Clinically Applicable Pan-Origin Cancer Detection for Lymph Nodes via Artificial Intelligence-Based Pathology.

INTRODUCTION: Lymph node metastasis is one of the most common ways of tumour metastasis. The presence or absence of lymph node involvement influences the cancer's stage, therapy, and prognosis. The integration of artificial intelligence systems in the histopathological diagnosis of lymph nodes after surgery is urgent. METHODS: Here, we propose a pan-origin lymph node cancer metastasis detection system. The system is trained by over 700 whole-slide images (WSIs) and is composed of two deep learning models to locate the lymph nodes and detect cancers. RESULTS: It achieved an area under the receiver operating characteristic curve (AUC) of 0.958, with a 95.2% sensitivity and 72.2% specificity, on 1,402 WSIs from 49 organs at the National Cancer Center, China. Moreover, we demonstrated that the system could perform robustly with 1,051 WSIs from 52 organs from another medical centre, with an AUC of 0.925. CONCLUSION: Our research represents a step forward in a pan-origin lymph node metastasis detection system, providing accurate pathological guidance by reducing the probability of missed diagnosis in routine clinical practice.

Cx43 overexpression reduce the incidence of obstructive sleep apnea associated atrial fibrillation via the CaMK⠡γ/HIF-1 axis.

BACKGROUND: Previous studies by our group have demonstrated chronic intermittent hypoxia (CIH) can decrease connexin 43 (Cx43) protein expression and thus increase atrial fibrillation (AF) inducibility. Cardiac sympathetic denervation (CSD) can reduce AF and increase Cx43 expression, however, the underlying molecular mechanisms and signaling pathways are still unclear. METHODS AND RESULTS: An obstructive sleep apnea (OSA) rat model in vivo experiments and CIH H9c2 cells model in vitro experiments were used to figure out the roles and underlying mechanisms of Cx43 on OSA-associated AF. In this study, we examined the expression of Cx43, CaMKⅡγ, Bax, Caspase 3, HIF-1 Bcl-2, Tunel, and CPB/p300, to discover the association between proteins and the mechanism of regulatory changes. The downstream proteins of Cx43 were calculated by gene sequencing and data analysis. We found Cx43 expression was significantly downregulated after CIH exposure in rat and H9c2 cells. Active caspase-3 and Bax at CIH+8 h group are high, but decreased at OE+8 h group. The Bcl-2 expression was higher in the N and OE+8 h group than CIH+8 h group. TUNEL-positive cells from the CIH+8 h group was markedly higher. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated Cx43 overexpression inhibited the CaMKIIγ expression, and CaMKIIγ was involved in the HIF-1 signaling pathway. In addition, we also found Cx43 overexpression remarkably decreased the HIF-1 protein and p300 mRNA expression, which inhibits the CaMKIIγ/HIF-1 signaling pathway. CONCLUSIONS: Taken together, these results suggested Cx43 overexpression inhibits the expression of calcium/calmodulin dependent protein CaMKⅡγ via the Cx43/CaMKIIγ/HIF-1 axis, which finally reduces the myocardial apoptosis and incidence of AF.

Updated efficacy of adjuvant epirubicin plus cyclophosphamide followed by taxanes versus carboplatin plus taxanes in early triple-negative breast cancer in phase 2 trial: 8.1-year median follow-up.

