Au nanorod assembly for sensitive SERS detection of airway inflammatory factors in sputum

In this paper, we demonstrate a surface-enhanced Raman spectroscopy (SERS) biosensor based on the self-assembly of gold nanorods (AuNRs) for the specific detection of airway inflammatory factors in diluted sputum. The AuNR surface was modified with an antibody that was able to specifically recognize an airway inflammatory factor, interleukin-5 (IL-5), so that a end-to-end self-assembly system could be obtained, resulting in an order of magnitude amplification of the Raman signal and greatly improved sensitivity. Meanwhile, the outer layer of the biosensor was coated with silicon dioxide, which improved the stability of the system and facilitated its future applications. When the detected concentration was in the range of 0.1-50 pg/mL, the SERS signal generated by the sensor showed a good linear relationship with the IL-5 concentration. Moreover, it had satisfactory performance in diluted sputum and clinical subjects with asthma, which could achieve sensitive detection of the airway inflammatory factor IL-5. Overall, the developed biosensor based on the SERS effect exhibited the advantages of rapid and sensitive detecting performance, which is suitable for monitoring airway inflammatory factors in sputum.

Natural killer cell-related prognostic risk model predicts prognosis and treatment outcomes in triple-negative breast cancer

Background

Natural killer (NK) cells are crucial to the emergence, identification, and prognosis of cancers. The roles of NK cell-related genes in the tumor immune microenvironment (TIME) and immunotherapy treatment are unclear. Triple-negative breast cancer (TNBC) is a highly aggressive malignant tumor. Hence, this study was conducted to develop a reliable risk model related to NK cells and provide a novel system for predicting the prognosis of TNBC.

Methods

NK cell-related genes were collected from previous studies. Based on TCGA and GEO database, univariate and LASSO cox regression analysis were used to establish the NK cell-related gene signature. The patients with TNBC were separated to high-risk and low-risk groups. After that, survival analysis was conducted and the responses to immunotherapies were evaluated on the basis of the signature. Moreover, the drug sensitivity of some traditional chemotherapeutic drugs was assessed by using the "oncoPredict" R package. In addition, the expression levels of the genes involved in the signature were validated by using qRT-PCR in TNBC cell lines.

Results

The patients with TNBC were divided into high- and low-risk groups according to the median risk score of the 5-NK cell-related gene signature. The low-risk group was associated with a better clinical outcome. Besides, the differentially expressed genes between the different risk groups were enriched in the biological activities associated with immunity. The tumor immune cells were found to be highly infiltrated in the low-risk groups. In accordance with the TIDE score and immune checkpoint-related gene expression analysis, TNBC patients in the low-risk groups were suggested to have better responses to immunotherapies. Eventually, some classical anti-tumor drugs were shown to be less effective in high-risk groups than in low-risk groups.

Conclusion

The 5-NK cell-related gene signature exhibit outstanding predictive performance and provide fresh viewpoints for evaluating the success of immunotherapy. It will provide new insights to achieve precision and integrated treatment for TNBC in the future.

Comprehensive analysis of transient receptor potential channels-related signature for prognosis, tumor immune microenvironment, and treatment response of colorectal cancer

BACKGROUND

Transient receptor potential channels (TRPC) play critical regulatory functions in cancer occurrence and progression. However, knowledge on its role in colorectal cancer (CRC) is limited. In addition, neoadjuvant treatment and immune checkpoint inhibitors (ICIs) have increasing roles in CRC management, but not all patients benefit from them. In this study, a TRPC related signature (TRPCRS) was constructed for prognosis, tumor immune microenvironment (TIME), and treatment response of CRC.

METHODS

Data on CRC gene expression and clinical features were retrospectively collected from TCGA and GEO databases. Twenty-eight TRPC regulators (TRPCR) were retrieved using gene set enrichment analysis. Different TRPCR expression patterns were identified using non-negative matrix factorization for consensus clustering, and a TRPCRS was established using LASSO. The potential value of TRPCRS was assessed using functional enrichment analysis, tumor immune analysis, tumor somatic mutation analysis, and response to preoperative chemoradiotherapy or ICIs. Moreover, an external validation was conducted using rectal cancer samples that received preoperative chemoradiotherapy at Fujian Cancer Hospital (FJCH) via qRT-PCR.

