Identification and analysis of lncRNA, microRNA and mRNA expression profiles and construction of ceRNA network in Talaromyces marneffei-infected THP-1 macrophage

METTL3-mediated NDUFB5 m6A modification promotes cell migration and mitochondrial respiration to promote the wound healing of diabetic foot ulcer

BACKGROUND

Diabetic foot ulcer (DFU) is the most devastating complication of diabetes mellitus (DM) and plays a major role in disability and death in DM patients. NADH: ubiquinone oxidoreductase subunit B5 (NDUFB5) plays an important role in maintaining mitochondrial respiration, but whether it is involved in regulating the progression of advanced glycation end products (AGEs)-mediated DFU is still unclear.

METHODS

Firstly, the role of AGEs on cell viability, migration, and mitochondrial respiration in human umbilical vein endothelial cells (HUVECs) was explored in vitro. Next, NDUFB5 expression was detected in human samples and AGEs-treated HUVECs, and NDUFB5's effect on AGEs-induced HUVECs injury and skin wound in diabetic mice was further clarified. In addition, the role of m6A modification mediated by methyltransferase-like 3 (METTL3) in regulating NDUFB5 expression and AGEs-induced HUVECs injury was investigated.

RESULTS

NDUFB5 promoted cell viability, migration, and mitochondrial respiration in AGEs-treated HUVECs, whereas mitochondrial fusion promoter M1 facilitated cell viability, migration, and mitochondrial oxiadative respiration in NDUFB5 knockdown HUVECs. Meanwhile, NDUFB5 promotes skin wound healing in diabetic mice. Besides, METTL3-mediated m6A modification and insulin like growth factor 2 mRNA binding protein 2 (IGF2BP2) enhanced NDUFB5 expression in HUVECs. Furthermore, METTL3 promoted cell viability, migration, and mitochondrial respiration in AGEs-treated HUVECs by increasing NDUFB5.

CONCLUSION

METTL3-mediated NDUFB5 m6A modification inhibits AGEs-induced cell injury in HUVECs. METTL3 and NDUFB5 might serve as potential targets for DFU therapy in the future.

Multi-omics approaches for drug-response characterization in primary biliary cholangitis and autoimmune hepatitis variant syndrome

BACKGROUND

Primary biliary cholangitis (PBC) and autoimmune hepatitis (AIH) variant syndrome (VS) exhibit a complex overlap of AIH features with PBC, leading to poorer prognoses than those with PBC or AIH alone. The biomarkers associated with drug response and potential molecular mechanisms in this syndrome have not been fully elucidated.

METHODS

Whole-transcriptome sequencing was employed to discern differentially expressed (DE) RNAs within good responders (GR) and poor responders (PR) among patients with PBC/AIH VS. Subsequent gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted for the identified DE RNAs. Plasma metabolomics was employed to delineate the metabolic profiles distinguishing PR and GR groups. The quantification of immune cell profiles and associated cytokines was achieved through flow cytometry and immunoassay technology. Uni- and multivariable logistic regression analyses were conducted to construct a predictive model for insufficient biochemical response. The performance of the model was assessed by computing the area under the receiver operating characteristic (AUC) curve, sensitivity, and specificity.

FINDINGS

The analysis identified 224 differentially expressed (DE) mRNAs, 189 DE long non-coding RNAs, 39 DE circular RNAs, and 63 DE microRNAs. Functional pathway analysis revealed enrichment in lipid metabolic pathways and immune response. Metabolomics disclosed dysregulated lipid metabolism and identified PC (18:2/18:2) and PC (16:0/20:3) as predictors. CD4+ T helper (Th) cells, including Th2 cells and regulatory T cells (Tregs), were upregulated in the GR group. Pro-inflammatory cytokines (IFN-γ, TNF-α, IL-9, and IL-17) were downregulated in the GR group, while anti-inflammatory cytokines (IL-10, IL-4, IL-5, and IL-22) were elevated. Regulatory networks were constructed, identifying CACNA1H and ACAA1 as target genes. A predictive model based on these indicators demonstrated an AUC of 0.986 in the primary cohort and an AUC of 0.940 in the validation cohort for predicting complete biochemical response.

