Bioinformatic analyzes and validation of cystathionine gamma-lyase as a prognostic biomarker and related to immune infiltrates in hepatocellular carcinoma.

Background: The role of cystathionine γ-lyase (CTH) in the prognosis and immune invasion of hepatocellular carcinoma (HCC) remains poorly understood. Methods: In this study, the clinical data of patients with HCC were analyzed, and the expression level of CTH was compared between HCC and normal tissues using the R package and various databases. Results: We found that CTH expression was significantly decreased in HCC compared with normal tissues, and its expression was associated with various clinicopathological factors, including tumor stage, gender, tumor status, residual tumor, histologic stage, race, alpha-fetoprotein (AFP), albumin, drinking, and smoking. Our results suggest that CTH might be a protective factor for the survival of patients with HCC. Further functional analysis revealed that high CTH expression was enriched in the Reactome signaling by interleukins and the Reactome neutrophil degranulation. Moreover, CTH expression was closely correlated with a variety of immune cells, including a negative correlation with the CD56 (bright) NK cells and follicular helper T cell (TFH), while a positive correlation with Th17 cells and central memory T cell (Tcm). High expression of CTH in immune cells predicted a better prognosis of HCC. Our findings further indicated Pyridoxal phosphate, l-cysteine, Carboxymethylthio-3-(3-chlorophenyl)-1,2,4-oxadiazol, 2-[(3-Hydroxy-2-Methyl-5-Phosphonooxymethyl-Pyridin-4-Ylmethyl)-Imino]-5-phosphono-pent-3-enoic acid and L-2-amino-3-butynoic acid as potential target candidate medications for HCC treatment based on CTH. Conclusion: Our study suggests that CTH can serve as a biomarker to predict the prognosis and immune infiltration of HCC.

Efficacy and safety of dietary polyphenols in rheumatoid arthritis: A systematic review and meta-analysis of 47 randomized controlled trials.

Objective: To evaluate safety and efficacy of dietary polyphenols in the treatment of rheumatoid arthritis (RA). Methods: CNKI, Pubmed, Cochrane library, Embase were searched to collect randomized controlled trials (RCTs) of dietary polyphenols in the treatment of RA. The databases were searched from the time of their establishment to November 8nd, 2022. After 2 reviewers independently screened the literature, extracted data, and assessed the risk of bias of the included studies, Meta-analysis was performed using RevMan5.4 software. Results: A total of 49 records (47 RCTs) were finally included, involving 3852 participants and 15 types of dietary polyphenols (Cinnamon extract, Cranberry extract, Crocus sativus L. extract, Curcumin, Garlic extract, Ginger extract, Hesperidin, Olive oil, Pomegranate extract, Puerarin, Quercetin, Resveratrol, Sesamin, Tea polyphenols, Total glucosides of paeony). Pomegranate extract, Resveratrol, Garlic extract, Puerarin, Hesperidin, Ginger extract, Cinnamon extract, Sesamin only involve in 1 RCT. Cranberry extract, Crocus sativus L. extract, Olive oil, Quercetin, Tea polyphenols involve in 2 RCTs. Total glucosides of paeony and Curcumin involve in more than 3 RCTs. These RCTs showed that these dietary polyphenols could improve disease activity score for 28 joints (DAS28), inflammation levels or oxidative stress levels in RA. The addition of dietary polyphenols did not increase adverse events. Conclusion: Dietary polyphenols may improve DAS28, reduce C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR), and improve oxidative stress, etc. However, more RCTs are needed to verify or modify the efficacy and safety of dietary polyphenols. Systematic review registration: https://www.crd.york.ac.uk/prospero/, identifier CRD42022315645.

Autophagy-related gene expression classification defines three molecular subtypes with distinct clinical and microenvironment cell infiltration characteristics in colon cancer.