BACKGROUND: Paclitaxel/docetaxel after doxorubicin plus cyclophosphamide (ECT) is considered as an adjuvant chemotherapy and improves the survival of early triple-negative breast cancer (TNBC) patients. We aim to assess whether carboplatin plus taxanes (TP) is non-inferior to ECT in prolonging the survival time. METHODS: TNBC patients were randomized (1:1) to receive ECT (90 mg/m2 epirubicin + 600 mg/m2 cyclophosphamide followed by 75 mg/m2 docetaxel or 175 mg/m2 paclitaxel every 3 weeks, n = 154) or TP (75 mg/m2 docetaxel or 175 mg/m2 paclitaxel + carboplatin AUC 5 every 3 weeks, n = 154). These expression of SPARC, PD-L1, and BRCA were studied. Patients were followed up for disease-free survival (DFS), overall survival (OS), and safety. RESULTS: We recruited 308 TNBC patients (median follow-up of 97.6 months). The median DFS and OS were not reached; the 8-year DFS rate of ECT and TP arms was 78.4% and 81.7%, respectively, while the 8-year OS rate were 87.2% and 89.1%, respectively. In the SPARC (> 50%) subgroup analysis, the TP arm had longer DFS (P = 0.049) and a tendency with better OS (P = 0.06) than ECT arm. No significant differences were observed in the DFS and OS between the ECT arm and TP arm in TNBC with SPARC (≤ 50%), PD-L1 (-) PD-L1 (+), and BRCA mutation or BRCA wild (all P values > 0.05). CONCLUSION: TP showed non-inferiority for DFS and OS compared with ECT in early TNBC. TP may be an effective alternative chemotherapy for TNBC patients whom the standard ECT regimen is not being used. TRAIL REGISTRATION: ClinicalTrials.gov identifier NCT01150513.

Distinct clinical phenotype and genetic testing strategy for Lynch syndrome in China based on a large colorectal cancer cohort.

Lynch syndrome (LS) is the most common hereditary colorectal cancer (CRC) predisposition syndrome. We performed a large-scale study to assess a screening strategy for identifying LS in Chinese CRC patients in routine clinical testing. A total of 4,195 eligible CRCs were universally screened. Then, 8.7% of CRCs were detected with dMMR. The incidence of LS was 2.7% (115 of 4,195) in this cohort; among patients over 70 years of age, only 0.3% (2 of 678) were diagnosed as LS. Then, 17.4% of LS cases showed large genomic deletions/duplications. LS probands developed CRCs predominantly at proximal colon location. The frequency of BRAF V600E mutation among Chinese CRCs was significantly lower than that among Western populations, and MLH1 promoter methylation significantly improved the efficiency of genetic screening for LS among MLH1-deficient patients. A comprehensive molecular testing strategy that includes detection of large genomic rearrangements is imperative for the diagnosis of LS. Among CRC patients aged 70 years or younger, a selective strategy for LS screening might be considered for routine clinical testing.

Carboplatin plus taxanes are non-inferior to epirubicin plus cyclophosphamide followed by taxanes as adjuvant chemotherapy for early triple-negative breast cancer.

PURPOSE: Platinum plays an important role in the treatment of triple-negative breast cancer (TNBC) in neoadjuvant and metastatic settings. However, its role in an adjuvant setting remains unclear. METHODS: In this non-inferior randomized phase 2 trial, we randomly assigned 308 chemotherapy-naive patients with histologically confirmed TNBC after primary surgery to receive either six cycles of TP (docetaxel: 75 mg/m2 or paclitaxel 175 mg/m2 d1; carboplatin AUC = 5, day 1), or four cycles of EC (epirubicin: 90 mg/m2; cyclophosphamide: 600 mg/m2, day 1) followed by four cycles of T (docetaxel: 75 mg/m2 or paclitaxel 175 mg/m2, day 1). The primary end point was the disease-free survival (DFS) rate at 5 years. Both regimens were repeated every 3 weeks. The prognostic and predictive value of germline breast cancer gene mutations and programmed death ligand-1 (PD-L1) expression was evaluated. RESULTS: At a median follow-up of 66.9 months, the 5-year DFS rate was 85.8% in the EC-T arm, and 84.4% in the TP arm (p non-inferiority = 0.034, p log-rank = 0.712). The 5-year overall survival (OS) rate was 94.4% in the EC-T arm and 93.5% in the TP arm (p = 0.770). Patients in the TP arm showed better compliance and experienced significantly lower frequencies of G3/4 neutrocytopenia and G3/4 alopecia, but higher rates of G1-4 thrombocytopenia than those in the EC-T arm. Patients with PD-L1 expressing tumors showed significantly improved DFS and OS. CONCLUSIONS: This study indicates that carboplatin plus taxanes could be a feasible adjuvant chemotherapy for patients with early TNBC who are cannot tolerate intensive chemotherapy with anthracycline.

An ultrasensitive and simple assay for the Hepatitis C virus using a reduced graphene oxide-assisted hybridization chain reaction.