CONCLUSION

A combined model integrating genomic, metabolic, and cytokinomic features demonstrated high accuracy in predicting insufficient biochemical response in patients with PBC/AIH VS. Early recognition of individuals at elevated risk for insufficient response allows for the prompt initiation of additional treatments.

ACACA reduces lipid accumulation through dual regulation of lipid metabolism and mitochondrial function via AMPK- PPARα- CPT1A axis

BACKGROUND

Non-alcoholic fatty liver disease (NAFLD) is a multifaceted metabolic disorder, whose global prevalence is rapidly increasing. Acetyl CoA carboxylases 1 (ACACA) is the key enzyme that controls the rate of fatty acid synthesis. Hence, it is crucial to investigate the function of ACACA in regulating lipid metabolism during the progress of NAFLD.

METHODS

Firstly, a fatty liver mouse model was established by high-fat diet at 2nd, 12th, and 20th week, respectively. Then, transcriptome analysis was performed on liver samples to investigate the underlying mechanisms and identify the target gene of the occurrence and development of NAFLD. Afterwards, lipid accumulation cell model was induced by palmitic acid and oleic acid (PA ∶ OA molar ratio = 1∶2). Next, we silenced the target gene ACACA using small interfering RNAs (siRNAs) or the CMS-121 inhibitor. Subsequently, experiments were performed comprehensively the effects of inhibiting ACACA on mitochondrial function and lipid metabolism, as well as on AMPK- PPARα- CPT1A pathway.

RESULTS

This data indicated that the pathways significantly affected by high-fat diet include lipid metabolism and mitochondrial function. Then, we focus on the target gene ACACA. In addition, the in vitro results suggested that inhibiting of ACACA in vitro reduces intracellular lipid accumulation, specifically the content of TG and TC. Furthermore, ACACA ameliorated mitochondrial dysfunction and alleviate oxidative stress, including MMP complete, ATP and ROS production, as well as the expression of mitochondria respiratory chain complex (MRC) and AMPK proteins. Meanwhile, ACACA inhibition enhances lipid metabolism through activation of PPARα/CPT1A, leading to a decrease in intracellular lipid accumulation.

CONCLUSION

Targeting ACACA can reduce lipid accumulation by mediating the AMPK- PPARα- CPT1A pathway, which regulates lipid metabolism and alleviates mitochondrial dysfunction.

The role and mechanisms of PD-L1 in immune evasion during Talaromyces marneffei infection

Talaromycosis, caused by Talaromyces marneffei (T. marneffei), is a systemic fungal disease that involves dissemination throughout the body. The ability of T. marneffei to evade the immune system is considered a crucial factor in its persistent infection, although the specific mechanisms are not yet fully understood. This study aims to investigate the molecular mechanisms underlying the occurrence of latent T. marneffei infection and immune evasion. The gene expression profile analysis in T. marneffei-infected mouse revealed that Pd-l1 exhibited the highest correlation strength with other hub genes, with a median of 0.60 (IQR: 0.50-0.69). T. marneffei infection upregulated the expression of PD-1 and PD-L1 in PBMCs from HIV patients, which was also observed in the T. marneffei-infected mouse and macrophage models. Treatment with a PD-L1 inhibitor significantly reduced fungal burden in the liver and spleen tissues of infected mice and in the kupffer-CTLL-2 co-culture system. PD-L1 inhibitor treatment increased CTLL-2 cell proliferation and downregulated the expression of PD-1, SHP-2, and p-SHP-2, indicating the activation of T cell viability and T cell receptor signaling pathway. Additionally, treatment with a PI3K inhibitor downregulated PD-L1 in T. marneffei-infected kupffer cells. Similar results were observed with treatment using the T. marneffei cell wall virulence factor β-glucan. Overall, T. marneffei infection upregulated PD-L1 expression in HIV / T. marneffei patients, mice, and kupffer cells. Treatment with a PD-L1 inhibitor significantly reduced fungal burden, while activating T cell activity and proliferation, thereby promoting fungal clearance. Furthermore, the PI3K signaling pathway may be involved in the regulation of PD-L1 by T. marneffei.

