Journal of Gene Medicine

BACKGROUND: Exosomal circRNAs played critical roles in tumor development and progression and might be novel biomarkers in the diagnosis and treatment of various cancers. However, the biological functions and clinical implications of exosomal circRNAs in breast cancer are unclear. METHODS: Expression profiles of exosomal circRNAs in exoRBase 2.0 database were used to identify differentially expressed exosomal circRNAs in breast cancer. The LASSO and SVM-RFE algorithm followed by multivariate logistic regression analysis were performed to construct the diagnostic model...

BACKGROUND: Hereditary spastic paraplegia-81 is a recently identified, rare autosomal recessive disease, caused due to biallelic pathogenic variants in the SELENOI gene, with only two families reported to date. The features documented in the two previous affected families include sensorineural deafness, blindness, cleft palate, delayed motor development, regression of motor skills, impaired intellectual development, poor speech and language acquisition, spasticity, hyperreflexia, white matter abnormalities, and cerebral and cerebellar atrophy...

Development of biological pacemaker cells is highly essential to avoid the long-term negative effects of pacemaker use such as pacemaker-induced heart failure. Differentiation of induced pluripotent stem cells (iPSCs) into cardiomyocytes (CMs) can be induced via the regulation of the Wnt signaling pathway. Real-time quantitative PCR (qPCR), western blotting, immunofluorescence staining, and patch-clamp technique were used to analyze the ability of ISL1 to induce the transformation of iPSC-CMs into pacemaker-like cells...

BACKGROUND: WD repeat domain 3 (WDR3) is involved in tumor growth and proliferation, but its role in the pathological mechanism of prostate cancer (PCa) is still unclear. METHODS: WDR3 gene expression levels were obtained by analyzing databases and our clinical specimens. The expression levels of genes and proteins were determined by RT-PCR, western blotting and immunohistochemistry, respectively. CCK8 assays were used to measure the proliferation of PCa cells. Cell transfection was used to study the role of WDR3 and USF2 in PCa...

Immunogenic cell death (ICD) is one of the mechanisms regulating cell death, which activates adaptive immunity in immunocompetent hosts and is associated with tumor progression, prognosis and therapeutic response. Endometrial cancer (EC) is one of the most common malignancies of the female genital tract, and the potential role of immunogenic cell death related genes (IRGs) in the tumor microenvironment (TME) remains unclear. We described the variation of IRGs and assessed expression patterns in EC samples from TCGA and GEO cohorts...

BACKGROUND: Acute rejection (AR) is a major problem following liver transplantation (LT). Extracellular vesicles (EVs) are involved in various pathological processes including liver disease. Effect of EVs derived from bone marrow mesenchymal stem cells (BMSCs) on AR injury after orthotopic liver transplantation (OLT) in mice was investigated in this study. METHODS: BMSCs and EVs were isolated and identified. OLT mouse model was established using Kamada's two cuff method and injected with EVs, followed by liver function detection and measurement of inflammatory cytokines (IL-10, IFN-γ, and TNF-α), M1 and M2 markers (TNF-α, iNOS, Retnla, and Arg1) were detected...

BACKGROUND: Esophageal adenocarcinoma (EAC) is one of the most common malignant tumors, and the number of patients is increasing year by year. T-cell exhaustion (TEX) is an important risk factor for tumor immunosuppression and invasion, but its underlying mechanism in the pathogenesis of EAC is not clear. METHODS: Unsupervised clustering was performed to screen relevant genes based on Gene Set Variation Analysis (GSVA) scores of the three pathways of the HALLMARK gene set IL2\IFNG\TNFA...

BACKGROUND: A growing number of studies have shown that inflammation-related components of the tumor microenvironment (TME) affect the clinical outcomes of cancer patients, and advances in radiomics may help predict survival and prognosis. METHODS: We performed a systematic analysis of inflammation-related genes (IRGs) in clear cell renal cell carcinoma (ccRCC) from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). and map their interaction network to assess the specific relationship between these DEIRGs and inflammation...

BACKGROUND: During infection, Mycobacterium abscessus (M. abscessus) encounters numerous environmental changes and adapts to them using a variety of complex mechanisms. Non-coding small RNAs (sRNAs) have been shown in other bacteria to be involved in post-transcriptional regulatory pathways, including environmental stress adaptation. However, the potential role of sRNAs in the resistance to oxidative stress in M. abscessus was not clearly described. METHODS: In this study, we analyzed putative sRNAs identified by RNA-seq experiments in M...

Adipocytes play a crucial role in the metabolism of lipids and sugars. Their response varies depending on the circumstances or other factors influenced by physiological and metabolic stresses. People living with HIV (PLWH) experience different effects of HIV and Highly Active Antiretroviral Therapy (HAART) on their body fat. Some patients respond well to ART, while others taking the similar regimens do not. The genetic makeup of patients has been strongly linked to the variable responses to HAART among PLWH...