Hepatitis C virus (HCV) is a major cause of chronic liver disease, which affects 2-3% of the world population. Until now, the early detection of HCV has been a great challenge, especially for those who live in developing countries. In this study, we developed a novel and ultrasensitive assay for the detection of HCV RNA based on the reduced graphene oxide nanosheets (rGONS) and hybridization chain reaction (HCR) amplification technique. This detection system contains a pair of single fluorophore-labeled hairpin probes that can freely exist in the solution in the absence of target RNA. The introduction of target RNA can robustly trigger a HCR with the two probes and produce long nanowires containing a double-stranded structure. The weak adsorption to rGONS makes the long nanowires emit a strong fluorescence. Using this enzyme-free amplification strategy, we developed a new method for the HCV RNA assay with a detection limit of 10 fM, which is far more sensitive than the common GO-based fluorescence method. Furthermore, the new method exhibits high selectivity for the discrimination of perfectly complementary and mismatched sequences. Finally, the new method was successfully used as a HCV RNA assay in biological samples with a strong anti-interference capability in complicated environments. In summary, these remarkable characteristics of the new method highlight its potential use in a clinical sample primary screening.

Reduced sensitivity to neutral feedback versus negative feedback in subjects with mild depression: Evidence from event-related potentials study.

Many previous event-related potential (ERP) studies have linked the feedback related negativity (FRN) component with medial frontal cortex processing and associated this component with depression. Few if any studies have investigated the processing of neutral feedback in mildly depressive subjects in the normal population. Two experiments compared brain responses to neutral feedback with behavioral performance in mildly depressed subjects who scored highly on the Beck Depression Inventory (high BDI) and a control group with lower BDI scores (low BDI). In the first study, the FRN component was recorded when neutral, negative or positive feedback was pseudo-randomly delivered to the two groups in a time estimation task. In the second study, real feedback was provided to the two groups in the same task in order to measure their actual accuracy of performance. The results of experiment one (Exp. 1) revealed that a larger FRN effect was elicited by neutral feedback than by negative feedback in the low BDI group, but no significant difference was found between neutral condition and negative condition in the High BDI group. The present findings demonstrated that depressive tendencies influence the processing of neutral feedback in medial frontal cortex. The FRN effect may work as a helpful index for investigating cognitive bias in depression in future studies.

[Association of genetic variantions of circadian clock genes and risk of breast cancer].

OBJECTIVE: To investigate the relationship between genetic variantions of circadian clock genes and risk of breast cancer. METHODS: A case-control study including 406 breast cancer patients and 412 controls was conducted and genes Clock (rs2070062) and Per2 (rs2304672, rs2304669, rs934945) were genotyped by TaqMan real-time PCR. Unconditional logistic regression model was used to analyze the association between the genetic polymorphisms and breast cancer. RESULTS: Individuals with the rs2304669-TT genotype showed significantly increased breast cancer risk with the OR of 2.33 when compared with the individuals with rs2304669-CC and CT genotypes (P = 0.001). In addition, the three haplotypes containing the risk T allele of rs2304669 were identified to be associated with increased breast cancer risk. However, it was found that rs2304672, rs2070062 and rs934945 polymorphisms were not related with breast cancer risk. CONCLUSIONS: The locus rs2304669 on Per2 gene is associated with breast cancer risk. Genetic variation of circadian clock genes may increase the susceptibility to breast cancer. Therefore, it may become an important biomarker of susceptibility to breast cancer.

Identification of potential biomarkers associated with CD4+ T cell infiltration in myocardial ischemia-reperfusion injury using bioinformation analysis.