Identification and characterization of CircRNA-associated CeRNA networks in moso bamboo under nitrogen stress

BACKGROUND

Nitrogen is a macronutrient element for plant growth and development. Circular RNAs (circRNAs) serve as pivotal regulators for the coordination between nutrient supply and plant demand. Moso bamboo (Phyllostachys edulis) is an excellent plant with fast growth, and the mechanism of the circRNA-target module in response to nitrogen remains unclear.

RESULTS

Deep small RNA sequencing results of moso bamboo seedlings under different concentrations of KNO₃ (N0 = 0 mM, N6 = 6 mM, N18 = 18 mM) were used to identify circRNAs. A total of 549 circRNAs were obtained, of which 309 were generated from corresponding parental coding genes including 66 new ones. A total of 536 circRNA-parent genes were unevenly distributed in 24 scaffolds and were associated with root growth and development. Furthermore, 52 differentially expressed circRNAs (DECs) were obtained, including 24, 33 and 15 DECs from three comparisons of N0 vs. N6, N0 vs. N18 and N6 vs. N18, respectively. Based on integrative analyses of the identified DECs, differentially expressed mRNAs (DEGs), and miRNAs (DEMs), a competitive endogenous RNA (ceRNA) network was constructed, including five DECs, eight DEMs and 32 DEGs. A regulatory module of PeSca_6:12,316,320|12,372,905-novel_miR156-PH02Gene35622 was further verified by qPCR and dual-luciferase reporter assays.

CONCLUSION

The results indicated that circRNAs could participate in multiple biological processes as miRNA sponges, including organ nitrogen compound biosynthesis and metabolic process regulation in moso bamboo. Our results provide valuable information for further study of circRNAs in moso bamboo under fluctuating nitrogen conditions.

Disseminated Talaromyces marneffei infection after renal transplantation: A case report and literature review

We reported a 31-year-old man who received renal transplantation for more than 2 years. He was admitted to our hospital on 9 March 2022 due to intermittent diarrhea accompanied by leukopenia for more than 1 month. The patient successively developed high fever, cough, anemia, weight loss, gastrointestinal bleeding, and liver function impairment. Computed tomography (CT) revealed a slight inflammation in the lower lobes of both lungs, enlargement of the lymph nodes in the retroperitoneal and the root of mesenteric areas, and hepatosplenomegaly. Talaromyces marneffei was detected by metagenomics next-generation sequencing (mNGS) in blood and bronchoalveolar lavage fluid, and the pathogen was subsequently verified by blood culture. After endoscopic hemostatic therapy and antifungal therapy with voriconazole and amphotericin B cholesteryl sulfate complex, the patient was successfully discharged. Oral voriconazole was given regularly after discharge. Diarrhea, fever, enlargement of the lymph nodes, and endoscopic evidence of erosion may indicate intestinal T. marneffei infection. Although the mortality of T. marneffei infection after renal transplantation is very high, timely and effective antifungal therapy with amphotericin B cholesteryl sulfate complex is still expected to improve its prognosis.

Three-Dimensional Organization of Chicken Genome Provides Insights into Genetic Adaptation to Extreme Environments

The high-throughput chromosome conformation capture (Hi-C) technique is widely used to study the functional roles of the three-dimensional (3D) architecture of genomes. However, the knowledge of the 3D genome structure and its dynamics during extreme environmental adaptations remains poor. Here, we characterized 3D genome architectures using the Hi-C technique for chicken liver cells. Upon comparing Lindian chicken (LDC) liver cells with Wenchang chicken (WCC) liver cells, we discovered that environmental adaptation contributed to the switching of A/B compartments, the reorganization of topologically associated domains (TADs), and TAD boundaries in both liver cells. In addition, the analysis of the switching of A/B compartments revealed that the switched compartmental genes (SCGs) were strongly associated with extreme environment adaption-related pathways, including tight junction, notch signaling pathway, vascular smooth muscle contraction, and the RIG-I-like receptor signaling pathway. The findings of this study advanced our understanding of the evolutionary role of chicken 3D genome architecture and its significance in genome activity and transcriptional regulation.

