Identified a disintegrin and metalloproteinase with thrombospondin motifs 6 serve as a novel gastric cancer prognostic biomarker by bioinformatics analysis

Cauchy hyper-graph Laplacian nonnegative matrix factorization for single-cell RNA-sequencing data analysis

Many important biological facts have been found as single-cell RNA sequencing (scRNA-seq) technology has advanced. With the use of this technology, it is now possible to investigate the connections among individual cells, genes, and illnesses. For the analysis of single-cell data, clustering is frequently used. Nevertheless, biological data usually contain a large amount of noise data, and traditional clustering methods are sensitive to noise. However, acquiring higher-order spatial information from the data alone is insufficient. As a result, getting trustworthy clustering findings is challenging. We propose the Cauchy hyper-graph Laplacian non-negative matrix factorization (CHLNMF) as a unique approach to address these issues. In CHLNMF, we replace the measurement based on Euclidean distance in the conventional non-negative matrix factorization (NMF), which can lessen the influence of noise, with the Cauchy loss function (CLF). The model also incorporates the hyper-graph constraint, which takes into account the high-order link among the samples. The CHLNMF model's best solution is then discovered using a half-quadratic optimization approach. Finally, using seven scRNA-seq datasets, we contrast the CHLNMF technique with the other nine top methods. The validity of our technique was established by analysis of the experimental outcomes.

Comprehensive Analysis of ADAMTS Gene Family in Renal Clear Cell Carcinoma and ADAMTS10 Research Combining Magnetic Resonance Imaging

Clear cell renal carcinoma (ccRCC) is one of the cancers that posed a severe threat to human life on a global scale. The ADAMTS family has been proven to be involved in a number of tumor types, although it is yet unknown how they relate to ccRCC. The mRNA expression matrix and other clinically relevant information of 607 ccRCC were sourced from TCGA database. The role of ADAMTS family genes in ccRCC was determined by differential gene expression analysis and gene set enrichment analysis (GSEA). Employing stage grading, gene mutation, and survival analysis, the genes most linked to the prognosis of ccRCC were identified. The influence of genes on the pathway was determined by Kyoto Encyclopedia of Genes and Genes (KEGG) analysis. Following that, the gene's impact on ccRCC was verified by qRT-PCR, WB, MTT, Transwell detection, and a wound healing assay. Bioinformatics analysis showed that ADAMTS10 was overexpressed in cancerous tissues of people with ccRCC and its expression increased with tumor grade. Mutation analysis showed that the main cause of mutation in the ADAMTS family gene was amplification. The prognosis and survival of the ADAMTS10 elevated expression group were lower than those of the poorly expressed group, as demonstrated by a survival analysis. On the basis of the findings of MRI, we examined 60 clinical patients and collected their cancer along with the surrounding tissues. The results of qPCR detection showed that the expression of ADAMTS10 was considerably higher in cancerous regions of 60 clinical users than it was in the tissues nearby. Inhibiting ADAMTS10 development prevents cancer cells from proliferating, invading, and migrating. The KEGG analysis links ADAMTS10 to the NF-κB signal pathway. WB experiment confirmed that inhibiting ADAMTS10 expression can inhibit the activation of the NF-κB signal pathway. ADAMTS10 may be a promising prognostic marker for ccRCC that can be employed independently.

Identification of a basement membrane-related genes signature to predict prognosis, immune landscape and guide therapy in gastric cancer

The basement membrane is an essential defense against cancer progression and is intimately linked to the tumor immune microenvironment. However, there is limited research comprehensively discussing the potential application of basement membrane-related genes (BMRGs) in the prognosis evaluation and immunotherapy of gastric cancer (GC). The RNA-seq data and clinical information of GC patients were collected from the TCGA and GEO database. Prognosis-associated BMRGs were filtered via univariate Cox regression analysis. The 4-BMRGs signatures were constructed by lasso regression. Prognostic predictive accuracy of the 4-BMRGs signature was appraised with survival analysis, receiver operating characteristic curves, and nomogram. Gene set enrichment analysis (GSEA), gene ontology, and gene set variation analysis were performed to dig out potential mechanisms and functions. The Estimate algorithm and ssGSEA were used for assessing the tumor microenvironment and immunological characteristics. Identification of molecular subtypes by consensus clustering. Drug sensitivity analysis using the "pRRophetic" R package. Immunotherapy validation with immunotherapy cohort. A 4-BMRGs signature was constructed, which could excellently predict the GC patient prognosis (5-year AUC value of 0.873). Kaplan-Meier and Cox regression analyses showed that the 4-BMRGs signature was an OS-independent prognostic factor, and that higher risk scores were associated with shorter OS. The high-risk subgroup exhibits a higher abundance of immune cell infiltration, such as macrophages. Additionally, we observed a strong correlation between 2 BMRGs (LUM, SPARC) and immune cells such as CD8 + T cells and macrophages. The high-risk subgroup appears to be more sensitive to Axitinib, DMOG, Gemcitabine and Docetaxel by pRRophetic analysis. Furthermore, the validation of the cohort that received immune therapy revealed that patients in the high-risk group who underwent immune checkpoint inhibitor treatment exhibited better response rates. Pan-cancer analysis also shows that risk scores are strongly associated with immune and carcinogenic pathways. The 4-BMRGs signature has demonstrated accuracy and reliability in predicting the GC patient's prognosis and could assist in the formulation of clinical strategies.

Function and prognostic value of basement membrane -related genes in lung adenocarcinoma

Background: Lung adenocarcinoma (LUAD) has become a common cause of cancer-related death. Many studies have shown that the basement membrane (BM) is associated with the development of cancer. However, BM-related gene expression and its relationship to LUAD prognosis remains unclear. Methods: BM-related genes from previous studies were used. Clinical and mRNA expression information were obtained from TCGA database. Cox, minimum absolute contraction, and selection operator regression were applied to analyze the selected genes affecting LUAD prognosis. A prognostic-risk model was then established. Furthermore, this study applied Kaplan-Meier analysis to assess the outcomes of high- and low-risk groups, then explored their differences in drug sensitivity. The DSigDB database was used to screen for therapeutic small-molecule drugs. Results: Fourteen prognostic models based on BM-related genes were successfully constructed and validated in patients with LUAD. We also found that independence was a prognostic factor in all 14 BM-based models. Functional analysis showed that the enrichment of BM-related genes mainly originated from signaling pathways related to cancer. The BM-based model also suggested that immune cell infiltration is associated with checkpoints. The low-risk patients may benefit from cyclopamine and docetaxel treatments. Conclusion: This study identified a reliable biomarker to predict survival in patients with LUAD and offered new insights into the function of BM-related genes in LUAD.

ADAMTS6: Emerging roles in cardiovascular, musculoskeletal and cancer biology

ADAMTS family members control mammalian development and disease, primarily through their function as proteases, by regulation of extracellular matrix composition. Until recently, ADAMTS6 was known as one of the orphan proteinases of the nineteen-member family with a relatively unknown expression pattern and function. Emerging focus on this enzyme has started to uncover these unknowns and revealed a vast importance and requirement of ADAMTS6 in cardiovascular and musculoskeletal development. In addition, ADAMTS6 has been linked to numerous disease settings including several types of cancer. This review summarizes the necessity of ADAMTS6 during development, its role in disease and requirement for essential prospective studies to fully realize its biological implications and potential for therapeutic intervention.