Background: Myocardial ischemia-reperfusion injury (MIRI) is often part of clinical events such as cardiac arrest, resuscitation, and reperfusion after coronary artery occlusion. Recently, more and more studies have shown that the immune microenvironment is an integral part of ischemia-reperfusion injury (IRI), and CD4+ T-cell infiltration plays an important role, but there are no relevant molecular targets for clinical diagnosis and treatment. Methods: The transcriptome data and matched group information were retrieved from the Gene Expression Omnibus (GEO) database. The ImmuCellAI-mouse (Immune Cell Abundance Identifier for mouse) algorithm was used to calculate each symbol's CD4+ T cell infiltration score. The time period with the greatest change in the degree of CD4+ T cell infiltration [ischemia-reperfusion 6 hours (IR6h)-ischemia-reperfusion 24 hours (IR24h)] was selected for the next analysis. Weighted gene co-expression network analysis (WGCNA) and differential expression analysis were performed to screen out CD4+ T cell-related genes and from which the gene CLEC5A was screened for the highest correlation with CD4+ T cell infiltration. The potential regulatory mechanism of CD4+ T cells in MIRI was discussed through various enrichment analysis. Finally, we analyzed the expression and molecular function (MF) of CLEC5A and its related genes in MIRI. Results: A total of 406 CD4+ T cell-related genes were obtained by intersecting the results of WGCNA and differential expression analysis. Functional enrichment analysis indicated that the CD4+ T cell-related genes were mainly involved in chemokine signaling pathway and cell cycle. By constructing a protein-protein interaction (PPI) network, a total of 12 hub genes were identified as candidate genes for further analysis. Through the correlation analysis between the 12 candidate genes found in the PPI network and CD4+ T cell infiltration fraction, we determined the core gene CLEC5A. Finally, a gene interaction network was constructed to decipher the biological functions of CLEC5A using GeneMANIA. Conclusions: In this study, RNA sequencing (RNA-Seq) data at different time points after reperfusion were subjected to a series of bioinformatics methods such as PPI network, WGCNA module, etc., and CLEC5A, a pivotal gene associated with CD4+ T-cells, was found, which may serve as a new target for diagnosis or treatment.

Age and treatment disparities in survival of primary malignant cardiac tumors: an analysis of over 40 years and 500 patients.

Background: Primary malignant cardiac tumors (PMCTs) are rare and tend to have a poor prognosis, due to their aggressive biological behavior and the inadequate expertise with the disease. This article compares the survival of patients with PMCT subtypes in the United States across age and treatment groups. Methods: Data of 529 patients diagnosed with PMCTs were analyzed. Chi-squared test was used to assess significance of the differences between proportions in demographic and tumor characteristics by age and treatment. Cox regression analysis was used to estimate survival from the Surveillance, Epidemiology, and End Results (SEER) follow-up data. Results: Survival rates for PMCTs differed significantly between age groups, with patients younger than 20 years surviving significantly longer than those older than 80 years. The median survival times of all patients with PMCTs were 22.5, 11, 5, and 1 month for ages less than 20, 20-50, 51-80, and greater than 80 years, respectively (global log-rank P=0.0026). In the treatment cohort, for all tumors [hazard ratio (HR) 1.52, P<0.001], sarcomas (HR 1.83, P=0.002), and other tumors (HR 2.24, P=0.017), survival was lower in patients who did not receive treatment than in those who received only surgery. Survival after diagnosis of sarcoma was lower in patients who received radiotherapy only than in those who received surgery only (HR 1.49, P=0.046). However, there was no significant association between treatment and survival for lymphoma and mesothelioma. Conclusions: This study confirms that PMCTs have limited treatment options and poor patient survival, especially for elderly patients and patients who receive no treatment. And patients with PMCTs of any age, whether treated or not, have poor survival rates. Techniques for early diagnosis and treatment may be necessary. Surgical treatment should have a higher priority for future treatment of patients with sarcomas.

Exploration of the shared genes and signaling pathways between lung adenocarcinoma and idiopathic pulmonary fibrosis.

