating miRNAs is altered during various pathologic conditions, such as inflammation, infection, and sepsis. Here, we summarize current findings on the role of circulating miRNAs in the diagnosis and staging of neonatal sepsis. The conclusions point to substantial diagnostic potential, and several miRNAs have been validated independently by different teams, namely miR-16a, miR-16, miR-96-5p, miR-141, miR-181a, and miR-1184.

Gene Co-Expression Analysis Identified Preserved and Survival-Related Modules in Severe Blunt Trauma, Burns, Sepsis, and Systemic Inflammatory Response Syndrome

Background

Severe trauma and burns accompanied by sepsis are associated with high morbidity and mortality. Little is known about the transcriptional similarity between trauma, burns, sepsis, and systemic inflammatory response syndrome (SIRS). Uncovering key genes and molecular networks is critical to understanding the biology of disease. Conventional analysis of gene changes (fold change) analysis is difficult for time-serial data such as post-injury blood transcriptome.

Methods

Weighted gene co-expression network analysis (WGCNA) was applied to the trauma dataset to identify modules and hub genes. Module stability was tested by half sampling. Module preservations of burns, sepsis, and SIRS were calculated using trauma as reference. Module functional enrichment was analyzed in gProfiler server. Candidate drugs were screened using Connectivity Map based on hub genes. The modules were visualized in Cytoscape.

Results

Seventeen modules were identified. The modules were robust to the exclusion of half the sample. They were involved in lymphocyte and platelet activation, erythrocyte differentiation, cell cycle, translation, and interferon signaling. In addition, highly connected hub genes were identified in each module, such as GUCY1B1, BCL11B, HMMR, and CEACAM6. High BCL11B (M13) or low CEACAM6 (M27) expression indicates better survival prognosis in sepsis patients regardless of endotype class and age. Network preservation in burns, sepsis, and SIRS showed a general similarity between trauma and burns. M4, M5, M13, M16, M20, and M27 were significantly associated with injury time in trauma and burns. High M13 (T cell activation), low M15 (cell cycle), and low M27 (neutrophil activation) indicate better survival of sepsis patients, regardless of endotype class and age. Moreover, the modules can efficiently separate patients with different diseases. Some modules and hub genes have good prognostic performance in sepsis. Based on the hub genes of each module, six candidate drugs were screened.

Conclusion

This study first compared the gene co-expression modules in trauma, burns, sepsis, and SIRS. The identified modules are useful for disease prognosis and drug discovery. BCL11B and CEACAM6 may be promising biomarkers for sepsis risk assessment.

Clinical significance of serum miR-101-3p expression in patients with neonatal sepsis

Aim: This study aimed to evaluate the levels and functions of miR-101-3p in neonatal sepsis (NS). Materials & methods: Quantitative real-time PCR was conducted to investigate the expression of miR-101-3p and the receiver operating characteristic curve was applied to manifest its diagnostic effects. Results: miR-101-3p was increased in the NS patients and the dysregulation of miR-101-3p was associated with levels of procalcitonin, CRP, IL-8 and TNF-α. The combination of miR-101-3p and procalcitonin could function as a promising indicator in distinguishing NS patients. The silenced miR-101-3p reversed the increased levels of TNF-α and IL-8 caused by lipopolysaccharide in vitro. DUSP1 was identified as a direct target gene of miR-101-3p in NS. Conclusion: The abundance of miR-101-3p facilitated the inflammation in NS by targeting DUSP1.

miRNomic Signature in Very Low Birth-Weight Neonates Discriminates Late-Onset Gram-Positive Sepsis from Controls

Background and Objectives. Neonatal sepsis is a serious condition with a high rate of mortality and morbidity. Currently, the gold standard for sepsis diagnosis is a positive blood culture, which takes 48–72 h to yield results. We hypothesized that identifying differentially expressed miRNA pattern in neonates with late-onset Gram-positive sepsis would help with an earlier diagnosis and therapy. Methods. This is a prospective observational study in newborn infants with late-onset Gram positive bacterial sepsis and non-septic controls. Complementary to blood culture, an aliquot of 0.5 mL of blood was used to determine small non-coding RNA expression profiling using the GeneChip miRNA 4.0 Array. Results. A total of 11 very low birth-weight neonates with late-onset Gram-positive sepsis and 16 controls were analyzed. Further, 217 differentially expressed miRNAs were obtained between both groups. Subsequently, a combined analysis was performed with these miRNAs and 4297 differentially expressed genes. We identified 33 miRNAs that regulate our mRNAs, and the most relevant biological processes are associated with the immune system and the inflammatory response. Conclusions. The miRNA profiling in very low birth-weight neonates distinguishes late-onset Gram-positive sepsis versus control neonates.

Hsa_circ_0000520 overexpression increases CDK2 expression via miR-1296 to facilitate cervical cancer cell proliferation

Background

Circular RNA (circRNA) has been demonstrated to participate in cervical cancer development. In this study, we analyzed the role of hsa_circ_0000520 in cervical cancer.