RESULTS

Among 834 CRC samples in the TCGA and meta-GEO cohorts, two TRPCR expression patterns were identified, which were associated with various immune infiltrations. In addition, 266 intersected genes from 5564 differentially expressed genes (DEGs) between two TRPC subtypes, 4605 DEGs between tumor tissue and adjacent non-tumor tissue (all FDR< 0.05, adjusted P< 0.001), and 1329 prognostic related genes (P< 0.05) were identified to establish the TRPCRS, which was confirmed in the TCGA cohort, two cohorts from GEO, and one qRT-PCR cohort from FJCH. According to the current signature, the high-TRPC score group had higher expressions of PD-1, PD-L1, and CTLA4, lower TIDE score, and improved response to anti-PD-1 treatment with better predictive ability. Compared to the high-TRPC score group, the low-TRPC score group comprised an immunosuppressive phenotype with increased infiltration of neutrophils and activated MAPK signaling pathway, but was more sensitive to preoperative chemoradiotherapy and associated with improved prognosis.

CONCLUSIONS

The current TRPCRS predicted the prognosis of CRC, evaluated the TIME in CRC, and anticipated the response to immune therapy and neoadjuvant treatment.

Case Report: Novel compound heterozygous variants in CHRNA1 gene leading to lethal multiple pterygium syndrome: A case report

Background: Lethal multiple pterygium syndrome (LMPS) is a rare autosomal recessive inherited disorder typically characterized by intrauterine growth retardation, multiple pterygia, and flexion contractures.

Case presentation: We herein report a Chinese case with a history of three adverse pregnancies demonstrating the same ultrasonic phenotypes, including increased nuchal translucency, edema, fetal neck cystoma, reduced movement, joint contractures, and other congenital features. Whole-exome sequencing (WES) revealed novel compound heterozygous variants in the CHRNA1 gene NM_000079.4: c.[1128delG (p.Pro377LeufsTer10)]; [505T>C (p.Trp169Arg)] in the recruited individual, and subsequent familial segregation showed that both parents transmitted their respective mutation.

Conclusion: For the first time, we identified an association between the CHRNA1 gene and the recurrent lethal multiple pterygium syndrome (LMPS) in a Chinese family. This finding may also enrich the mutation spectrum of the CHRNA1 gene and promote the applications of WES technology in etiologic diagnosis of ultrasound anomalies in prenatal examination.

Identification of endoplasmic reticulum stress-associated genes and subtypes for prediction of Alzheimer’s disease based on interpretable machine learning

Introduction: Alzheimer’s disease (AD) is a severe dementia with clinical and pathological heterogeneity. Our study was aim to explore the roles of endoplasmic reticulum (ER) stress-related genes in AD patients based on interpretable machine learning.

Methods: Microarray datasets were obtained from the Gene Expression Omnibus (GEO) database. We performed nine machine learning algorithms including AdaBoost, Logistic Regression, Light Gradient Boosting (LightGBM), Decision Tree (DT), eXtreme Gradient Boosting (XGBoost), Random Forest, K-nearest neighbors (KNN), Naïve Bayes, and support vector machines (SVM) to screen ER stress-related feature genes and estimate their efficiency of these genes for early diagnosis of AD. ROC curves were performed to evaluate model performance. Shapley additive explanation (SHAP) was applied for interpreting the results of these models. AD patients were classified using a consensus clustering algorithm. Immune infiltration and functional enrichment analysis were performed via CIBERSORT and GSVA, respectively. CMap analysis was utilized to identify subtype-specific small-molecule compounds.

Results: Higher levels of immune infiltration were found in AD individuals and were markedly linked to deregulated ER stress-related genes. The SVM model exhibited the highest AUC (0.879), accuracy (0.808), recall (0.773), and precision (0.809). Six characteristic genes (RNF5, UBAC2, DNAJC10, RNF103, DDX3X, and NGLY1) were determined, which enable to precisely predict AD progression. The SHAP plots illustrated how a feature gene influence the output of the SVM prediction model. Patients with AD could obtain clinical benefits from the feature gene-based nomogram. Two ER stress-related subtypes were defined in AD, subtype2 exhibited elevated immune infiltration levels and immune score, as well as higher expression of immune checkpoint. We finally identified several subtype-specific small-molecule compounds.

Conclusion: Our study provides new insights into the role of ER stress in AD heterogeneity and the development of novel targets for individualized treatment in patients with AD.

