Human blood DNA methylation patterns reflect individual lifestyle

Obesity is driven by modifiable lifestyle factors whose effects may be mediated by epigenetics. Therefore, we investigated lifestyle effects (diet, physical activity, smoking and alcohol) on blood DNA methylation in participants of the LIFE-Adult study, a well-characterized population-based cohort from Germany. Fifty subjects with an extremely healthy and 50 with an extremely unhealthy lifestyle were selected for genome-wide DNA methylation analysis in blood samples. Whereas obesity was only marginally related to variability in DNA methylation pattern, comparisons between lifestyle categories resulted in 145 Differentially Methylated Positions (DMPs) and 4682 Differentially Methylated Regions (DMRs) annotated to 4426 unique genes. Intersection analysis showed that diet, physical activity, smoking and alcohol intake are equally contributing to the observed differences, which particularly affects pathways related to glutamatergic synapse and axon guidance. DNA methylation patterns help discriminate individuals with a healthy vs. unhealthy lifestyle, which may mask subtle methylation differences derived from obesity.

CircularLRRC7 is a Potential Tumor Suppressor Associated With miR-1281 and PDXP Expression in Glioblastoma

Circular RNAs (circRNAs) are usually enriched in neural tissues, yet about 80% circRNAs have lower expression in gliomas relative to normal brains, highlighting the importance of circRNAs as tumor suppressors. However, the clinical impact as well as the pathways regulated by the tumor-suppressive circRNAs remain largely unknown in glioblastoma (GBM). Through bioinformatic analysis followed by experimental validation, we found that hsa_circ_0114014 (circLRRC7) was dramatically down-regulated in GBM when compared with normal brain tissues (p < 0.0001). GBM patients with a lower circLRRC7 expression had poorer progression-free survival (PFS, p < 0.05) and overall survival (OS, p < 0.05). Analyses of the predicted target miRNAs of circLRRC7 in CSCD and CRI databases, in combination with the miRNA expression data in GBMs and normal brains from GSE database, revealed miR-1281 as a potential downstream target of circLRRC7. Subsequently, the target genes of hsa-mir-1281 were predicted by TargetScan, miRDB and miRNATAR databases. Intersection analysis and correlation test indicated that PDXP was a potential target of miR-1281. In summary, circLRRC7 may be a tumor suppressor that associated with miR-1281 and PDXP expression in GBM, which may provide novel therapeutic targets for GBM treatment.

A Novel Immune and Stroma Related Prognostic Marker for Invasive Breast Cancer in Tumor Microenvironment: A TCGA Based Study

BackgroundBreast cancer (BC) is the most frequent cancer in women. The tumor microenvironment (TME), consisting of blood vessels, immune cells, fibroblasts, and extracellular matrix, plays a pivotal role in tumorigenesis and progression. Increasing evidence has emphasized the importance of TME, especially the immune components, in patients with BC. Nevertheless, we still lack a deep understanding of the correlation between tumor invasion and TME status.MethodsTranscriptome and clinical data were retrieved from The Cancer Genome Atlas (TCGA) database. ESTIMATE algorithm was applied for quantifying stromal and immune scores. Then we screened out the differentially expressed genes (DEGs) through the intersection analysis. Furthermore, the establishment of protein-protein interaction (PPI) network and univariate COX regression analysis were utilized to determine the core genes in DEGs. In addition, we also performed Gene Set Enrichment Analysis (GSEA) and CIBERSORT analysis to distinguish the function of crucial gene expression and the proportion of tumor-infiltrating immune cells (TICs), respectively.ResultsA total of 1178 samples (112 normal samples and 1066 tumor samples) were extracted from TCGA for calculation, and 226 DEGs were obtained from this assessment. Further intersection analysis revealed eight key genes, including ITK, CD3E, CCL19, CD2, SH2D1A, CD5, SLAMF6, SPN, which were proven to correlate with BC status. Moreover, ITK was picked out for further study. The results illustrated that high expression of BC patients had a more prolonged overall survival (OS) time than ITK low expression BC patients (p = 0.009), and ITK expression also presented the statistical significance in age, TNM staging, tumor size classification, and metastasis classification. Additionally, GSEA and CIBERSORT analysis indicated that ITK expression had an association with immune activity in TME.ConclusionITK may be a potential indicator for prognosis prediction in patients with BC, and its biological behavior may promote our understanding of the molecular mechanism of tumor progression and targeted therapy.