Methods

Fifty-two pairs of cervical cancer and adjacent normal tissue samples were collected, and five human cervical cancer cell lines were obtained followed by the detection of hsa_circ_0000520 expression. Nuclear-cytoplasmic isolation and fluorescence in situ hybridization were performed to analyze the subcellular localization of hsa_circ_0000520 while linear RNA was digested by RNase R. Gain- or loss-of function experiments on hsa_circ_0000520 were performed, followed by detection of cell proliferation and cell cycle by EdU, Cell Counting Kit-8, colony formation assay, and flow cytometry respectively.

Results

Hsa_circ_0000520 and cyclin-dependent kinase 2 (CDK2) were highly expressed in cervical cancer tissues. Binding sites between microRNA-1296 (miR-1296) and hsa_circ_0000520 or CDK2 were verified. Antibody to Argonaute 2 (Ago2) could precipitate hsa_circ_0000520, indicating that hsa_circ_0000520 could competitively bind to miR-1296 via Ago2. Silencing hsa_circ_0000520 inhibited cervical cancer cell proliferation and promoted the inhibitory effects of miR-1296 on CDK2, thereby blocking cell cycle progression and promoting apoptosis.

Conclusion

These results support the premise that targeting hsa_circ_0000520 can be a potential approach to combat cervical cancer.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-021-02953-9.

MiR-96-5p alleviates inflammatory responses by targeting NAMPT and regulating the NF-κB pathway in neonatal sepsis

Neonatal septicemia is a serious infectious disease in the neonatal period. MicroRNAs (miRNAs) have been reported to participate in the inflammatory responses in neonatal sepsis. The aim of the present study was to explore the effects and molecular mechanism of miR-96-5p on regulating the inflammatory responses in neonatal sepsis. MiR-96-5p was low expressed while nicotinamide phosphoribosyltransferase (NAMPT) was high expressed in the serum of neonatal septicemia patients. The expression of miR-96-5p was decreased in LPS-induced inflammatory responses. Besides, miR-95-5p relieved LPS-induced inflammatory responses in RAW264.7 cells. NAMPT was demonstrated as a potential target of miR-96-5p, and knockdown of NAMPT reduced inflammatory in RAW264.7 cells stimulated with LPS. Moreover, overexpression of NAMPT reversed the effects of miR-96-5p on LPS-induced inflammatory responses. In addition, miR-96-5p inhibited nuclear factor (NF)-κB signaling pathway in RAW264.7 cells stimulated with LPS. MiR-96-5p alleviated inflammatory responses via targeting NAMPT and inhibiting NF-κB pathway in neonatal sepsis.

Screening of Key Genes of Sepsis and Septic Shock Using Bioinformatics Analysis

Objective

Sepsis is a disease associated with high mortality. We performed bioinformatic analysis to identify key biomarkers associated with sepsis and septic shock.

Methods

The top 20% of genes showing the greatest variance between sepsis and controls in the GSE13904 dataset (children) were screened by co-expression network analysis. The differentially expressed genes (DEGs) were identified through analyzing differential gene expression between sepsis patients and control in the GSE13904 (children) and GSE154918 (adult) data sets. Intersection analysis of module genes and DEGs was performed to identify common DEGs for enrichment analysis, protein-protein interaction network (PPI network) analysis, and Short Time-series Expression Miner (STEM) analysis. The PPI network genes were ranked by degree of connectivity, and the top 100 sepsis-associated genes were identified based on the area under the receiver operating characteristic curve (AUC). In addition, we evaluated differences in immune cell infiltration between sepsis patients and controls in children (GSE13904, GSE25504) and adults (GSE9960, GSE154918). Finally, we analyzed differences in DNA methylation levels between sepsis patients and controls in GSE138074 (adults).

Results

The common genes were associated mainly with up-regulated inflammatory and metabolic responses, as well as down-regulated immune responses. Sepsis patients showed lower infiltration by most types of immune cells. Genes in the PPI network with AUC values greater than 0.9 in both GSE13904 (children) and GSE154918 (adults) were screened as key genes for diagnosis. These key genes (MAPK14, FGR, RHOG, LAT, PRKACB, UBE2Q2, ITK, IL2RB, and CD247) were also identified in STEM analysis to be progressively dysregulated across controls, sepsis patients and patients with septic shock. In addition, the expression of MAPK14, FGR, and CD247 was modified by methylation.

Conclusion

This study identified several potential diagnostic genes and inflammatory and metabolic responses mechanisms associated with the development of sepsis.

Analysis of the Role and Regulation Mechanism of hsa-miR-147b in Lung Squamous Cell Carcinoma Based on The Cancer Genome Atlas Database

Objective: This study aimed to explore the role and regulatory mechanism of hsa-miR-147b in lung squamous cell carcinoma (LUSC) through The Cancer Genome Atlas (TCGA) database. Methods: The expression and clinical value of miR-147b in LUSC were analyzed in the TCGA database. The target genes of miR-147b were screened via miRWalk 2.0 and verified in TCGA database. Gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed to analyzed the differential target genes of miR-147b. Kaplan-Meier survival analysis and Cox regression were used to screen the prognosis-related target genes. Results: The expression of miR-147b in LUSC tissues increased, and was associated with poor prognosis, gender, and stage of LUSC patients. The area under the curve (AUC) of miR-147b was 0.8478 by the receiver-operating characteristic curve. There were 428 differentially expressed genes of miR-147b that played a critical role in drug transport, DNA binding, calcium signaling pathway, and Ras signaling pathway through GO and KEGG. PTGIS, SUSD4, ARC, HTR2C, SHISA9, and PLA2G4D were independent risk factors for poor prognosis in LUSC patients. LUSC patients in the high-risk group had a higher risk of death. The time-dependent AUC was 0.673. Conclusions: MiR-147b might be a potential molecular marker for poor prognosis in patients with LUSC.

