Pseudogene AK4P1 promotes pancreatic ductal adenocarcinoma progression through relieving miR-375-mediated YAP1 degradation

MiR-375 Inhibitor Alleviates Inflammation and Oxidative Stress by Upregulating the GPR39 Expression in Atherosclerosis

Atherosclerosis may be caused or developed by an immune response and antioxidation imbalance. MicroRNA-375 (miR-375) or G-protein-coupled receptor 39 (GPR39) is involved in vascular endothelial cell injury, but their role in atherosclerosis is unknown. This experiment aimed to determine the action of the miR-375/GPR39 axis in atherosclerosis.Human aortic endothelial cells (HAECs) were treated with 10 ng/mL of oxidised low-density lipoprotein (ox-LDL) for 24 hours to induce HAEC injury, which was treated by the miR-375 inhibitor, GPR39 inhibitor, or agonist. High-fat diet (HFD) -induced ApoE-/- mice were made as an atherosclerosis model for miR-375 inhibitor treatment. Cell Counting Kit-8 was applied to detect HAEC viability. HAEC apoptosis and ROS levels were measured using flow cytometry. Vascular histopathology and the GPR39 expression were detected using hematoxylin-eosin and immunohistochemistry. The expressions of interleukin (IL) -6, IL-1β, and tumour necrosis factor-α (TNF-α) were assessed using an enzyme-linked immunosorbent assay. The miR-375, GPR39, NOX-4, and p-IκBα/IκBα levels were measured using quantitative reverse transcription polymerase chain reaction or western blot.MiR-375 and GPR39 levels increased and decreased in ox-LDL-treated HAECs, respectively. The miR-375 inhibitor or GPR39 agonist promoted cell viability and inhibited apoptosis in ox-LDL-induced HAEC injury. The miR-375 inhibitor also significantly downregulated the IL-6, IL-1β, TNF-α, p-IκBα/IκBα, ROS, and NOX-4 expressions to alleviate oxidative stress and inflammation, which were reversed by the GPR39 inhibitor. An in vivo experiment proved that the miR-375 inhibitor upregulated the GPR39 expression and improved inflammation, oxidative stress, and endothelial cell damage associated with atherosclerosis.The miR-375 inhibitor improved inflammation, oxidative stress, and cell damage in ox-LDL-induced HAECs and HFD-induced ApoE-/- mice by promoting the GPR39 expression, which provided a new theoretical basis for the clinical treatment of atherosclerosis.

Functional and Potential Therapeutic Implication of MicroRNAs in Pancreatic Cancer

The alarmingly low five-year survival rate for pancreatic cancer presents a global health challenge, contributing to about 7% of all cancer-related deaths. Late-stage diagnosis and high heterogeneity are the biggest hurdles in treating pancreatic cancer. Thus, there is a pressing need to discover novel biomarkers that could help in early detection as well as improve therapeutic strategies. MicroRNAs (miRNAs), a class of short non-coding RNA, have emerged as promising candidates with regard to both diagnostics and therapeutics. Dysregulated miRNAs play pivotal roles in accelerating tumor growth and metastasis, orchestrating tumor microenvironment, and conferring chemoresistance in pancreatic cancer. The differential expression profiles of miRNAs in pancreatic cancer could be utilized to explore novel therapeutic strategies. In this review, we also covered studies on recent advancements in various miRNA-based therapeutics such as restoring miRNAs with a tumor-suppressive function, suppressing miRNA with an oncogenic function, and combination with chemotherapeutic drugs. Despite several challenges in terms of specificity and targeted delivery, miRNA-based therapies hold the potential to revolutionize the treatment of pancreatic cancer by simultaneously targeting multiple signaling pathways.

Integration of RNA-Seq and Machine Learning Identifies Hub Genes for Empagliflozin Benefitable Heart Failure with Reduced Ejection Fraction

Purpose

This study aimed to analyze the hub genes of heart failure with reduced ejection fraction (HFrEF) treated with Empagliflozin using RNA sequencing (RNA-seq) and bioinformatics methods, including machine learning.

