HLA-DMB restricts human T-cell leukemia virus type-1 (HTLV-1) protein expression via regulation of ATG7 acetylation

HLA-DMB correlates with antitumor immunity and an improved prognosis in endometrial carcinoma tumors

Introduction

Endometrial Carcinoma (UCEC) is a prevalent malignant tumor within the female reproductive system. HLA-DMB, the beta chain of the non-classical MHC class II protein HLA-DM, has been implicated in the progression of various cancers. However, its role in the development of endometrial carcinoma remains unclear. Therefore, we conducted a preliminary exploration of the prognostic value and potential mechanisms of HLA-DMB in uterine corpus endometrial carcinoma (UCEC).

Methods

The differential expression of HLA-DMB was analyzed in 554 tumor samples and 35 normal samples obtained from the TCGA database. The differential expression of HLA-DMB across various cancers, along with immune infiltration analysis, was conducted using the TIMER2.0 database. Additionally, the expression of HLA-DMB in endometrial carcinoma was examined in the GEPIA2 database, along with its relationship to prognosis. Furthermore, TISIDB was utilized to predict the relationships between HLA-DMB and various immune enhancement factors as well as immunosuppressive factors. Gene Ontology (GO) analysis and Gene Set Enrichment Analysis (GSEA) were employed to explore the signaling pathways associated with HLA-DMB in endometrial cancer. Univariate COX regression analysis was performed to identify prognostic factors for endometrial carcinoma (EC), and a multivariate COX proportional hazards regression model was used to confirm that HLA-DMB can serve as an independent prognostic factor for EC. The protein interaction network of HLA-DMB was constructed using the STRING database, and the chemical drugs related to HLA-DMB were predicted through the CTD database. Finally, the expression of HLA-DMB was validated by qPCR and immunohistochemistry.

Results

The expression of HLA-DMB at both mRNA and protein levels is significantly higher in UCEC tissues compared to normal tissues. Prognostic analyses indicate that increased expression of HLA-DMB correlates with improved patient prognosis, suggesting its potential as an independent prognostic factor for UCEC. Furthermore, in endometrial cancer, elevated levels of HLA-DMB are associated with higher immune infiltration scores and are closely related to various immune-enhancing factors. Mechanistically, HLA-DMB primarily participates in CD22-mediated regulation of B cell receptors (BCR), leading to BCR antigen activation and the production of second messengers. In our drug analysis, we identified several chemical agents associated with HLA-DMB, including cisplatin, dexamethasone, and ethinylestradiol.

Discussion

This study elucidates the function and underlying mechanisms of HLA-DMB in UCEC, providing a potential biomarker and target for immunotherapy in this disease.

Elucidating common biomarkers and pathways of osteoporosis and aortic valve calcification: insights into new therapeutic targets

BACKGROUND

Osteoporosis and aortic valve calcification, prevalent in the elderly, have unclear common mechanisms. This study aims to uncover them through bioinformatics analysis.

METHODS

Microarray data from GEO was analyzed for osteoporosis and aortic valve calcification. Differential expression analysis identified co-expressed genes. SVM-RFE and random forest selected key genes. GO and KEGG enrichment analyses were performed. Immunoinfiltration and GSEA analyses were subsequently performed. NetworkAnalyst analyzed microRNAs/TFs. HERB predicted drugs, and molecular docking assessed targeting potential.

RESULTS

Thirteen genes linked to osteoporosis and aortic valve calcification were identified. TNFSF11, KYNU, and HLA-DMB emerged as key genes. miRNAs, TFs, and drug predictions offered therapeutic insights. Molecular docking suggested 17-beta-estradiol and vitamin D3 as potential treatments.

CONCLUSION

The study clarifies shared mechanisms of osteoporosis and aortic valve calcification, identifies biomarkers, and highlights TNFSF11, KYNU, and HLA-DMB. It also suggests 17-beta-estradiol and vitamin D3 as potential effective treatments.

Insights on E1-like enzyme ATG7: functional regulation and relationships with aging-related diseases

Autophagy is a dynamic self-renovation biological process that maintains cell homeostasis and is responsible for the quality control of proteins, organelles, and energy metabolism. The E1-like ubiquitin-activating enzyme autophagy-related gene 7 (ATG7) is a critical factor that initiates classic autophagy reactions by promoting the formation and extension of autophagosome membranes. Recent studies have identified the key functions of ATG7 in regulating the cell cycle, apoptosis, and metabolism associated with the occurrence and development of multiple diseases. This review summarizes how ATG7 is precisely programmed by genetic, transcriptional, and epigenetic modifications in cells and the relationship between ATG7 and aging-related diseases.