Upregulation of miR-150-5p alleviates LPS-induced inflammatory response and apoptosis of RAW264.7 macrophages by targeting Notch1

Circulating miR-150-5p has been identified as a prognostic marker in patients with critical illness and sepsis. Herein, we aimed to further explore the role and underlying mechanism of miR-150-5p in sepsis. Quantitative real-time-PCR assay was performed to detect the expression of miR-150-5p upon stimulation with lipopolysaccharide (LPS) in RAW264.7 cells. The levels of tumor necrosis factor-α, interleukin (IL)-6 and IL-1β were measured by ELISA assay. Cell apoptosis was determined using flow cytometry. Western blot was used to assess notch receptor 1 (Notch1) expression in LPS-induced RAW264.7 cells. Dual-luciferase reporter assay was employed to validate the target of miR-150-5p. Our data showed that miR-150-5p was downregulated and Notch1 was upregulated in LPS-stimulated RAW264.7 cells. miR-150-5p overexpression or Notch1 silencing alleviated LPS-induced inflammatory response and apoptosis in RAW264.7 cells. Moreover, Notch1 was a direct target of miR-150-5p. Notch1 abated miR-150-5p-mediated anti-inflammation and anti-apoptosis in LPS-induced RAW264.7 cells. miR-150-5p alleviated LPS-induced inflammatory response and apoptosis at least partly by targeting Notch1 in RAW264.7 cells, highlighting miR-150-5p as a target in the development of anti-inflammation and anti-apoptosis drugs for sepsis treatment.

Screening and identification of key gene in sepsis development: Evidence from bioinformatics analysis

Sepsis is one of the leading causes of mortality in intensive care units (ICU). The growing incidence rate of sepsis and its high mortality rate result are very important sociosanitary problems. Sepsis is a result of infection which can cause systemic inflammatory and organ failure. But the pathogenesis and the molecular mechanisms of sepsis is still not well understood. The aim of the present study was to identify the candidate key genes in the progression of sepsis.Microarray datasets GSE28750, GSE64457, and GSE95233 were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified, and function enrichment analyses were performed. The protein-protein interaction network (PPI) was constructed and the module analysis was performed using STRING and Cytoscape. Furthermore, to verify the results of the bioinformatics analyses, the expression levels of selected DEGs were quantified by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) in libobolysaccharide (LPS)-induced Human Umbilical Vein Endothelial Cells (HUVECs) to support the result of bioinformatics analysis.Thirteen hub genes were identified and biological process analysis revealed that these genes were mainly enriched in apoptotic process, inflammatory response, innate immune response. Hub genes with high degrees, including MAPK14, SLC2A3, STOM, and MMP8, were demonstrated to have an association with sepsis. Furthermore, RT-PCR results showed that SLC2A3 and MAPK14 were significantly upregulated in the HUVECs induced by LPS compared with controls.In conclusion, DEGs and hub genes identified in the present study help us understand the molecular mechanisms of sepsis, and provide candidate targets for diagnosis and treatment of sepsis.

Identification of key miRNA‑mRNA pairs in septic mice by bioinformatics analysis

Sepsis is one of the most common causes of death among critically ill patients in intensive care units worldwide; however, the microRNAs (miRNAs/miRs) involved in the sepsis process (and their target genes) are largely unknown. The present study integrated miRNA and mRNA datasets to elucidate key sepsis-related miRNA-mRNA pairs. The datasets, GSE74952 and GSE55238 were downloaded from the Gene Expression Omnibus. By performing bioinformatics analysis such as GEO2R, miRNA target gene prediction, Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes pathway analysis and miRNA-mRNA network analysis, a total of four sepsis-related miRNA-mRNA pairs were successfully obtained. Mmu-miR-370-3p, cluster of differentiation (CD)8a, CD247, Zap70 and inhibitor of nuclear factor κ B kinase subunit β (Ikbkb) were identified as the components involved in these pairs, and these genes were enriched in the T-cell receptor signaling pathway. Finally, reverse transcription-quantitative PCR results validated that the expression levels of the four genes (CD8a, CD247, Zap70 and Ikbkb) in the sepsis model mice were consistent with the microarray analysis. In conclusion, the present study identified four sepsis-related miRNA-mRNA pairs using bioinformatics analysis. These results indicated that the candidate miRNA-mRNA pairs may be involved in the regulation of immunity in sepsis, which may in turn act as indicators or therapeutic targets for sepsis.