Critical Reviews in Eukaryotic Gene Expression最新文献

The complement system (CS) is linked to the progression of gastric cancer (GC), which has a high mortality rate, though its mechanisms in GC remain unclear. This study aims to identify CS-related prognostic genes with causal links to GC, and to investigate their mechanisms. The intersection between differentially expressed genes (DEGs) obtained from the TCGA-STAD dataset and CS-related genes (CRGs) was defined as differentially expressed CRGs (DCRGs). Prognostic genes with a causal association with GC (pCDCRGs) were sequentially identified via Mendelian randomization (MR) analysis and Cox and least absolute shrinkage and selection operator (LASSO) regression analyses, followed by expression analysis. A gene signature and a nomogram were then established based on pCDCRGs and independent prognostic factors. Subsequent analyses focused on functional enrichment, immune relevance, drug sensitivity, gene interactions, and molecular regulatory networks. Eventually, reverse transcription-quantitative PCR (RT-qPCR) was employed to validate expression of pCDCRGs. DCRGs were obtained from the intersection of 8,418 DEGs and 241 CRGs. Among 12 DCRGs with causal association (CDCRGs) with GC, 7 genes were identified as pCDCRGs, including FANCG, FANCF, F2R, C4BPA, SERPINF2, PROC, and CD59. Notably, CD59 was markedly highly expressed in the normal group, whereas the other genes were markedly highly expressed in the GC group. Afterward, an accurate pCDCRG signature was developed. Risk score, age, and stage were recognized as independent risk factors, and the constructed nomogram demonstrated strong predictive accuracy. Additionally, analyses indicated that these 7 pCDCRGs may influence GC by affecting pathways such as complement and coagulation cascades, immune cell infiltration, immune characteristics, immunotherapy responses, and drug sensitivity. These effects may be linked to gene interactions and the regulatory roles of lncRNAs like RMRP and miRNAs such as hsa-mir-613. RT-qPCR showed C4BPA, PROC, F2R, and SERPINF2 were markedly up-regulated, whereas CD59 was markedly down-regulated in GC tissues. This study identified seven complement system-related prognostic genes with causal links to GC, based on which we developed a highly predictive 7-pCDCRG signature, providing valuable insights for clinical prognostic prediction and immunotherapy in GC patients.

Diabetic kidney disease (DKD) is the most common complication of diabetes and a leading cause of chronic kidney disease that frequently leads to end-stage renal disease (ESRD). The pathogenesis of DKD is complex and is not fully understood. This study was designed to identify key targets for DKD diagnosis and explore the underlying molecular mechanisms.

Methods: DKD-specific clusters were selected from single-cell datasets. Gene modules were identified using hairpin-dynamic weighted gene co-expression network analysis (hdWGCNA). Multiple machine learning algorithms were applied to model and screen hub genes from two bulk datasets. Rat model of DKD was built using optical microscopes to observe the histopathological changes in the kidney by HE, PAS, and Masson staining. The expression of RASGRP3, PDE3B, and CD247 in DKD-Rat was verified by RT-PCR, and the expression of RASGRP3, PDE3B, and CD247 in the serum samples of DKD patients was verified by ELISA. The results of sex and age, RASGRP3, PDE3B, CD247 were calculated by multivariate logistic regression analysis.

Results: Three hub genes were obtained through screening single-cell and two bulk datasets. In-depth exploration of the potential molecular mechanisms of the hub genes was conducted using gene set variation analysis (GSVA), immune infiltration analysis, and single-cell correlation analysis. Receiver operating characteristic (ROC) curve confirmed a high diagnostic value of the hub biomarkers, and a high-efficiency diagnostic model was constructed and mutually validated in the two datasets. We found that damaged tubular number and interstitial fibrotic percentage were significantly increased in DKD rat. As shown by HE, PAS and Masson staining, the mRNA levels of PDE3B and CD247 were markedly upregulated in DKD rat compared with those in the control group. Lower expression levels of RASGRP3 mRNA were manifested in DKD. The levels of RASGRP3, PDE3B, CD247 in DKD patients by ELISA were statistically significant (p < 0.05). PDE3B and CD247 had an AUC value greater than 0.9,RASGRP3 had an AUC value greater than 0.7.

Conclusion: This study identified 3 T cell-related hub biomarkers, providing references for the early diagnosis of DKD and changes in T cells during DKD progression.