BACKGROUND: We aimed to provide a new typing method for Osteosarcoma (OS) based on single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data from the perspective of lipid metabolism and examine its potential mechanisms in the onset and progression of OS. METHODS: Scores for six lipid metabolic pathways were calculated by single-sample gene set enrichment analysis (ssGSEA) based on a scRNA-seq dataset and three microarray expression profiles. Subsequently, cluster typing was conducted using unsupervised consistency clustering...

UNLABELLED: Background and aims This study performed a network pharmacology analysis to explore the potential anti-cancer activity of baicalein against oral squamous cell carcinoma (OSCC). METHODS: The differentially expressed genes in OSCC were identified by the Linear Models for Microarray Data method, and the key module related to OSCC was acquired by the Weighted Gene Co-expression Network Analysis from GSE30784. Baicalein targets were obtained from GeneCards, SwissTargetPrediction, and TCMSP (traditional Chinese medicine systems pharmacology database and analysis platform) databases...

BACKGROUND: Glycosylation has been proposed as a new cancer hallmark. However, focusing on specific glycans or glycoproteins may lose much data relevant to glycosylation alterations. This study aimed to first comprehensively investigate the expression and mutation profiles of glycosylation-related genes (GRgenes) in prostate cancer (PCa) and then develop a glycosylation signature and explore its role in predicting the progression and immunotherapeutic response of PCa. METHODS: Based on the Cancer Genome Atlas database, we comprehensively screened potential prognostic GRgenes and analyzed their expression and mutation profiles in PCa...

BACKGROUND: Cuproptosis is implicated in regulating tricarboxylic acid cycle and associated with tumor therapeutic sensitivity, patient outcomes and tumorigenesis. However, the classification and prognostic effect of cuproptosis-associated genes (CAGs), the relationship between cuproptosis and tumor microenvironment (TME) as well as the treatment of lower-grade glioma (LrGG) remain enigmatic. METHODS: The genetic and transcriptional alterations, prognostic value and classification related to cuproptosis were systematically analyzed...

BACKGROUND: Intervertebral disc degeneration (IDD) is a primary health problem worldwide that involves oxidative stress, ferroptosis, and lipid metabolism. However, the underlying mechanism remains unclear. We investigated whether the transcription factor BACH1 affected IDD progression by regulating HMOX1/GPX4-mediated ferroptosis and lipid metabolism in nucleus pulposus cells (NPCs). METHODS: A rat IDD model was created to detect BACH1 expression in intervertebral disc tissues...

BACKGROUND AND AIMS: Long non-coding RNAs (lncRNAs) have been established to promote or inhibit the oncogenic and tumorigenic potential of various cancers, acting as competing endogenous RNAs (ceRNAs) for specific microRNAs. The primary objective of the study was to investigate the underlying mechanism by which LINC02027/miR-625-3p/PDLIM5 axis affects the proliferation, migration and invasion in hepatocellular carcinoma (HCC). METHODS: The differentially expressed gene was selected based on gene sequencing and bioinformation database analysis of HCC and adjacent nontumor tissues...

BACKGROUND: Although great progress has been made in studying the function of long non-coding RNA (lncRNA) in various tumors, including gastric cancer (GC). However, there are still numerous lncRNAs that have not yet been studied and explored for their roles in GC, and their important functions need to be further revealed. METHODS: Through analyzing The Cancer Genome Atlas (TCGA) database combined with bioinformatics survival tools, a novel GC-related lncRNA LGALS8-AS1 was identified...

BACKGROUND: Great improvement has been made for the prognosis of esophageal cancer (ESCA) with the applying of chemotherapy and immunotherapy. But the majority of cases remain to be resistant to these regimens. Hence it is in urgent need to characterize the subtypes of ESCA with favorable survival outcome and drug responsiveness. METHODS: We characterized the malignant cells of ESCA and explored their communication with immune cells by Cellchat algorithm. The ligand-receptors interaction pairs were then used as inputting information to identify the subtypes of ESCA by unsupervised clustering analysis...

BACKGROUND: Polypropylene is a thermoplastic polymer playing the role of an endocrine disruptor that interferes with the union, emission, transport, or elimination of normal hormones. Epidemiological information indicated the relation of endocrine-disturbing chemicals with prostate cancer, testis tumor, and diminished fertility. p53 is a key tumor silencer gene. The present study aims to evaluate Luteinizing hormone (LH) and Follicle-stimulating hormone (FSH) levels and the risk of p53 mutations due to exposure to Polypropylene in non-tumorous adult male factory workers...

BACKGROUND: Osteoporosis (OP) is a metabolic bone disease involving reduced bone mass. Adipose-derived stem cells (ASCs) play an important role in bone regeneration. Emerging evidence suggests that Methyltransferase-like 3(METTL3) plays a significant role in bone development and metabolism. Therefore, this study investigates changes to METTL3 in the osteogenic differentiation of adipose stem cells in osteoporotic rats (OP-ASCs) and explores ways to enhance their osteogenic ability. METHODS: An animal model of osteoporosis was established by removing both ovaries in rats (OVX)...