Identification of Candidate Genes Associated with Development of Vascular Cognitive Impairment by Integrated Bioinformatics Analysis Combined with Biological Experiments.

The morbidity and mortality associated with vascular cognitive impairment (VCI) generally increase steeply, and health systems will face increasing demand for services. The present study aims to screen key genes to give new insight into the mechanisms and treatment of VCI based on bioinformatic approaches combined with biological experiments in rats. The gene expression data of VCI patients contained in the GSE122063 dataset were downloaded from the GEO. We performed a weighted gene co-expression network analysis (WGCNA) to identify a hub module and 44 hub genes.277 differentially expressed genes (DEGs) were analyzed using R software by the "limma" package. STRING database was used to construct protein-protein interaction (PPI) network, after which 36 hub genes were identified through Cytoscape. Functional enrichment analysis revealed that these genes from the yellow module and 277 DEGs were mainly associated with these pathways, such as staphylococcus aureus infection, complement, and coagulation cascades. These biological functions are related to inflammatory cell activation and inflammatory response. The key genes of VCI were the overlapping hub genes from the yellow module and the PPI network. The expressions of hub genes in rats were determined by qRT-PCR, western blot, immunohistochemistry, and immunofluorescence. In conclusion, C1QA, C1QB, C1QC, CD163, and FCGR2A were highly expressed in the hippocampus of VCI rats, and they can serve as candidate biomarkers for the diagnosis and prognosis of VCI. Finally, molecular docking results suggested that five genes interact with Bisphenol A. These findings open a new avenue to investigate molecular mechanisms for preventing or treating vascular cognitive impairment.

Correlation between right-to-left shunt and sudden sensorineural hearing loss: protocol for a case-control study.

BACKGROUND AND PURPOSE: Sudden sensorineural hearing loss (SSNHL) is a neurological and otolaryngological emergency during which rapid diagnosis and early treatment are of great importance. Clinical experience indicates that a considerable number of patients with SSNHL have concurrent right-to-left shunt (RLS). With limited reports, the association between SSNHL and RLS is yet unclear and there is a need for large observational studies to explore their latent relationship. METHODS AND ANALYSIS: This proposed study is a prospective, observational case-control study. A total of 194 eligible participants matched in age and sex will be divided equally into two groups: 97 patients with SSNHL included in the case group and 97 individuals without SSNHL in the control group. Medical evaluations, including clinical characteristics, laboratory examination, audiological examination and ultrasonography examination, will be performed in all subjects. The primary outcome of the study is the difference in RLS rates between the groups. Differences in patent foramen ovale rates and other measured variables will be further assessed. A conditional logistic regression as a correlation analysis will be used to evaluate the relationship between RLS and SSNHL. DISCUSSION: This study may provide evidence on the correlation between RLS and SSNHL in order to enrich the aetiology of SSNHL. ETHICS AND DISSEMINATION: The study protocol has been approved by the Ethics Committee of Peking University Shenzhen Hospital. A written informed consent form will be signed and dated by the participants and the researchers before the study begins. The results will be disseminated in peer-reviewed publications. TRIAL REGISTRATION NUMBER: ChiCTR2200064067.

Genetic analysis of potential biomarkers and therapeutic targets in age-related hearing loss.

Age-related hearing loss (ARHL) or presbycusis is the phenomenon of hearing loss due to the aging of auditory organs with age. It seriously affects the cognitive function and quality of life of the elderly. This study is based on comprehensive bioinformatic and machine learning methods to identify the critical genes of ARHL and explore its therapy targets and pathological mechanisms. The ARHL and normal samples were from GSE49543 datasets of the Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was applied to obtain significant modules. The Limma R-package was used to identify differentially expressed genes (DEGs). The 15 common genes of the practical module and DEGs were screened. Functional enrichment analysis suggested that these genes were mainly associated with inflammation, immune response, and infection. Cytoscape software created the protein-protein interaction (PPI) layouts and cytoHubba, support vector machine-recursive feature elimination (SVM-RFE), and random forests (RF) algorithms screened hub genes. After validating the hub gene expressions in GSE6045 and GSE154833 datasets, Clec4n, Mpeg1, and Fcgr3 are highly expressed in ARHL and have higher diagnostic efficacy for ARHL, so they were identified as hub genes. In conclusion, Clec4n, Mpeg1, and Fcgr3 play essential roles in developing ARHL, and they might become vital targets in ARHL diagnosis and anti-inflammatory therapy.