Background: Idiopathic pulmonary fibrosis (IPF), a type of interstitial lung disease (ILD), is a chronic disease with an unknown etiology. The occurrence of lung cancer (LC) is one of the main causes of death in patients with IPF. However, the pathogenesis driving these malignant transformations remains unclear; therefore, this study aimed to identify the shared genes and functional pathways associated with both disease conditions. Methods: Data were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. To identify overlapping genes in both diseases, the "limma" package in R software and weighted gene coexpression network analysis (WGCNA) were used. Venn diagrams were used to obtain the shared genes. The diagnostic value of the shared genes was assessed using receiver operating characteristic (ROC) curve analysis. Gene Ontology (GO) term enrichment was performed on the shared genes between lung adenocarcinoma (LUAD) and IPF, and the genes were also functionally enriched using Metascape. A protein-protein interaction (PPI) network was created using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. Finally, the link between shared genes and common antineoplastic medicines was investigated using the CellMiner database. Results: The coexpression modules associated with LUAD and IPF were discovered using WGCNA, and 148 genes were found to overlap. In addition, 74 upregulated and 130 downregulated overlapping genes were obtained via differential gene analysis. Functional analysis of the genes revealed that these genes are primarily engaged in extracellular matrix (ECM) pathways. Furthermore, COL1A2, POSTN, COL5A1, CXCL13, CYP24A1, CXCL14, and BMP2 were identified as potential biomarkers in patients with LUAD secondary to IPF showing good diagnostic values. Conclusions: ECM-related mechanisms may be the underlying link between LC and IPF. A total of 7 shared genes were identified as potential diagnostic markers and therapeutic targets for LUAD and IPF.

Identification of a polycomb group-related gene signature for predicting prognosis and immunotherapy efficacy in lung adenocarcinoma.

Background: Several studies have reported the role of polycomb group (PcG) genes in human cancers; however, their role in lung adenocarcinoma (LUAD) is unknown. Methods: Firstly, consensus clustering analysis was used to identify PcG patterns among the 633 LUAD samples in the training dataset. The PcG patterns were then compared in terms of the overall survival (OS), signaling pathway activation, and immune cell infiltration. The PcG-related gene score (PcGScore) was developed using Univariate Cox regression and the least absolute shrinkage and selection operator (LASSO) algorithm to estimate the prognostic value and treatment sensitivity of LUAD. Finally, the prognostic ability of the model was validated using a validation dataset. Results: Two PcG patterns were obtained by consensus clustering analysis, and the two patterns showed significant differences in prognosis, immune cell infiltration, and signaling pathways. Both the univariate and multivariate Cox regression analyses confirmed that the PcGScore was a reliable and independent predictor of LUAD (P<0.001). The high- and low-PCGScore groups showed significant differences in the prognosis, clinical outcomes, genetic variation, immune cell infiltration, and immunotherapeutic and chemotherapeutic effects. Lastly, the PcGScore demonstrated exceptional accuracy in predicting the OS of the LUAD patients in a validation dataset (P<0.001). Conclusions: The study indicated that the PcGScore could serve as a novel biomarker to predict prognosis, clinical outcomes, and treatment sensitivity for LUAD patients.

Identification of a potential bioinformatics-based biomarker in keloids and its correlation with immune infiltration.

Keloid formation is a pathological consequence resulting from cutaneous irritation and injury, primarily attributed to excessive collagen matrix deposition and fibrous tissue proliferation. Chronic inflammation, left uncontrolled over an extended period, also stands as a substantial contributing factor. The precise mechanisms underlying keloid formation remain unclear. Therefore, this study aimed to identify key genes for diagnostic purposes. To achieve this, we used two Gene Expression Omnibus (GEO) data sets to identify differentially expressed genes. We identified one particular gene, homeobox C9 (HOXC9), using a thorough strategy involving two algorithms (least absolute shrinkage and selection operator and support vector machine-recursive feature elimination) and weighted gene co-expression network analysis. We then assessed its expression in normal and keloid tissues. In addition, we explored its temporal expression patterns via Mfuzz time clustering analysis. In our comprehensive analysis, we observed that immune infiltration, as well as cell proliferation, are crucial to keloid formation. Thus, we investigated immune cell infiltration in the keloid and normal groups, as well as the correlation between HOXC9 and these immune cells. It was found that HOXC9 was closely associated with the immune microenvironment of keloids. This shows that HOXC9 can serve as a potential biomarker and therapeutic target for keloids.

Identification of lysosomal genes associated with prognosis in lung adenocarcinoma.

