5-Hydroxymethylcytosine in circulating cell-free DNA as a potential diagnostic biomarker for SLE.

BACKGROUND: SLE is a complex autoimmune disease with heterogeneous manifestations and unpredictable outcomes. Early diagnosis is challenging due to non-specific symptoms, and current treatments only manage symptoms. Epigenetic alternations, including 5-Hydroxymethylome (5hmC) modifications, are important contributors to SLE pathogenesis. However, the 5hmC modification status in circulating cell-free DNA (cfDNA) of patients with SLE remains largely unexplored. We investigated the distribution of 5hmC in cfDNA of patients with SLE and healthy controls (HCs), and explored its potential as an SLE diagnosis marker. METHODS: We used 5hmC-Seal to generate genome-wide 5hmC profiles of plasma cfDNA and bioinformatics analysis to screen differentially hydroxymethylated regions (DhMRs). In vitro mechanistic exploration was conducted to investigate the regulatory effect of CCCTC-binding factor (CTCF) in 5hmC candidate biomarkers. RESULTS: We found distinct differences in genomic regions and 5hmC modification motif patterns between patients with SLE and HCs, varying with disease progression. Increased 5hmC modification enrichment was detected in SLE. Additionally, we screened 151 genes with hyper-5hmC, which are significantly involved in SLE-related processes, and 5hmC-modified BCL2, CD83, ETS1 and GZMB as SLE biomarkers. Our findings suggest that CTCF regulates 5hmC modification of these genes by recruiting TET (ten-eleven translocation) protein, and CTCF knockdown affected the protein expression of these genes in vitro. CONCLUSIONS: Our findings demonstrate the increased 5hmC distribution in plasma cfDNA in different disease activity in patients with SLE compared with HCs and relating DhMRs involved in SLE-associated pathways. Furthermore, we identified a panel of SLE relevant biomarkers, and these viewpoints could provide insight into the pathogenesis of SLE.

Variations in antibiotic resistance genes and removal mechanisms induced by C/N ratio of substrate during composting.

For a comprehensive insight into the potential mechanism of the removal of antibiotic resistance genes (ARGs) removal induced by initial substrates during composting, we tracked the dynamics of physicochemical properties, bacterial community composition, fungal community composition, the relative abundance of ARGs and mobile genetic genes (MGEs) during reed straw and cow manure composting with different carbon to nitrogen ratio. The results showed that the successive bacterial communities were mainly characterized by the dynamic balance between Firmicutes and Actinobacteria, while the fungal communities were composed of Ascomycota. During composting, the interactions between bacteria and fungi were mainly negative. After composting, the removal efficiency of ARGs in compost treatment with C/N ≈ 26 (LL) was higher than that in compost treatment with C/N ≈ 35 (HL), while MGEs were completely degraded in HL and enriched by 2.3% in LL. The large reduction in the relative abundance of ARGs was possibly due to a decrease in the potential host bacterial genera, such as Advenella, Tepidimicrobium, Proteiniphilum, Acinetobacter, Pseudomonas, Flavobacteria and Arcbacter. Partial least-squares path modeling (PLS-PM) revealed that the succession of bacterial communities played a more important role than MGEs in ARGs removal, while indirect factors of the fungal communities altered the profile of ARGs by affecting the bacterial communities. Both direct and indirect factors were affected by composting treatments. This study provides insights into the role of fungal communities in affecting ARGs and highlights the role of different composting treatments with different carbon to nitrogen ration on the underlying mechanism of ARGs removal.

Association between IDH1/2 mutations and brain glioma grade.