BACKGROUND: Multiple molecular subtypes with distinct clinical outcomes in colon cancer have been identified in recent years. Nonetheless, the autophagy-related molecular subtypes as well as its mediated tumor microenvironment (TME) cell infiltration characteristics have not been fully understood. METHODS: Based on the seven colon cancer cohorts with 1580 samples, we performed a comprehensive genomic analysis to explore the molecular subtypes mediated by autophagy-related genes. The single-sample gene-set enrichment analysis (ssGSEA) was used to quantify the relative abundance of each cell infiltration in the TME. Unsupervised methods were used to perform autophagy subtype clustering. Least absolute shrinkage and selection operator regression (LASSO) was used to construct autophagy characterization score (APCS) signature. RESULTS: We determined three distinct autophagy-related molecular subtypes in colon cancer. The three autophagy subtypes presented significant survival differences. Microenvironment analyses revealed the heterogeneous TME immune cell infiltration characterization between three subtypes. Cluster 1 autophagy subtype was characterized by abundant innate and adaptive immune cell infiltration. This subtype exhibited an enhanced stromal activity including activated pathways of epithelial-mesenchymal transition, TGF-ß and angiogenesis, and an increased infiltration of fibroblasts and endothelial cells. The expression of immune checkpoint molecules was also significantly up-regulated, which may mediate immune escape in Cluster 1 subtype. Cluster 2 subtype was characterized by relatively lower TME immune cell infiltration and enhanced DNA damage repair pathways. Cluster 3 subtype was characterized by the suppression of immunity. Patients with high APCS, with poorer survival, presented a significantly positive correlation with TME stromal activity. Low APCS, relevant to activated damage repair pathways, showed enhanced responses to anti-PD-1/PD-L1 immunotherapy. Two immunotherapy cohorts confirmed patients with low APCS exhibited prominently enhanced clinical response and treatment advantages. CONCLUSIONS: This study may help understand the molecular characterization of autophagy-related subtypes. We demonstrated the autophagy genes in colon cancer could drive the heterogeneity of TME immune cell infiltration. Our study represented a step toward personalized immunotherapy in colon cancer.

Wide-ranging analysis of survival-related alternative splicing events in invasive breast carcinoma.

Invasive breast carcinoma (BRCA) is a serious disease that threatens the survival time of those affected. Alternative splicing (AS) involved in BRCA pathogenesis may be a potential therapeutic target. However, to the best of our knowledge, a systematic analysis of survival-related alternative splicing events (SREs) has not yet been reported. The aim of the present study was to identify SREs and analyze their potential biological functions as BRCA prognostic biomarkers. An UpSet plot demonstrated AS global characteristics. Cox's proportional hazards regression model quantitatively demonstrated the prognostic relevance of AS events. Functional enrichment analysis investigated the potential pathways through which AS events affect BRCA progression. The receiver operating characteristic curve model determined the clinical significance of AS events represented using percent-spliced-in (PSI) values. The regulatory network of splicing factors (SFs) and AS events laid the foundation for studying the role of SFs in BRCA. The present study identified 1,215 SREs and their distribution characteristics, suggesting that AS events in exon skipping (ES) primarily exerted normal physiological functions, while AS events in alternative terminator sites had the most significant prognostic effect. The present study demonstrated that survival-associated genes are involved primarily in certain biological processes of ribosomal proteins. In the diagnostic model, the alternative acceptor site, alternative donor site, alternative promoter site and ES performed well. ELAVL4 was the key gene associated with prognosis and SREs. In conclusion, a number of AS events affect BRCA initiation, progression and prognosis. The PSI value of AS events has the potential to diagnose BRCA and predict a prognosis; however, this must be confirmed in additional studies.

Association between retinol binding protein 4 and diabetic retinopathy among type 2 diabetic patients: a meta-analysis.

AIMS: The aim of this study was to investigate the association between retinol-binding protein 4 (RBP4) and diabetic retinopathy (DR) among patients with type 2 diabetes mellitus (T2DM). METHODS: Databases PubMed, Embase, Web of Science, Chinese National Knowledge Infrastructure, VIP, and Wangfang were searched to July 30, 2019. The Newcastle-Ottawa Scale was applied to assess the quality of all identified studies, and those qualified were included in the meta-analysis. The Chi squared Q test and I2 statistics were conducted to evaluate heterogeneity. Standardized mean differences (SMD) and 95% confidence intervals (CI) among RBP4 within the DR and T2DM without retinopathy (DWR) groups were pooled using the random effects model depending on the heterogeneity. Subgroup analyses were conducted among the groups having different diabetes duration, detection methods, body mass index, and total cholesterol and triglyceride levels. The funnel plot was used to assess publication bias. RESULTS: Nineteen observational studies were included in our meta-analysis. RBP4 was significantly higher in both nonproliferative DR (SMD: 0.72, 95% CI 0.48-0.95, P < 0.00001) and proliferative DR (SMD: 2.68, 95% CI 1.69-3.67, P < 0.00001) groups despite high heterogeneity (I2 = 87 and 97% in DR and PDR groups, respectively). Significant differences were noted among most subgroups (P < 0.05). Among those accompanied by hypercholesterolemia, the association between RBP4 and DR were unclear (P = 0.09). CONCLUSIONS: Elevated RBP4 is strongly associated with DR and may play an essential role in its progression. Additional large-scale controlled studies are needed to confirm these findings.