Background: Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer, representing 40% of all cases of this tumor. Despite immense improvements in understanding the molecular basis, diagnosis, and treatment of LUAD, its recurrence rate is still high. Methods: RNA-seq data from The Cancer Genome Atlas (TCGA) LUAD cohort were download from Genomic Data Commons Portal. The GSE13213 dataset from Gene Expression Omnibus (GEO) was used for external validation. Differential prognostic lysosome-related genes (LRGs) were identified by overlapping survival-related genes obtained via univariate Cox regression analysis with differentially expressed genes (DEGs). The prognostic model was built using Kaplan-Meier curves and least absolute shrinkage and selection operator (LASSO) analyses. In addition, univariate and multivariate Cox analyses were employed to identify independent prognostic factors. The responses of patients to immune checkpoint inhibitors (ICIs) were further predicted. The pRRophetic package and rank-sum test were used to compute the half maximal inhibitory concentrations (IC50) of 56 chemotherapeutic drugs and their differential effects in the low- and high-risk groups. Moreover, quantitative real-time polymerase chain reaction, Western blot, and human protein atlas (HPA) database were used to verify the expression of the four prognostic biomarkers in LUAD. Results: Of the nine candidate differential prognostic LRGs, GATA2, TFAP2A, LMBRD1, and KRT8 were selected as prognostic biomarkers. The prediction of the risk model was validated to be reliable. Cox independent prognostic analysis revealed that risk score and stage were independent prognostic factors in LUAD. Furthermore, the nomogram and calibration curves of the independent prognostic factors performed well. Differential analysis of ICIs revealed CD276, ICOS, PDCD1LG2, CD27, TNFRSF18, TNFSF9, ENTPD1, and NT5E to be expressed differently in the low- and high-risk groups. The IC50 values of 12 chemotherapeutic drugs, including epothilone.B, JNK.inhibitor.VIII, and AKT.inhibitor.VIII, significantly differed between the two risk groups. KRT8 and TFAP2A were highly expressed, while GATA2 and LMBRD1 were poorly expressed in LUAD cell lines. In addition, KRT8 and TFAP2A were highly expressed, while GATA2 and LMBRD1 were poorly expressed in tumor tissues. Conclusions: Four key prognostic biomarkers-GATA2, TFAP2A, LMBRD1, and KRT8-were used to construct a significant prognostic model for LUAD patients.

[Docetaxel plus carboplatin versus EC-T as adjuvant chemotherapy for triple-negative breast cancer: safety data from a phase III randomized open-label trial].

OBJECTIVE: Triple-negative [estrogen receptor (ER)-/progesterone receptor (PR)-/HER2-] breast cancer (TNBC) accounts for ∼ 15% of overall breast cancer and associated with a poor prognosis. There is a short of standard adjuvant chemotherapy regimens for TNBC. A number of studies have shown that TNBC might be sensitive to cisplatin and carboplatin on the basis that dysfunction of BRCA1 and its pathway is associated with a specific DNA-repair defect, but data of adjuvant setting about this is limited. METHODS: From January 2010 to September 2011, 95 early triple-negative breast cancer patients confirmed by pathology were randomly assigned to receive TP (docetaxel 75 mg/m², carboplatin AUC = 5, day 1, 21 days a cycle for 6 cycles) or EC-T (epirubicin 90 mg/m², cyclophosphamide 600 mg/m², d1, 21 days a cycle for 4 cycles, followed by docetaxel 80 mg/m², d1, 21 days a cycle for 4 cycles) chemotherapy. Adjuvant radiation therapy was given selectively after chemotherapy. Here we report a preliminary safety analysis with the chi-square test. RESULTS: Seventy-six out of the 95 patients had completed the chemotherapy and could be assessed for the safety profiles of the regimens. Thirty-seven of them were in the EC-T group with a median age of 47 years, and 21 out of these 37 patients were premenopausal (56.8%). Another 39 patients came from the TP group with a median age of 46 years, and 22 out of these 39 patients were premenopausal (56.4%). All of the 37 patients in EC-T group completed the planned treatment whereas 2 patients of the 39 cases in TP group did not because of bone marrow suppression. During the treatments, 9 patients had dose adjustment in each group. Adverse events of grade 1/2 were common. Specific incidence of adverse events with grade 3/4 in each group was as follows: alopecia, 29.7% vs. 10.3% (P = 0.033), vomiting 21.6% vs. 7.7% (P = 0.085), leukopenia 54.1% vs.25.6% (P = 0.011) and neutropenia 51.4% vs. 35.9% (P = 0.174). Other grade 3/4 toxicities were rare. All the adverse events (except peripheral neuropathy and pigmentation) recovered within 1 month after the chemotherapy. CONCLUSION: Both EC-T and TP regimens as adjuvant chemotherapy are safe and tolerable for the treatment of triple-negative breast cancer patients, while the TP regimen has advantages with less grade III/IV alopecia and leukopenia.