Genetic analysis of potential biomarkers and therapeutic targets in neuroinflammation from sporadic Creutzfeldt-Jakob disease.

This study aimed to identify hub genes and pathological mechanisms related to neuroinflammation in Sporadic Creutzfeldt-Jakob disease (SCJD) based on comprehensive bioinformatics. SCJD and normal samples were collected from GSE160208. Weighted gene co-expression network analysis (WGCNA) and Limma R package were used to obtain key genes, which were used for enrichment and immune cell infiltration analyses. Protein-protein interaction (PPI) network, cytoHubba, and machine learning were used to screen the central genes of SCJD. The chemicals related to hub genes were predicted and explored by molecular docking. 88 candidate genes were screened. Enrichment analysis showed they were mainly related to bacterial and viral infection and immune cell activation. Immune cell infiltration analysis suggested that immune cell activation and altered activity of the immune system are involved in the progression of SCJD. After identifying hub genes, KIT and SPP1 had higher diagnostic efficacy for SCJD (AUC > 0.9), so they were identified as central genes. The molecular docking results showed hub genes both docked well with Tretinoin. KIT, SPP1, and Tretinoin are essential in developing neuroinflammation in SCJD and may provide new ideas for diagnosing and treating SCJD.

The correlation between medial pattern of intracranial arterial calcification and white matter hyperintensities.

BACKGROUND AND AIMS: Despite reported correlations between intracranial arterial calcification (IAC) and white matter hyperintensities (WMH), little is known about the relationship between IAC pattern and WMH. By differentiating intimal and medial IAC, we aimed to investigate the relationship between IAC pattern and WMH. METHODS: Consecutive acute stroke patients were included. IAC pattern was categorized as intimal or medial on plain brain CT. The number of cerebral arteries involved by IAC for each patient was recorded. IAC severity was defined as focal or diffuse. On brain MRI, the burden of WMH was visually graded and classified as absent mild, moderate and severe. Multiple logistic regression was performed to examine the relationship between IAC and WMH. RESULTS: Among 265 patients, intimal IAC was detected in 54.7% patients and medial IAC in 48.5% patients. Diffuse IAC was present in 27.9% patients, all of which were medial. WMH was found in 75.5% patients, including 39.6% patients with mild WMH, 26.0% with moderate WMH, and 9.8% with severe WMH. The severity of medial IAC was correlated with WMH occurrence (p < 0.001). Chi-square linear trend suggested the number of arteries involved by medial IAC (p < 0.001) and the severity of medial IAC (p < 0.001) were correlated with WMH burden. Multiple ordinal logistic regression demonstrated a positive correlation of WMH burden with the number of arteries involved by medial IAC (p < 0.001) and the severity of medial IAC (p < 0.001). CONCLUSIONS: Medial IAC was correlated with WMH. The dose-effect relationship between medial IAC and WMH suggests underlying shared mechanisms of intracranial large artery disease and small vessel disease.

Cardiocerebrovascular risk in sensorineural hearing loss: results from the National Health and Nutrition Examination Survey 2015 to 2018.

Objective: This study aims to determine whether the risks of cardiocerebrovascular disease are relevant to sensorineural hearing loss (SNHL) based on a national database. Methods: A total of 1,321 participants aged from 18 to 69 with complete data including medical history and audiometry from the NHANES database (2015-2018) were analyzed. All included participants had available hearing data and the average thresholds of the hearing data were measured and calculated as low-frequency pure-tone average (LFPTA; 500, 1,000, and 2,000 Hz) and high-frequency pure-tone average (HFPTA; 3,000, 4,000, 6,000, and 8,000 kHz). SNHL was defined as an average pure tone of more than or equal to 20 dB in at least one better ear. Multivariable models to assess the association between cardiocerebrovascular risks and SNHL were used in this study. Results: The prevalence of stroke was 1.6% in individuals with SNHL and 0.4% in individuals without SNHL (p = 0.023). A higher cardiovascular risk score was observed in SNHL patients compared to participants without SNHL (1.58 vs. 0.90, p < 0.001). Stroke was associated with a 3.67-fold increase in the risk of SNHL (95% CI: 1.12-12.00, p = 0.032) in univariable logistic regression, and the association (OR = 4.22, 95%CI = 1.28-13.93, p = 0.020) remained significant after adjusting for several covariates. Multivariable logistic regression models indicated a positive correlation between cardiovascular risk and SNHL (OR = 1.66, 95% CI = 1.40-1.96, p < 0.001), but no significant relationship was shown with all covariates adjusted. However, significant associations were found between SNHL and both age and sex in both univariable and multivariable logistic regression models. Conclusion: Our findings suggested that a higher cardiocerebrovascular risk burden was associated with an increased risk of SNHL, and the relationship may be influenced by age and sex. Future longitudinal studies are needed to investigate the mechanistic and pathologic vascular hypothesis of SNHL.