Breast cancer (BC) is the leading malignancy affecting women globally, characterized by significant heterogeneity. Therefore, our objective was to explore potential targets within the context of intra-tumor heterogeneity (ITH) to modulate the response of tumor-associated macrophages (TAMs) to treatment in BC patients. The TCGA database was used to integrate and analyze human BC samples, from which the ITH score was extracted to identify genetic differences. Using non-negative matrix factorization clustering analysis, we successfully identified two distinct molecular subtypes, referred to as C1 and C2. Notably, subtype C1 exhibited a significantly more favorable prognosis compared with subtype C2. Further investigation of immune cell infiltration using the CIBERSORT algorithm revealed a significant correlation between both subtypes and the infiltration of TAMs. Additionally, we identified SPIB as a key factor influencing TAM infiltration within the model. Notably, SPIB is expressed at low levels in BC and is associated with an unfavorable prognosis for patients. Interestingly, overexpression of SPIB led to increased infiltration of M1 macrophages. In conclusion, this study sheds light on the characteristics of BC and immune cell infiltration within its microenvironment. SPIB emerges as a promising therapeutic candidate, with potential to modulate the immunosuppressive nature of the BC microenvironment and improve patient outcomes.

Keloid formation is an undesirable outcome of wound healing and is detrimental to patients' physical and mental health, while the molecular regulators of its pathogenesis, especially non-coding RNAs (ncRNAs), are largely unknown. In this study, we integrated and analyzed RNA-seq and miRNA microarray datasets of skin samples from keloid-prone and healthy normal individuals to detect the dysregulated long ncRNAs (lncRNAs) and miRNAs. We excavated 583 and 104 keloid-specific lncRNAs and miRNAs, respectively. Moreover, the molecular functions of these ln-cRNAs and miRNAs are all related to ossification. Next, we constructed the relationship between lncRNAs and immune cell infiltration, and found the macrophages, NK cells, and dendritic cells were specifically dysregulated in keloid-prone or normal groups during wound healing. We constructed the potential regulatory network between these cell types and 20 dysregulated lncRNAs, suggesting their regulatory function in keloid formation. At last, we constructed the competitive endogenous RNA network and found two hub lncRNAs and five miRNAs, including DLEU1 and SLC25A21-AS1, miR-197-5p, miR-940, miR-6765-5p, miR-711, and miR-4284, which were highly dysregulated during keloid formation. In summary, these results demonstrate that lncRNAs and miRNAs play important roles and form a regulatory network in the pathogenesis, immune infiltration, and development of keloid formation.

The members of the network (interactome) that controls cancer needs to be known. This network consists of proteins and non-coding, single-stranded RNAs, such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and transfer RNAs (tRNAs). miRNAs are 21-23 nucleotides-long, and degrade messenger RNAs (mRNAs) and lncRNAs. lncRNAs are longer than 200 nucleotides, and sponge (sequester) miRNAs.

Non-small cell lung cancer (NSCLC) has a high global incidence and mortality rate. Although circRNAs have significant attention in tumor research, it's role in NSCLC is uncertain. QRT-PCR and Western blotting were utilized to quantify the expression of circCNKSR2, miR-138-5p, and PLEK2 in NSCLC tissues and cells. The characteristics and subcellular localization of circCNKSR2 were determined using RNase R analysis and qRT-PCR. In vitro functional experiments determined the biological functions of circCNKSR2. The specific binding interactions among circCNKSR2, miR-138-5p, and PLEK2 were evaluated through bioinformatics analysis, luciferase reporter, and rescue assays. In vivo xenograft model was established to examine the impact of circCNKSR2, which was significantly increased in NSCLC tissues and cells. Functional studies demonstrated that silencing circCNKSR2 significantly inhibited NSCLC malignant phenotype and Warburg effect. Bioinformatics analysis and rescue experiments verification indicated circCNKSR2 functioned as a miR-138-5p sponge, and inhibiting miR-138-5p reversed the suppressive effect of silencing circCNKSR2 in NSCLC. Additionally, PLEK2 identified as a miR-138-5p target gene. The potential regulatory role of circCNKSR2 in NSCLC progression and Warburg effect via the miR-138-5p/PLEK2 pathway was demonstrated.

Background: The HECT, C2, and WW domain-containing E3 ubiquitin protein ligase 1 (HECW1) gene is a member of the HECT family of E3 ubiquitin ligases. While HECW1 has been implicated in various cancers, its role in gastric cancer (GC) remains unclear.

Methods: Bioinformatics approaches were employed to investigate HECW1's role in GC. Functional assays, including the CCK-8, transwell migration, and wound healing assays, were performed to assess its impact on GC cell proliferation, invasion, and migration.

Results: HECW1 expression was significantly upregulated in GC tissues compared to normal controls, correlating with specific clinical characteristics. Cox regression analyses identified HECW1 as an independent prognostic factor for GC. Prognostic nomograms accurately predicted 1-, 3-, and 5-year survival rates, with calibration curves closely aligned with the ideal diagonal line. Elevated HECW1 expression was associated with poorer overall survival and disease progression outcomes. ROC analyses demonstrated that HECW1 had strong predictive power for outcomes (AUC = 0.746, CI = 0.683-0.808) and five-year survival rates (AUC = 0.734, CI = 0.600-0.869). Enrichment analysis suggested HECW1's involvement in protein processing and interactions with substrates such as SMAD4, TTF1, DVL1, and NEDD4. Functional assays showed that HECW1 knockdown significantly reduced GC cell proliferation, invasion, and migration.