Characteristics of circadian rhythm-related genes and establishment of a prognostic scoring system for lung adenocarcinoma with experimental verification: a bioinformatics analysis.

Background: Non-small cell lung cancer (NSCLC) is one of the most common malignant tumors worldwide. Lung adenocarcinoma (LUAD), the main subtype of NSCLC, has a poor prognosis. In recent years, circadian rhythm (CR)-related genes (CRRGs) have demonstrated associations with tumor occurrence and development, but the relationship between CRRGs and LUAD is not clear. Because of the correlation between CRRGs and tumors, we have reason to believe that CRRGs will become an important prognostic indicator for LUAD and guide the treatment of LUAD prognosis. Methods: Based on data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, we explored the biological function and immune cell infiltration of LUAD in different CR clusters and quantified CR genes using principal component analysis (PCA). Then, we built a CR scoring system (CRscore) to explore the relationship between CRRGs and LUAD prognosis. Results: Patients were divided into three clusters (A, B, and C). Biological characteristics, such as survival, immune cell infiltration, and gene enrichment, were significantly different among the three clusters (P<0.001). We then established the usefulness of the CR score, which could probably predict the prognosis of LUAD. Specifically, patients with a high CR score had a better prognosis and were more sensitive to chemotherapy than those with a low CR score. Conclusions: It is possible to use CRRGs to assess the prognosis of patients with LUAD. Quantification of CR using the CRscore tool in patients with LUAD maybe help to guide personalized cancer immunotherapy strategies in the future. Thus, the CRscore may be a prognostic tool for LUAD.

Histone acetylation modification regulator-mediated tumor microenvironment infiltration characteristics and prognostic model of lung adenocarcinoma patients.

Background: The incidence rate of lung adenocarcinoma (LUAD) is rapidly increasing. Recent studies have reported that histone acetylation modification plays an important role in the occurrence and development of tumors. However, the potential role of modification of histone acetylation modification in the development of tumor immune microenvironment is still unclear. Methods: In this study, we comprehensively evaluated the acetylation modification patterns of LUAD samples obtained from various different databases based on 36 histone modification regulators, and constructed a prognostic model based on The Cancer Genome Atlas (TCGA) LUAD cohort using the Cox regression method. The close relationship between histone acetylation and tumor immune characteristics was further studied, including immune infiltration, immune escape and immunotherapy. Finally, we combined three cohort (GSE30219, GSE72094 and GSE50081) from Gene Expression Omnibus (GEO) database to verify the above results. Results: We analyzed the expression, mutation and interaction of 36 histone acetylation regulated genes. After Univariate Cox regression analysis and least absolute shrinkage and selection operator regression (LASSO), 5 genes (KAT2B, SIRT2, HDAC5, KAT8, HDAC2) were screened to establish the prognosis model and calculate the risk score. Then, patients in the TCGA cohort were divided into high- and low-risk groups based on the risk scores. Further analysis indicated that patients in the high-risk group exhibited significantly reduced overall survival (OS) compared with those in the low-risk group. The high- and low-risk groups exhibited significant differences in terms of tumor immune characteristics, such as immune infiltration, immune escape and immunotherapy. The high-risk group had lower immune score, less immune cell infiltration and higher clinical stage. Moreover, multivariate analysis revealed that this prognostic model might be a powerful prognostic predictor for LUAD. In addition, drugs sensitive for this classification were identified. Finally, the efficacy of the prognostic model was validated by cohort (GSE30219, GSE72094 and GSE50081) from GEO database. Conclusions: Our study provided a robust signature for predicting changing prognosis of patients with LUAD. Thus, it appears to be a potentially useful prognostic tool. Moreover, the important relationship between histone acetylation and tumor immune microenvironment was revealed.

Analysis of prognostic model based on immunotherapy related genes in lung adenocarcinoma.