The signature of immune-subtype specific driving transcription factors suggest potential drugs for refractory glioblastoma.

Immunocharacteristics-based typing strategies can be used to reflect the similar status of tumors. Therefore, we aimed to demonstrate whether the immune subtypes of GBM have independent prognostic efficacy and whether these subtypes can be used as clinical guidance for predicting the progression of GBM and determining drug sensitivity. In this study, we found that patients with GBM were divided into three conserved immune-related subtypes based on the infiltration level of immune cells, including immunosuppressed, moderate immunoactivity, and high immunoactivity. Regarding the relevant clinical significance, the high immunoactivity in GBM indicates the worst survival, which exhibited the highest levels of oncogenic activity, including angiogenesis, tumor-associated macrophages and tumor-associated fibroblasts, indicated worst survival. The immunosuppressive subtype of GBM was more likely to carry epidermal growth factor receptor mutations and MGMT methylation, and belong to the classical and proneural subtypes; however, but the high immunoactivity subtype was not. The immune subtype-specific transcription factors (TFs) regulatory network indicates that specific TFs drive the construction of each immune subtype, and that these subtype-specific TFs are more prone to internal TFs regulation. Furthermore, the immunosuppressed and moderate immunoactivity subtypes were significantly correlated with the drugs sensitivity, whereas the high immunoactivity subtype was not, indicating that GBMs with high immunoactivity were refractory. We also found that obatoclax mesylate, NPK76-II-72-1, gemcitabine, TAK-715 are potential drugs for the treatment of refractory GBM based on drug sensitivity models of different immune subtypes. Therefore, we demonstrated that the immune subtypes of GBM have independent prognostic efficacy and can be used as clinical guidance for predicting the progression of GBM and drug sensitivity. Most importantly, this study is expected to provide a pathway for the development of effective drugs for treatment of refractory GBM.

The correlation between intracranial arterial calcification and the outcome of reperfusion therapy.

OBJECTIVE: Intracranial arterial calcification (IAC) is a risk factor of ischemic stroke. However, the relationship between IAC patterns and clinical outcome of ischemic stroke remains controversial. We aimed to investigate the correlation between IAC patterns and the effects of reperfusion therapy among acute stroke patients. METHODS: Consecutive acute ischemic stroke patients who underwent reperfusion therapy were included. IAC was categorized as intimal or medial. Based on its involvement, IAC was further classified as diffuse or focal. Neurologic dysfunction was assessed by the National Institute of Health stroke scale (NIHSS). Clinical outcome including favorable neurologic outcome (FNO) and early neurologic deterioration (END) were assessed. RESULTS: Of 130 patients, 117 had IAC. Intimal IAC was identified in 74.6% of patients and medial IAC was present in 64.6% of patients. Diffuse IAC was present in 31.5% of patients. All diffuse IACs were medial pattern. Diffuse IAC was associated with higher baseline NIHSS (p = 0.011) and less FNO (p = 0.047). Compared with patients with focal or single diffuse IAC, patients with multiple diffuse IAC had higher baseline NIHSS (p = 0.002) and less FNO (p = 0.024). Multivariable linear regression (p < 0.001) and logistic regression (p = 0.027) suggested that multiple diffuse IAC was associated with higher baseline NIHSS and less FNO. No significant association was found between END and different IAC patterns. INTERPRETATION: Multiple diffuse medial IAC may predict severer neurologic dysfunction and less favorable neurologic outcome after reperfusion therapy in acute stroke patients.