Identification of Potential miRNA-mRNA Regulatory Network Associated with Pig Growth Performance in the Pituitaries of Bama Minipigs and Landrace Pigs

Pig growth performance is one of the criteria for judging pork production and is influenced by genotype and external environmental factors such as feeding conditions. The growth performance of miniature pigs, such as Bama minipigs, differs considerably from that of the larger body size pigs, such as Landrace pigs, and can be regarded as good models in pig growth studies. In this research, we identified differentially expressed genes in the pituitary gland of Bama minipigs and Landrace pigs. Through the pathway enrichment analysis, we screened the growth-related pathways and the genes enriched in the pathways and established the protein-protein interaction network. The RNAHybrid algorithm was used to predict the interaction between differentially expressed microRNAs and differentially expressed mRNAs. Four regulatory pathways (Y-82-ULK1/CDKN1A, miR-4334-5p-STAT3/PIK3R1/RPS6KA3/CAB39L, miR-4331-SCR/BCL2L1, and miR-133a-3p-BCL2L1) were identified via quantitative real-time PCR to detect the expression and correlation of candidate miRNAs and mRNAs. In conclusion, we revealed potential miRNA-mRNA regulatory networks associated with pig growth performance in the pituitary glands of Bama minipigs and Landrace pigs, which may help to elucidate the underlying molecular mechanisms of growth differences in pigs of different body sizes.

Derivation, Comprehensive Analysis, and Assay Validation of a Pyroptosis-Related lncRNA Prognostic Signature in Patients With Ovarian Cancer

Background

Pyroptosis is regulated by long non-coding RNAs (lncRNAs) in ovarian cancer (OC). Therefore, a comprehensive analysis of pyroptosis-related lncRNAs (PRLs) in OC is crucial for developing therapeutic strategies and survival prediction.

Methods

Based on public database raw data, mutations in the landscape of pyroptosis-related genes (PRGs) in patients with OC were investigated thoroughly. PRLs were identified by calculating Pearson correlation coefficients. Cox and LASSO regression analyses were performed on PRLs to screen for lncRNAs participating in the risk signature. Furthermore, receiver operating characteristic (ROC) curves, Kaplan-Meier survival analyses, decision curve analysis (DCA) curves, and calibration curves were used to confirm the clinical benefits. To assess the ability of the risk signature to independently predict prognosis, it was included in a Cox regression analysis with clinicopathological parameters. Two nomograms were constructed to facilitate clinical application. In addition, potential biological functions of the risk signature were investigated using gene function annotation. Subsequently, immune-related landscapes and BRCA1/2 mutations were compared in different risk groups using diverse bioinformatics algorithms. Finally, we conducted a meta-analysis and in-vitro assays on alternative lncRNAs.

Results

A total of 374 patients with OC were randomized into training and validation cohorts (7:3). A total of 250 PRLs were selected from all the lncRNAs. Subsequently, a risk signature (DICER1-AS1, MIR600HG, AC083880.1, AC109322.1, AC007991.4, IL6R-AS1, AL365361.1, and AC022098.2) was constructed to distinguish the risk of patient survival. The ROC curve, K-M analysis, DCA curve, and calibration curve indicated excellent predictive performance for determining overall survival (OS) based on the risk signature in each cohort (p < 0.05). The Cox regression analysis indicated that the risk signature was an independent prognostic factor for OS (p < 0.05). Moreover, significant differences in the immune response and BRCA1 mutations were identified in different groups distinguished by the risk signature (p < 0.05). Interestingly, in-vitro assays showed that an alternative lncRNA (DICER1-AS1) could promote OC cell proliferation.