Conclusions: HECW1 acts as an oncogene in GC and represents a potential prognostic indicator. Targeting HECW1 may inhibit GC progression, providing a promising therapeutic strategy.

Helicobacter pylori (H. pylori) infection promotes the progression of gastric cancer. The purpose of this study is to investigate the effects of H. pylori infection on gastric cancer and the underlying mechanisms. mRNA levels were determined by reverse transcription quantitative PCR (RT-qPCR). Protein expression was detected by Western blot. Cell viability was detected by Cell Counting Kit-8 assay. Cell proliferation was detected by colony formation assay. Cell mobility was detected by transwell assay. The co-localization of NEDD8 activating enzyme E1 subunit 1 (NAE1) and transferrin receptor 1 (TFR1) was determined by fluorescence in situ hybridization (FISH) assay. TFR1 neddylation was determined using in vitro neddylation assay. H. pylori infection contributed to the proliferation, migration, and invasion of gastric cancer. Moreover, H. pylori infection inhibited erastin-induced ferroptosis of gastric cancer cells. H. pylori infection downregulated NAE1, which promoted the neddylation and protein stability of TFR1. Intriguingly, overexpressed NAE1 inhibited the metastasis as well as promoted the ferroptosis of gastric cancer. H. pylori infection mediates malignant behaviors of gastric cancer via inactivating NAE1/TFR1 signaling. Therefore, targeting NAE1/TFR1 signaling may provide a novel strategy for gastric cancer.

Dysregulated microRNAs (miRNAs) are a hallmark of chronic rhinosinusitis, especially chronic rhinosinusitis with nasal polyps (CRSwNP). This study aimed to investigate the role of miR-143-3p in chronic rhinosinusitis. miR-143-3p and mRNA levels were calculated by reverse transcription quantitative polymerase chain reaction (RT-qPCR). Protein expressed was determined by Western blot. The infiltration of CD4 cells and eosinophils was analyzed using immunohistochemistry and hematoxylin and eosin staining. The binding sites between miR-143-3p and TET1 were predicted with TargetScan and verified using luciferase assay. The DNA methylation of interferon-gamma (IFN-γ) was predicted using DNA methylation-specific RT-qPCR assay. The interaction between TET1 and IFN-γ was confirmed using the chromatin immunoprecipitation assay. CD4+ T cell polarization was analyzed using flow cytometry. miR-143-3p was downregulated in CRSwNP patients, mediating nasal polyp presence. Overexpressed miR-143-3p promoted the differentiation of T helper 1 (Th1) cells. miR-143-3p targeted and downregulated the expression of TET1, which was upregulated in CRSwNP patients. TET1-mediated DNA methylation of IFN-γ, inducing its downregulation. Overexpressed TET1 inhibited Th1 differentiation and promoted the Th1 cell to Th2 polarization. miR-143-3p promotes the differentiation of anti-inflammatory Th1 cells in CRSwNP via regulating TET1/IFN-γ axis.

Background: Cystic fibrosis (CF) is common genetic disorder in Europe and North America but rarer in Asian populations.

Objective: To explore the clinical manifestations and gene mutations of cystic fibrosis.

Methods: This case series study enrolled children with CF diagnosed in the pediatric respiratory department of Shandong Provincial Hospital affiliated to Shandong First Medical University between June 2016 and August 2022.

Results: Seven children, including 6 girls and 1 boy, were enrolled. All 7 patients had recurrent wet cough and (chronic) pneumonia. Six patients suffered from chronic sinusitis, 4 patients had recurrent wheezing; 2 patients had chronic diarrhea, malnutrition and growth lag; 2 patients were complicated by allergic bronchopulmonary aspergillosis; and 1 patient had pancreatic insufficiency. Bronchiectasis, thickening of bronchial wall and mucous impaction, were seen in the chest CT of 7 children. Six patients showed a large amount of viscous sputum adhered to the bronchial wall by bronchoscopy. Infection of Pseudomonas aeruginosa was found in 6 cases, Staphylococcus aureus in 2 cases, and Aspergillus fumigatus in 2 cases by bronchoalveolar lavage fluid or sputum culture. Sweat sodium chloride test was performed in 3 cases, and the result showed that Cl-> 60 mmol/L. CFTR gene mutations were found in 7 cases, which were rare mutations of Caucasians, including 2 cases with new mutation sites (c.325T>G and 326A>G).

Conclusions: The major clinical presentations of CF could be chronic and recurrent upper and lower respiratory tract infections, malnutrition, and digestive tract diseases. The rare and even new mutations of Caucasians on CFTR gene may occur in Chinese children.