Analisis Kinerja Lalu Lintas Simpang Tak Bersinyal untuk Penentuan Tingkat Pelayanan di Jalan Klampis Jaya Surabaya

Klampis Jaya Road, Surabaya City, has a fairly heavy traffic flow, especially during working hours. This resulted in congestion on Klampis Jaya Road and not a few motorists who violated traffic regulations such as turning around Mleto Road. This study aimed to determine the current traffic flow performance and in 2024 at the intersection on Klampis Jaya Road, Surabaya City, predicted the traffic flow performance around the road and intersection on Klampis Jaya Road Surabaya City. The research method used was non-signalized intersection analysis using the Indonesian Road Capacity Manual. The calculation of the traffic performance of the four intersections in Klampis Jaya showed the Degree of Saturation (DS) and Service Level (TP) of each intersection. Traffic performance for the four intersections in 2021 was DS = 0.752 and TP = C (Enough), with the characteristics of stable traffic flow, was restricted movement. The traffic performance for the four intersections in 2024 was DS = 0.95 and TP = D (Less), with the characteristics of traffic flow stable movement being limited.

Network Pharmacology-Based Mechanistic Investigation of Jinshui Huanxian Formula Acting on Idiopathic Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is a chronic respiratory disease with high incidence, morbidity, and mortality rates. Jinshui Huanxian formula (JHF) is an empirical formula that targets the pathogenesis of lung-kidney qi deficiency and phlegm-blood stasis in pulmonary fibrosis (PF). The purpose of this study was to explore JHF’s potential pharmacological mechanisms in IPF therapy using network intersection analysis. JHF’s primary active components and corresponding target genes were predicted using various databases. Two sets of IPF disease genes were obtained from the DisGeNET and GEO databases and two sets of IPF drug targets were collected. The disease and drug target genes were analyzed. The JHF target genes that intersected with IPF’s differentially expressed genes were identified to predict JHF’s targets of action in IPF. The functions and pathways of predicted targets acting on IPF were analyzed using the DAVID and KEGG pathway databases. Finally, the resulting drug target mechanisms were validated in a rat model of PF. The initial analyses identified 494 active compounds and 1,304 corresponding targets for JHF. The intersection analysis revealed four common genes for the JHF targets, IPF disease, and anti-IPF drugs in the KEGG database. Furthermore, these genes were targeted by several JHF compounds. Seventy-two JHF targets were closely related to IPF, which suggests that they are therapeutically relevant. Target screening revealed that they regulate IPF through 18 pathways. The targets’ molecular functions included regulation of oxidoreductase activity, kinase regulator activity, phosphotransferase activity, and transmembrane receptor protein kinase activity. In vivo experiments showed that JHF alleviated the degree of PF, including decreases in collagen deposition and epithelial-mesenchymal transition. This study systematically explored JHF’s mechanisms to identify the specific target pathways involved in IPF. The generated pharmacological network, paired with in vivo validation, elucidates the potential roles and mechanisms of JHF in IPF therapy.

CCR2 and PTPRC are regulators of Tumor Microenvironment and potential prognostic biomarkers of lung adenocarcinoma

Tumor microenvironment (TME) plays an essential role in lung adenocarcinoma (LUAD) development and metastasis. With the development of TME research, it has been proved that differences in tumor-infiltrating immune cells (TICs) and gene expression profile are related to the prognosis of cancer. Our study aimed to identify key genes affecting immune state in TME of LUAD. We downloaded the RNA-seq data of LUAD cases from the TCGA database. ImmuneScore, StromalScore and ESTIMATEScore of each LUAD sample were calculated using ESTIMATE algorithm. Based on the median of different scores, LUAD samples were divided into high and low score groups. Differentially expressed genes (DEGs) between groups were obtained, and univariate Cox regression analysis and protein-protein interaction (PPI) network were used to screen shared DEGs generating in the intersection analysis. CIBORSORT algorithm was performed to calculate the relative contents of TICs for each LUAD sample, and correlation analysis between TICs and key genes was used to determine the influence of key genes to the TME. Finally, CCR2 and PTPRC, affecting the immune status of TME and the prognosis of LUAD, were acquired. Analysis based on the CIBERSORT algorithm suggested that CCR2 and PTPRC were correlated with a variety of TICs, and closely related to the clinical characteristics of the LUAD patients. Our research showed that CCR2 and PTPRC may be potential prognostic markers in LUAD, which may affect function of γδT cells and other immune cells by participating in the regulation of TME immune state.