Identification of hub genes and pathophysiological mechanism related to acute unilateral vestibulopathy by integrated bioinformatics analysis.

Background: Although many pathological mechanisms and etiological hypotheses of acute unilateral vestibulopathy (AUVP) have been reported, but the actual etiology remains to be elucidated. Objective: This study was based on comprehensive bioinformatics to identify the critical genes of AUVP and explore its pathological mechanism. Methods: Gene expression profiles of AUVP and normal samples were collected from GSE146230 datasets of the Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was constructed, and the WGCNA R-package extracted significant modules. The limma R-package was applied to identify differentially expressed genes (DEGs). The common genes of practical modules and DEGs were screened for GO and KEGG pathways analysis. The protein-protein interaction (PPI) layout and hub genes validation was created by Cytoscape software using the link from the STRING database. The functions of hub genes were predicted through the CTD (comparative genetics database). Results: A total of 332 common genes were screened from practical modules and DEGs. Functional enrichment analysis revealed that these genes were predominantly associated with inflammation and infection. After construction of PPI, expressions of hub genes, and drawing ROC curves, LILRB2, FPR1, AQP9, and LILRA1 are highly expressed in AUVP (p < 0.05) and have a certain diagnostic efficacy for AUVP (AUC > 0.7), so they were selected as hub genes. The functions of hub genes suggested that the occurrence of AUVP may be related to inflammation, necrosis, hepatomegaly, and other conditions in CTD. Conclusion: LILRB2, FPR1, AQP9, and LILRA1 may play essential roles in developing AUVP, providing new ideas for diagnosing and treating AUVP.

Identification of Hub Genes Related to Alzheimer's Disease and Major Depressive Disorder.

BackgroundAlthough many studies reported a close relationship between depression and Alzheimer's disease (AD), the underlying pathophysiological mechanism remains unclear. The present study aimed to investigate the mechanism of AD and major depressive disorder (MDD). Method: The datasets were downloaded from the Gene Expression Omnibus. After screening differentially expressed genes (DEGs), gene ontology and pathway analysis were performed and protein-protein interaction, TF-target gene, and miRNA-target gene networks were established. Results: 171 DEGs of AD-related datasets and 79 DEGs shared by AD and MDD were detected. Functional analysis revealed that AD and MDD common genes were significantly enriched in circadian entrainment and long-term depression signaling pathways. Five hub genes were identified after construction of networks and validation of hub gene signatures. In conclusion, DYNC1H1, MAPRE3, TTBK2, ITGB1, and WASL may be potential targets for the diagnosis and treatment of AD and MDD.

A novel antisense oligonucleotide anchored on the intronic splicing enhancer of hTERT pre-mRNA inhibits telomerase activity and induces apoptosis in glioma cells.

INTRODUCTION: Alternative splicing of hTERT pre-mRNA is an important step in the regulation of telomerase activity, but the regulation mechanisms and functions remain unclear. METHODS: RT-PCR analysis was used to detect hTERT splicing in glioma cell lines and brain tissues. TRAP assay was used to detect the telomerase activity. Then, we designed and synthesized 2'-O-methyl-RNA phosphorothioate AONs and transfected them into glioma cells to detect the changes in telomerase activity. MTT assay, plate colony formation assay, western blotting and Annexin V/PI assay were used to detect cell proliferation and apoptosis. At last, bioinformatics analyses were used to predict the expression and function of splicing protein SRSF2 in gliomas. RESULTS: hTERT splicing occurs both in glioma cell lines and glioma patients' tissues. The telomerase activity was related to the expression level of the full-length hTERT, rather than the total hTERT transcript level. AON-Ex726 was complementary to the sequence of the intronic splicing enhancer (ISE) in intron six, and significantly altered the splicing pattern of hTERT pre-mRNA, reducing the expression level of the full-length hTERT mRNA and increasing the expression level of the -ß hTERT mRNA. After transfection with AON-Ex726, the level of apoptosis was increased, while telomerase activity and cell proliferation were significantly decreased. By bioinformatic predictions, we found the AON-Ex726 anchoring sequence in ISE overlaps the binding site of SRSF2 protein, which is up-regulated during the development of gliomas. CONCLUSIONS: Our findings provided new targets and important clues for the gene therapy of gliomas by regulating the alternative splicing pattern of hTERT pre-mRNA.