Emergence of a Salmonella Rissen ST469 clinical isolate carrying blaNDM-13 in China

New Delhi metallo-β-lactamase-13 (NDM-13) is an NDM variant that was first identified in 2015 and has not been detected in Salmonella species prior to this study. Here we describe the first identification of a Salmonella Rissen strain SR33 carrying bla_NDM-13. The aim of this study was to molecularly characterize SR33’s antimicrobial resistance and virulence features as well as investigate the genetic environment of bla_NDM-13. The Salmonella Rissen SR33 strain was isolated from a patient with fever and diarrhea. SR33 belonged to ST469, and it was found to be multidrug-resistant (MDR) and to carry many virulence genes. Phylogenetic analysis showed that SR33 shared a close relationship with most of the Chinese S. Rissen ST469 strains. bla_NDM-13 was located in a transmissible IncI1 plasmid pNDM13-SR33. Sequence analysis of bla_NDM-13-positive genomes downloaded from GenBank revealed that a genetic context (ΔISAba125-bla_NDM-13-ble_MBL-trpF) and a hybrid promoter (consisting of −35 sequences provided by ISAba125 and −10 sequences) were conserved. ISAba125 was truncated by IS1294 in three plasmids carrying bla_NDM-13, including pNDM13-SR33. To our knowledge, this is the first report of bla_NDM-13 carried by Salmonella. The emergence of bla_NDM-13 in a clinical MDR S. Rissen ST469 strain highlights the critical need for monitoring and controlling the dissemination of bla_NDM-13. bla_NDM-13 carried by a transmissible IncI1 plasmid may result in an increased risk of bla_NDM-13 transmission. IS1294 may be involved in the movement of bla_NDM-13.

Abnormal Changes of Monocyte Subsets in Patients With Sjögren’s Syndrome

Background

Recent studies have proven the existence of distinct monocyte subsets, which play a significant role in the development of some rheumatic diseases such as systemic lupus erythematosus (SLE). This study was performed to define the changes of monocyte subsets in patients with Sjögren’s Syndrome (SjS).

Methods

Single cell RNA-sequencing (scRNA-seq) data of monocytes from SjS patients and controls were analyzed. The transcriptomic changes in monocyte subsets between SjS and controls were identified and potential key functional pathways involved in SjS development were also explored.

Results

A total of 11 monocyte subsets were identified in the scRNA-seq analyses of monocytes. A new monocyte subset characterized by higher expression of VNN2 (GPI-80) and S100A12 (Monocyte cluster 3) was identified, and it was increased in SjS patients. Compared with controls, almost all monocyte subsets from SjS patients had increased expression of TNFSF10 (TRAIL). Moreover, interferon (IFN)-related and neutrophil activation-associated pathways were main up-regulated pathways in the monocytes of SjS patients.

Conclusion

This study uncovered the abnormal changes in monocyte subsets and their transcriptomic changes in SjS patients, and identified TNFSF10 ^high/+ monocytes as a potential key player in SjS pathogenesis and a promising target for SjS treatment.

SNRPD1/E/F/G Serve as Potential Prognostic Biomarkers in Lung Adenocarcinoma

Objectives: Sm proteins (SNRPB/D1/D2/D3/E/F/G), involved in pre-mRNA splicing, were previously reported in the tumorigenesis of several cancers. However, their specific role in lung adenocarcinoma (LUAD) remains obscure. Our study aims to feature abnormal expressions and mutations of genes for Sm proteins and assess their potential as therapeutic targets via integrated bioinformatics analysis.

Methods: In this research, we explored the expression pattern and prognostic worth of genes for Sm proteins in LUAD across TCGA, GEO, UALCAN, Oncomine, Metascape, David 6.8, and Kaplan-Meier Plotter, and confirmed its independent prognostic value via univariate and multivariate cox regression analysis. Meanwhile, their expression patterns were validated by RT-qPCR. Gene mutations and co-expression of genes for Sm proteins were analyzed by the cBioPortal database. The PPI network for Sm proteins in LUAD was visualized by the STRING and Cytoscape. The correlations between genes for Sm proteins and immune infiltration were analyzed by using the “GSVA” R package.

Results: Sm proteins genes were found upregulated expression in both LUAD tissues and LUAD cell lines. Moreover, highly expressed mRNA levels for Sm proteins were strongly associated with short survival time in LUAD. Genes for Sm proteins were positively connected with the infiltration of Th2 cells, but negatively connected with the infiltration of mast cells, Th1 cells, and NK cells. Importantly, Cox regression analysis showed that high SNRPD1/E/F/G expression were independent risk factors for the overall survival of LUAD.

Conclusion: Our study showed that SNRPD1/E/F/G could independently predict the prognostic outcome of LUAD and was correlated with immune infiltration. Also, this report laid the foundation for additional exploration on the potential treatment target’s role of SNRPD1/E/F/G in LUAD.