Prognostic Value and Immune Infiltration of Novel Biomarkers in Glioma: Evidence From a Comprehensive Analysis of Tumor Microenvironment

BackgroundIn the glioma microenvironment, infiltrating immune cells has been shown to possess beneficial effects for tumor progression. Immune cells and stromal cells dominate the tumor microenvironment in glioma. The complex interplay between the tumor progression with immune cells or stromal cells was still unknown. MethodsIn this study, we used Estimation of stromal and immune cells in malignant tumor tissues using expression data (ESTIMATE) calculations to calculate the proportion of tumour-infiltrating immune cells (TIC) and the number of immune and stromal components in glioma cases from the cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) databases. Differentially expressed genes (DEG) were analyzed by COX regression analysis and protein-protein interaction (PPI) network construction. Then, JAK3, IL2RB and CD3E were identified as predictors by the intersection analysis of univariate COX and PPI, and further analysis showed that the expression of them were positively correlated with survival and clinicopathological characteristics of glioma patients. Finally, the Cell type Identification By Estimating Relative Subsets Of known RNA Transcripts (CIBERSORT) deconvolution algorithm was applied to quantify the fraction and infiltration of 22 types of immune cells in glioma. ResultsOur results showed that ESTIMATEScores Were Correlated with the Survival of glioma Patients, DEGs Shared by ImmuneScore and StromalScore were predominantly presented as the enrichment of immune-related genes gene set enrichment analysis (GSEA). The intersection analysis of PPI network and univariate COX regression enabled us to identify three genes (JAK3, IL2RB and CD3E) that had never been reported before, whose expression was correlated with clinical characteristics such as survival and WHO grading of these patients. CITICSORT analysis of TIC ratio showed that B cell memory and CD8 + T cells were positively correlated with JAK3, IL2RB and CD3E expression, suggesting that these genes may be responsible for maintaining the immunodominant state of TME. CIBERSORT analysis for the proportion of TICs revealed that the levels of JAK3, IL2RB and CD3E affected the immune activity of TME.ConclusionOur results confirmed that the JAK3, IL2RB and CD3E can be used as diagnostic and prognostic biomarkers for glioma and may be used as therapeutic targets in the future.

Mechanisms and Molecular Targets of the Tao-Hong-Si-Wu-Tang Formula for Treatment of Osteonecrosis of Femoral Head: A Network Pharmacology Study

The Tao-Hong-Si-Wu-Tang (THSWT) formula, a classic prescription of traditional Chinese medicine, has long been used for the treatment of osteonecrosis of femoral head (ONFH). However, its mechanisms of action and molecular targets are not comprehensively clear. In the present study, the Traditional Chinese Medicine System Pharmacology (TCMSP) database was employed to retrieve the active compounds of each herb included in the THSWT formula. After identifying the drug targets of active compounds and disease targets of ONFH, intersection analysis was conducted to screen out the shared targets. The protein-protein network of the shared targets was built for further topological analysis. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis were then carried out. A gene pathway network was constructed to screen the core target genes. We identified 61 active compounds, 155 drug targets, and 5443 disease targets. However, intersection analysis only screened out 37 shared targets. Kaempferol, luteolin, and baicalein regulated the greatest number of targets associated with ONFH. The THSWT formula may regulate osteocyte function through specific biological processes, including responses to toxic substances and oxidative stress. The regulated pathways included the relaxin, focal adhesion, nuclear factor-κB, toll-like receptor, and AGE/RAGE signaling pathways. RELA, VEGFA, and STAT1 were the important target genes in the gene network associated with the THSWT formula for the treatment of ONFH. Therefore, the present study suggested that the THSWT formula has an action mechanism involving multiple compounds and network targets for the treatment of ONFH.