Methods

From February 2021 to February 2023, nine patients with HFrEF were enrolled from our hospital's cardiovascular department. In addition to routine drug treatment, these patients received 10 mg of Empagliflozin once daily for two months. Efficacy was assessed and RNA-seq was performed on peripheral blood before and after treatment with empagliflozin. HFrEF-related hub genes were identified through bioinformatics analyses including differential gene expression analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, immune infiltration analysis, machine learning, immune cell correlation analysis and clinical indicator correlation analysis.

Results

The nine patients included in this study completed a two-month treatment regimen, with an average age of 62.11 ± 6.36 years. By performing bioinformatics analysis on the transcriptome from the treatment groups, 42 differentially expressed genes were identified, with six being up-regulated and 36 being down-regulated (|log2FC|>1 and adj.pvalue<0.05). Immune infiltration analysis of these genes demonstrated a significant difference in the proportion of plasma between the pre-treatment and post-treatment groups (p<0.05). Two hub genes, GTF2IP14 and MTLN, were finally identified through machine learning. Further analysis of the correlation between the hub genes and immune cells suggested a negative correlation between GTF2IP14 and naive B cells, and a positive correlation between MTLN and regulatory T cells and resting memory CD4+ T cells (p<0.05).

Conclusion

Through RNA-seq and bioinformatics analysis, this study identified GTF2IP14 and MTLN as the hub genes of HFrEF, and their mechanisms may be related to immune inflammatory responses and various immune cells.

Pseudogenes in Cancer: State of the Art

Pseudogenes are duplicates of protein-coding genes that have accumulated multiple detrimental alterations, rendering them unable to produce the protein they encode. Initially disregarded as "junk DNA" due to their perceived lack of functionality, research on their biological roles has been hindered by this assumption. Nevertheless, recent focus has shifted towards these molecules due to their abnormal expression in cancer phenotypes. In this review, our objective is to provide a thorough overview of the current understanding of pseudogene formation, the mechanisms governing their expression, and the roles they may play in promoting tumorigenesis.

Profiling of a novel circadian clock-related prognostic signature and its role in immune function and response to molecular targeted therapy in pancreatic cancer

BACKGROUND

Pancreatic ductal adenocarcinoma (PADA) represents a devastating type of pancreatic cancer with high mortality. Defining a prognostic gene signature that can stratify patients with different risk will benefit cancer treatment strategies.

METHODS

Gene expression profiles of PADA patients were acquired from the Cancer Genome Atlas and Gene Expression Omnibus, including GSE62452 and GSE28735. Differential expression analysis was carried out using the package edgeR in R. Intro-tumor immune infiltrates were quantified by six different computational algorithms XCELL, TIMER, QUANTISEQ, MCPCOUNTER, EPIC, and CIBERSORT. Biological processes were investigated based on R package "clusterProfiler".

RESULTS

13 genes (ARNTL2, BHLHE40, FBXL17, FBXL8, PPP1CB, RBM4B, ADRB1, CCAR2, CDK1, CSNK1D, KLF10, PSPC1, SIAH2) were eligible for the development of a prognostic gene signature. Performance of the prognostic gene signature was assessed in the discovery set (n = 210), validation set (n = 52), and two external data set (GSE62452, n = 65, and GSE28735, n = 84). Area under the curve (AUC) for predicting 3-year overall survival was 0.727, 0.732, 0.700, and 0.658 in the training set, the validation set, and the two test sets, respectively. KM curve revealed that the low-risk group had an improved prognosis than the high-risk group in all four datasets. PCA analysis demonstrated that the low-risk group was apparently separated from the high-risk group. CD8 T cell and B cell were significantly reduced in the high-risk group than in the low-risk group, while neutrophils were significantly augmented in the high-risk group than in the low-risk group. BMS-536924, Foretinib, Linsitinib, and Sabutoclax were more sensitive in the low-risk group, whereas Erlotinib was more effective in the high-risk group.

CONCLUSIONS

We successfully established and verified a novel circadian clock-related gene signature, which could stratify patients with different risk and be reflective of the therapeutic effect of molecular targeted therapy. Our findings could incorporate the pharmacological modulation of circadian clock into future therapeutic strategies.