Integration of multiple key molecules in lung adenocarcinoma identifies prognostic and immunotherapeutic relevant gene signatures.

BACKGROUND: Although multiple key molecules in lung adenocarcinoma (LUAD) have been identified in recent years, the overall tumor microenvironment (TME) immune cell infiltration characterizations mediated by multiple key molecules remain little known. This study aimed to integrate the roles of multiple key molecules to evaluate patient prognosis and TME cell infiltration characterization as well as responses to immunotherapy. METHODS: Using combined LUAD cancer cohorts with 228 normal samples and 913 tumor samples, we comprehensively dissected the differences of genomic and TME cell infiltration landscapes between normal lung tissues and tumor tissues. The single-sample gene-set enrichment analysis (ssGSEA) was used to quantify the relative abundance of 24 cell infiltration. The riskScore signature was constructed using a least absolute shrinkage and selection operator (LASSO) Cox regression mode. RESULTS: Seven novel key molecules with significantly up-regulated expression in LUAD were determined. Survival analyses revealed their important prognostic values. LUAD microenvironment presented a markedly decreased infiltration of immune cells compared to normal lung tissues. We found tumors with up-regulated expression of these key molecules exhibited a significantly decreased TME cell infiltration and increased immune checkpoint molecule expression. The high riskScore subtype was characterized by decreased innate and adaptive immune cell infiltration. Activation of p53 signaling pathway and regulator T cells were observed in the high riskScore subtype, which were regarded as T-cell suppressive and could be responsible for poorer prognosis in this subtype (HR 1.83(1.27-2.63)). Multivariate analyses demonstrated the riskScore was a robust and independent prognostic biomarker, and its value in predicting immunotherapeutic outcomes was also confirmed (HR 1.70(1.22-2.37)). CONCLUSIONS: This study reveal a novel gene signature significantly related to patient prognosis and TME cell infiltration in LUAD. We demonstrated the integrated roles of multiple key molecules played a crucial role in shaping TME cell infiltration diversity and complexity. Evaluating the integrated characterization of multiple key molecules could contribute to predicting patients' response to immunotherapy and guiding more effective immunotherapy strategies.

Computer aided diabetic retinopathy detection based on ophthalmic photography: a systematic review and Meta-analysis.

AIM: To ensure the diagnostic value of computer aided techniques in diabetic retinopathy (DR) detection based on ophthalmic photography (OP). METHODS: PubMed, EMBASE, Ei village, IEEE Xplore and Cochrane Library database were searched systematically for literatures about computer aided detection (CAD) in DR detection. The methodological quality of included studies was appraised by the Quality Assessment Tool for Diagnostic Accuracy Studies (QUADAS-2). Meta-DiSc was utilized and a random effects model was plotted to summarize data from those included studies. Summary receiver operating characteristic curves were selected to estimate the overall test performance. Subgroup analysis was used to identify the efficiency of CAD in detecting DR, exudates (EXs), microaneurysms (MAs) as well as hemorrhages (HMs), and neovascularizations (NVs). Publication bias was analyzed using STATA. RESULTS: Fourteen articles were finally included in this Meta-analysis after literature review. Pooled sensitivity and specificity were 90% (95%CI, 85%-94%) and 90% (95%CI, 80%-96%) respectively for CAD in DR detection. With regard to CAD in EXs detecting, pooled sensitivity, specificity were 89% (95%CI, 88%-90%) and 99% (95%CI, 99%-99%) respectively. In aspect of MAs and HMs detection, pooled sensitivity and specificity of CAD were 42% (95%CI, 41%-44%) and 93% (95%CI, 93%-93%) respectively. Besides, pooled sensitivity and specificity were 94% (95%CI, 89%-97%) and 87% (95%CI, 83%-90%) respectively for CAD in NVs detection. No potential publication bias was observed. CONCLUSION: CAD demonstrates overall high diagnostic accuracy for detecting DR and pathological lesions based on OP. Further prospective clinical trials are needed to prove such effect.