Isocitrate dehydrogenase 1/2 (IDH)1/2 mutations are frequently detected in glioma. The aim of the present study was to investigate the association between IDH1/2 mutations and glioma grades. The current study was retrospective and used samples from 206 patients with brain glioma and 9 patients with spinal cord glioma as a control. Patients were diagnosed and graded according to the World Health Organization classification of tumors of the central nervous system. The association of patient age with glioma grade was evaluated, and IDH1/2 mutations were also examined and analyzed in different grades. On average, brain glioma grade tended to increase with increasing patient age; patients with grade IV (primary) gliomas had a significantly higher mean age than those with grades I and II (P<0.05), and patients with grade II glioma had a significantly lower mean age than those with grade III (P<0.05). The majority of brain gliomas with mutations in IDH1/2 in grade II, II-III and III occurred in adults, rather than adolescents. IDH1/2 mutations occurred most frequently in grade II, II-III and III gliomas, and these mutation frequencies differed significantly between brain glioma grades (P<0.001). In summary, mutations in IDH1/2 were associated with grade II, II-III and III brain gliomas, and possibly with the progression of brain glioma from grade II to grade III.

Bioinformatics analysis of the molecular mechanism of diffuse intrinsic pontine glioma.

The present study aimed to elucidate key molecular mechanisms in the progression of diffuse intrinsic pontine glioma (DIPG). The gene expression profile GSE50021, which consisted of 35 pediatric DIPG samples and 10 normal brain samples, was downloaded from the Gene Expression Omnibus database. The differentially-expressed genes (DEGs) in the pediatric DIPG samples were identified. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome pathways of DEGs were enriched and analyzed. The protein-protein interaction (PPI) network of the DEGs was constructed and functional modules of the PPI network were disclosed using ClusterONE. A total of 679 DEGs (454 up- and 225 downregulated) were identified in the pediatric DIPG samples. DEGs were significantly enriched in various GO terms, and KEGG and Reactome pathways. The PPI network of upregulated (153 nodes and 298 connections) and downregulated (71 nodes and 124 connections) DEGs, and two crucial modules, were obtained. Downregulated genes in module 2, such as cholecystokinin (CCK), gastrin (GAST), adenylate cyclase 2 (brain) (ADCY2) and 5-hydroxytryptamine (serotonin) receptor 7 (HTR7), were significantly enriched in the calcium signaling pathway, the neuroactive ligand-receptor interaction pathway and in GO terms, such as the G-protein coupled receptor (GPCR) signaling pathway, while upregulated genes in module 1 were not enriched in any pathways or GO terms. CCK and GAST associated with the GPCR signaling pathway, HTR7 enriched in the neuroactive ligand-receptor interaction, and ADCY2 and HTR7 involved in the calcium signaling pathway may be key mechanisms playing crucial roles in the development and progression of DIPG.

[CT appearance and p16 gene abnormality of peripheral lung cancer].

OBJECTIVE: To investigate the relationship between the mutation and abnormal expression of p16 gene in peripheral lung carcinoma and its CT manifestations. METHODS: Immunohistochemistry and PCR-SSCP were used to detect P16 protein expression and p16 gene mutation of 52 cases of peripheral lung cancer. All patients were scanned with spiral CT before the operation and proved by pathology. RESULTS: Of the 52 cases of lung cancer tissues, the negative expression rate of p16 gene protein was 53.8% (28/52), and the deletion or mutation rate of the exon 2 was 23.1% (12/52). There were significant statistical differences of p16 gene defect and its protein loss rates among groups of different clinical stages (P < 0.05), but among groups of different tissue types, different differentiation degree p16 gene defect and its protein loss rates showed no significant statistical difference (P > 0.05). In lung cancer patients with CT appearances of thin spicule, speculated protuberance, pleural indentation, and metastasis of lymph node, p16 gene and its protein loss rates were much higher than those without CT manifestations mentioned above (P < 0.05). However, there were no statistical differences among groups of different tumor sizes, with or without lobulation, with or without cavity, and different contrast enhanced CT values (P > 0.05). CONCLUSION: p16 gene mutation and abnormal expression may play an important role in the occurrence and development of lung cancer, and it is relative to CT appearances of lung cancer. p16 gene may be used as a predicting index for clinical diagnosis and prognosis assessment.