Conclusion

The PRL risk signature could independently predict overall survival and guide treatment in patients with OC.

Serum Exosomal microRNA Profiling in AIDS Complicated with Talaromyces marneffei Infection

Introduction

In order to find the early diagnostic markers of AIDS combined with TM infection, we detected and analyzed the serum exosomal miRNAs of AIDS patients with or without TM infection.

Materials and Methods

We profiled the expression levels of miRNAs via RNA sequencing in serum exosomes from the pooled samples of 17 AIDS patients combined without TM infection and 15 AIDS combined with TM infection patients. For external validation, we validated these results using real-time quantification polymerase chain reaction (qRT-PCR) in an independent cohort of 35 AIDS patients combined without TM infection and 33 AIDS combined with TM infection patients. Finally, bioinformatics was used to predict the target genes and pathways of meaningful miRNAs.

Results

A total of 131 serum exosomal miRNAs including 73 up-regulated and 59 down-regulated miRNAs were found to be differentially expressed (log2FC≥1 and FDR <0.01) in the two groups. A validation analysis revealed that three miRNAs (miR-192-5p, miR-194-5p and miR-1246) were upregulated in exosomes from AIDS combined with TM infection patients. ROC analyses showed that the AUC in combined diagnosis of the three miRNAs was 0.742, and the diagnostic sensitivity and specificity were 0.568 and 0.861, respectively. In the biological process analysis, all the 3 miRNAs were involved in transcription, DNA-templated and positive regulation of transcription from RNA polymerase II promoter. At the same time, the related pathways were involved in TGF-β signaling pathway, AMPK signaling pathway, Wnt signaling pathway, MAPK signaling pathway, cGMP-PKG and cAMP signaling pathway, etc.

Conclusion

miR-192-5p, miR-194-5p and miR-1246 in serum exosomes might be a potential biomarker for AIDS combined with TM infection patients, which may be involved in TGF-β signaling pathway, AMPK signaling pathway, Wnt signaling pathway, MAPK signaling pathway, cGMP-PKG and cAMP signaling pathway, etc. Further research is needed on the biological functions and mechanisms of these miRNAs.

Long non-coding RNA anti-differentiation non-coding RNA affects proliferation, invasion, and migration of breast cancer cells by targeting miR-331

We aimed to evaluate the effects of long-chain non-coding RNA (lncRNA) anti-differentiation non-coding RNA (ANCR) on the proliferation, invasion, and migration of breast cancer cells by targeting miR-331. Forty-eight breast cancer and paracancerous tissue samples were collected. LncRNA ANCR expressions in breast cancer and adjacent tissues, human breast cancer cells and mammary epithelial cells, and miR-331 expressions in interfering cell line MDA-MB-231 (MCF-7)-shANCR, negative control MDA-MB-231 (MCF-7)-shNC and blank control MDA-MB-231 (MCF-7) were detected by real-time quantitative PCR. The correlations between lncRNA ANCR expression and clinicopathological characteristics were analyzed. Cell proliferation was detected by MTT and colony formation assays. Invasion and migration were tested by Transwell and scratch assays, respectively. The targeting relationship between ANCR and miR-331 was analyzed using the TargetScan database, and their interaction was studied using a dual-luciferase reporter assay. The expression of lncRNA ANCR in breast cancer tissue was significantly lower than that in adjacent normal tissue (p < 0.05). LncRNA ANCR was lowly expressed in various human breast cancer cell lines, being lowest in high-metastatic cell line (MDA-MB-231HM) (p < 0.05). Silencing lncRNA ANCR significantly enhanced the proliferation and invasion capacities of breast cancer cells, and promoted their tumor formation abilities in nude mice (p < 0.05). ANCR bound miR-331 targetedly, and the former negatively regulated the expression of the latter. LncRNA ANCR is lowly expressed upon breast cancer, and inhibits cell proliferation, invasion, and migration in vitro and in vivo. LncRNA ANCR exerts antitumor effects by targetedly binding miR-331 and then inhibiting its expression.