TRIM7/RNF90 promotes autophagy via regulation of ATG7 ubiquitination during L. monocytogenes infection

L. monocytogenes is a widely used infection model for the research on pathogenesis and host defense against gram-positive intracellular bacteria. Emerging evidence indicates that posttranslational modifications play a critical role in the regulation of macroautophagy/autophagy. However, little is known about the posttranslational modifications of ATG7, the essential protein in the autophagy process. In this study, we demonstrated that the RING-type E3 ligase TRIM7/RNF90 positively regulated autophagosome accumulation by promoting the ubiquitination of ATG7 at K413, thereby affecting L. monocytogenes infection. TRIM7 expression was induced by a variety range of conditions, including starvation, rapamycin stimulation, and L. monocytogenes infection. TRIM7 deficiency in mice or cells resulted in elevated innate immune responses and increased L. monocytogenes infection. ATG7 was associated with TRIM7 and the positive regulatory role of TRIM7 in L. monocytogenes infection-, starvation- or rapamycin-induced autophagosome accumulation was suggested by TRIM7 deficiency, TRIM7 overexpression, and TRIM7 knockdown. Further mechanistic investigation indicated that TRIM7 promoted the K63-linked ubiquitination of ATG7 at K413 and ubiquitination at this site was required for the function of ATG7 in autophagy and L. monocytogenes infection. Thus, our findings suggested a new regulator in intracellular bacterial infection and autophagy, with a novel posttranslational modification targeting ATG7. This research may expand our understanding of host anti-bacterial defense and the role of autophagy in intracellular bacterial infection.Abbreviations: ATG3: autophagy related 3; ATG5: autophagy related 5; ATG7: autophagy related 7; ATG10: autophagy related 10; ATG12: autophagy related 12; ATG16L1: autophagy related 16 like 1; Baf A1: bafilomycin A1; CQ: chloroquine; BMDC: bone marrow-derived dendritic cell; BMDM: bone marrow-derived macrophage; CFUs: colony-forming units; CXCL10/IP-10: C-X-C motif chemokine ligand 10; EBSS: Earle's balanced salt solution; ELISA: enzyme-linked immunosorbent assay; IFIT1/ISG56: interferon induced protein with tetratricopeptide repeats 1; IFNB/IFN-β: interferon beta; IL6: interleukin 6; IRF3, interferon regulatory factor 3; Lm: L. monocytogenes; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; MOI: multiplicity of infection; PLA: proximity ligation assay; PMA: phorbol myristate acetate; PMA-THP1, PMA-differentiated THP1; PMs: peritoneal macrophages; PTMs: posttranslational modifications; STING1, stimulator of interferon response cGAMP interactor 1; TBK1, TANK binding kinase 1; TNF/TNF-α: tumor necrosis factor; TRIM7/RNF90: tripartite motif containing; Hainan Provincial Natural Science Foundation of China.

Construction and validation of a novel immune and tumor mutation burden-based prognostic model in lung adenocarcinoma

Lung adenocarcinoma (LUAD), the most common type of cancer, is hard to diagnose and has an unfavorable prognosis. Tumor mutation burden (TMB) is a useful predictor and can also determine the efficacy of immunotherapy in various cancers. The present study focused on unraveling the association between immune infiltration and TMB and developing an immune- and TMB-related prognostic model to predict LUAD patients' prognosis. The results revealed that the immune-related prognostic model (IPM) based on TMB was capable of classifying LUAD patients in all cohorts into different risk groups. The IPM was useful and had a significant correlation with LUAD patients' overall survival (OS). Based on the multivariate Cox analysis results, the IPM was proved to be an independent predictive biomarker. Furthermore, the five hub genes and the immune-related model were related to different immune infiltrating cells. The IPM was related to immune checkpoints. At last, an effective nomogram was established to predict LUAD patients' prognosis. To conclude, our IPM is effective in predicting LUAD patients' prognosis and provides novel insights into immunotherapy for LUAD.

The Optimization and Biological Significance of a 29-Host-Immune-mRNA Panel for the Diagnosis of Acute Infections and Sepsis

In response to the unmet need for timely accurate diagnosis and prognosis of acute infections and sepsis, host-immune-response-based tests are being developed to help clinicians make more informed decisions including prescribing antimicrobials, ordering additional diagnostics, and assigning level of care. One such test (InSep™, Inflammatix, Inc.) uses a 29-mRNA panel to determine the likelihood of bacterial infection, the separate likelihood of viral infection, and the risk of physiologic decompensation (severity of illness). The test, being implemented in a rapid point-of-care platform with a turnaround time of 30 min, enables accurate and rapid diagnostic use at the point of impact. In this report, we provide details on how the 29-biomarker signature was chosen and optimized, together with its molecular, immunological, and medical significance to better understand the pathophysiological relevance of altered gene expression in disease. We synthesize key results obtained from gene-level functional annotations, geneset-level enrichment analysis, pathway-level analysis, and gene-network-level upstream regulator analysis. Emerging findings are summarized as hallmarks on immune cell interaction, inflammatory mediators, cellular metabolism and homeostasis, immune receptors, intracellular signaling and antiviral response; and converging themes on neutrophil degranulation and activation involved in immune response, interferon, and other signaling pathways.