Lung cancer is one of the most common malignant tumors, and ranks high in the list of mortality due to cancers. Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer. Despite progress in the diagnosis and treatment of lung cancer, the prognosis of these patients remains dismal. Therefore, it is crucial to identify the predictors and treatment targets of lung cancer to provide appropriate treatments and improve patient prognosis. In this study, the gene modules related to immunotherapy were screened by weighted gene co-expression network analysis (WGCNA). Using unsupervised clustering, patients in The Cancer Genome Atlas (TCGA) were divided into three clusters based on the gene expression. Next, gene clustering was performed on the prognosis-related differential genes, and a six-gene prognosis model (comprising PLK1, HMMR, ANLN, SLC2A1, SFTPB, and CYP4B1) was constructed using least absolute shrinkage and selection operator (LASSO) analysis. Patients with LUAD were divided into two groups: high-risk and low-risk. Significant differences were found in the survival, immune cell infiltration, Tumor mutational burden (TMB), immune checkpoints, and immune microenvironment between the high- and low-risk groups. Finally, the accuracy of the prognostic model was verified in the Gene Expression Omnibus (GEO) dataset in patients with LUAD (GSE30219, GSE31210, GSE50081, GSE72094).

A modified screening strategy for Lynch syndrome among MLH1-deficient CRCs: Analysis from consecutive Chinese patients in a single center.

BACKGROUND: The low prevalence of the BRAF V600E mutation in colorectal cancers (CRCs) in Chinese populations has stimulated concern about the efficacy of BRAF mutation analysis for Lynch syndrome (LS) screening. METHODS: In total, 169 of 4104 consecutive CRC patients with absent MLH1 staining were analyzed to compare the utility of the BRAF V600E mutation testing with MLH1 promoter methylation analysis in the Chinese population. Germline genetic testing was performed in patients with wild-type BRAF/methylated MLH1. RESULTS: Compared with BRAF genotyping, the use of MLH1 methylation testing alone to evaluate patients with MLH1 deficiency reduced referral rates for germline testing by 1.8-fold (82.8% vs. 47.1%). However, 6 patients harboring MLH1 promoter methylation were verified to have LS through germline genetic testing. It is notable that all 6 patients had a family history of CRC in at least 1 first-degree relative (FDR) or second-degree relative (SDR). The combination of MLH1 promoter methylation analysis and a family history of CRC could preclude significantly more patients from germline genetic testing than from BRAF mutation testing alone (45.5% vs. 17.2%, p<0.001) and decrease the number of misdiagnosed LS patients with MLH1 promoter methylation. CONCLUSION: The combination of a family history of CRC with MLH1 promoter methylation analysis showed better performance than BRAF mutation testing in the selection of patients in the Chinese population for germline genetic testing.

Nrf2 Promotes Inflammation in Early Myocardial Ischemia-Reperfusion via Recruitment and Activation of Macrophages.

Cardiomyocyte apoptosis in response to inflammation is a primary cause of myocardial ischemia-reperfusion injury (IRI). Nuclear factor erythroid 2 like 2 (Nrf2) reportedly plays an important role in myocardial IRI, but the underlying mechanism remains obscure. Expression data from the normal heart tissues of mice or heart tissues treated with reperfusion for 6 h after ischemia (IR6h) were acquired from the GEO database; changes in biological function and infiltrating immune cells were analyzed. The binding between the molecules was verified by chromatin immunoprecipitation sequencing. Based on confirmation that early myocardial ischemia-reperfusion (myocardial ischemia/reperfusion for 6 hours, IR6h) promoted myocardial apoptosis and inflammatory response, we found that Nrf2, cooperating with Programmed Cell Death 4, promoted transcription initiation of C-C Motif Chemokine Ligand 3 (Ccl3) in myocardial tissues of mice treated with IR6h. Moreover, Ccl3 contributed to the high signature score of C-C motif chemokine receptor 1 (Ccr1)-positive macrophages. The high signature score of Ccr1-positive macrophages leads to the release of pro-inflammatory factors interleukin 1 beta and interleukin 6. This study is the first to elucidate the damaging effect of Nrf2 via remodeling of the immune microenvironment in early myocardial ischemia-reperfusion, which provides us with new perspectives and treatment strategies for myocardial ischemia-reperfusion.