The Role of CXCL10 in Prognosis of Patients with Colon Cancer and Tumor Microenvironment Remodeling

Background: In the past few years, tumor microenvironment (TME) has gradually become a hot topic in tumor research, which has important significance in the diagnosis, prevention and prognosis of tumors. Importantly, the immune system is a major contributing factor in TME, and studies have shown that tumors are partially infiltrated with various immune cell subsets. The immune characteristics of the TME play an essential role in evaluating the prognosis of patients. The immune scoring system based on the distribution of tumor local immune cell subsets and cell density has been an essential indicator in the evaluation of patient prognosis and has been verified in various tumor studies. TME is indispensable in the occurrence and development of Colorectal cancer (CRC). However, understanding the dynamic regulation of immunity and matrix components in TME of CRC is still a challenge and should be investigated further.Methods: In this study, we collected transcriptome RNA-seq data of 521 Colon adenocarcinoma (COAD) patients from The Cancer Genome Atlas (TCGA) data portal. We then estimate the fraction of stromal and immune cells in COAD cases by ESTIMATE algorithms [1]. A total of 1109 stromal-immune score-related differentially expressed genes (DEGs) were identified and used to generate a high-confidence protein–protein intersection (PPI) network and univariate COX regression analysis. Intersection analysis of the data from PPI network and univariate COX regression analysis showed the core gene. Then we performed Gene set enrichment analysis (GSEA), survival analysis and clinical analysis for CXCL10, and applied CIBERSORT algorithms to estimate the tumor-infiltrating immune cells (TICs) proportion in COAD cases.Results: The proportion of immune and stromal components in TME are associated with the progression of COAD. For example, tumor metastasis is inversely proportional to immune score. A total of 1109 DEGs were obtained by analyzing the low-score shared genes and the high-score shared genes by intersection analysis which might be the determinant of TME status. The GO enrichment analysis indicated that DEGs are associated with immune-related terms. KEGG pathway enrichment analysis showed that these DEGs are mainly enriched in cytokine cytokine receptor signaling pathway etc. Therefore, DEGs are related to immune regulation, which indicates that the participation of immune factors is the main characteristic of TME in COAD. Moreover, the expression level of CXCL10 has significantly connection with the prognosis of patients and the progression of COAD. Conclusion: Taken together, we conducted a comprehensive analysis of the TME in COAD, and predicted a prognostic indicator for COAD, which provided a novel insight for therapeutics of COAD.

A Comparison of Traffic Flow Performance of Roundabouts and Signalized Intersections: A Case Study in Nigde

Background: Intersections affect the safety and capacity of urban traffic. Therefore, the design and selection of the type of intersection need to be made very carefully. According to the demand level, a different intersection can be designed. Signalized intersections are one of the intersection types in which the sequence and duration of the flow at the intersection are provided by the lights. Generally, this type of intersection is used on roads with high traffic volume. Modern roundabouts are one of the types of circular intersections that provide advantages over other types of intersection in terms of smooth operation and safety. Modern roundabouts exist in several types today worldwide. In practice, the distinction about the kinds of roundabouts would not be fully clarified; as a result, queuing and delay can be seen as negative effects. Methods: In this study, to make a distinction and clarify the kinds of roundabouts, first, the roundabouts types are introduced according to geometric and operational aspects. A signalized intersection, where a circular island is placed and also signalized, was investigated in terms of capacity, delay, and emissions located in Niğde. The traffic flow performance of the current state (nested signalized roundabout) was calculated with HCM Method (for signalized intersection) using SIDRA and compared with roundabout solutions of the intersection with HCM6 (for roundabout) method using SIDRA Intersection analysis software. Results: From the results of the intersection capacity analysis study based on HCM6, it was seen that the application of a roundabout scenario (intersection considered as a modern roundabout) showed higher performance at the intersections than the intersection having a secondary signal. Capacity increased to 67.8%, the average delay decreased to 72.8% and 95th percentile queue dropped to 82.2%. Conclusion: Roundabout controlling instead of a nested signal system can be an example of the increase in the performance of traffic flow. This highlights the importance of choosing the appropriate roundabout design.