Prognostic Significance of Prostaglandin-Endoperoxide Synthase-2 Expressions in Human Breast Carcinoma: A Multiomic Approach

Functional Profiling of Soft Tissue Sarcoma Using Mechanistic Models

Soft tissue sarcoma is an umbrella term for a group of rare cancers that are difficult to treat. In addition to surgery, neoadjuvant chemotherapy has shown the potential to downstage tumors and prevent micrometastases. However, finding effective therapeutic targets remains a research challenge. Here, a previously developed computational approach called mechanistic models of signaling pathways has been employed to unravel the impact of observed changes at the gene expression level on the ultimate functional behavior of cells. In the context of such a mechanistic model, RNA-Seq counts sourced from the Recount3 resource, from The Cancer Genome Atlas (TCGA) Sarcoma project, and non-diseased sarcomagenic tissues from the Genotype-Tissue Expression (GTEx) project were utilized to investigate signal transduction activity through signaling pathways. This approach provides a precise view of the relationship between sarcoma patient survival and the signaling landscape in tumors and their environment. Despite the distinct regulatory alterations observed in each sarcoma subtype, this study identified 13 signaling circuits, or elementary sub-pathways triggering specific cell functions, present across all subtypes, belonging to eight signaling pathways, which served as predictors for patient survival. Additionally, nine signaling circuits from five signaling pathways that highlighted the modifications tumor samples underwent in comparison to normal tissues were found. These results describe the protective role of the immune system, suggesting an anti-tumorigenic effect in the tumor microenvironment, in the process of tumor cell detachment and migration, or the dysregulation of ion homeostasis. Also, the analysis of signaling circuit intermediary proteins suggests multiple strategies for therapy.

Identification and validation of a novel ferroptosis-related gene signature for prognosis and potential therapeutic target prediction in cholangiocarcinoma

Cholangiocarcinoma (CCA) is a highly heterogeneous and aggressive malignancy of the bile ducts with a poor prognosis and high mortality rate. Effective targeted therapy and accurate prognostic biomarkers are still lacking. Ferroptosis is a form of regulated cell death implicated in cancer progression and has emerged as a potential therapeutic target in various cancers. However, a comprehensive analysis of ferroptosis-related genes (FRGs) for predicting CCA prognosis and therapeutic targets and determining the role of ferroptosis in CCA remain to be performed. Here, we developed a prognostic FRG signature using a least absolute shrinkage and selection operator Cox regression analysis in a training cohort. We then validated it using four independent public datasets. The six-FRG signature was developed to predict CCA patient survival, stratifying them into low-risk and high-risk groups based on survival time. Significantly, the high-risk CCA patients had shorter overall survival. A receiver operating characteristic curve analysis further confirmed the prognostic FRG signature's strong predictive ability, indicating that it was an independent prognostic indicator for CCA patients. Furthermore, the high-risk group was associated with fluke infection and high clinical stages. Cancer-associated fibroblast (CAF) score and CAF markers were significantly higher in the high-risk group than the low-risk group. Moreover, our FRG signature could predict immune checkpoint markers for immunotherapy and drug sensitivity. The mRNA expression levels of the six-FRG signature was validated in 10 CCA cell lines and dividing them into low-risk and high-risk groups using the FRG signature. We further showed that high-risk CCA cell lines were more resistant to ferroptosis inducers, including erastin and RSL3, than the low-risk CCA cell lines. Our study constructed a novel FRG signature model to predict CCA prognoses which might provide prognostic biomarkers and potential therapeutic targets for CCA patients. Ferroptosis sensitivity in high-risk and low-risk CCA cell lines suggests that ferroptosis resistance is associated with high-risk group CCA. Therefore, ferroptosis could be a promising therapeutic target for precision therapy in CCA patients.

NTD-DR: Nonnegative tensor decomposition for drug repositioning

Computational drug repositioning aims to identify potential applications of existing drugs for the treatment of diseases for which they were not designed. This approach can considerably accelerate the traditional drug discovery process by decreasing the required time and costs of drug development. Tensor decomposition enables us to integrate multiple drug- and disease-related data to boost the performance of prediction. In this study, a nonnegative tensor decomposition for drug repositioning, NTD-DR, is proposed. In order to capture the hidden information in drug-target, drug-disease, and target-disease networks, NTD-DR uses these pairwise associations to construct a three-dimensional tensor representing drug-target-disease triplet associations and integrates them with similarity information of drugs, targets, and disease to make a prediction. We compare NTD-DR with recent state-of-the-art methods in terms of the area under the receiver operating characteristic (ROC) curve (AUC) and the area under the precision and recall curve (AUPR) and find that our method outperforms competing methods. Moreover, case studies with five diseases also confirm the reliability of predictions made by NTD-DR. Our proposed method identifies more known associations among the top 50 predictions than other methods. In addition, novel associations identified by NTD-DR are validated by literature analyses.

Comprehensive Analysis of Prognostic Value and Immune Infiltration of NLRC4 and CASP1 in Colorectal Cancer

Introduction

Nod-like receptor C4 (NLRC4) is a member of the Nod-like receptor (NLR) family, and its expression mediates the activation of caspase-1 (CASP1). Abnormal expression of NLRC4 and CASP1 is associated with multiple tumors. However, the expression differences, prognostic value and immune correlation of NLRC4 and CASP1 in colorectal cancer (CRC) remain to be determined.

Methods

In this study, TCGA, CCLE, HPA, PrognoScan, STRING and GeneMANIA databases were used to analyze differences in expression, prognostic value, genetic alterations and immune cell infiltration of NLRC4 and CASP1 in CRC patients. Then, we further validated the expression of NLRC4 and CASP1 in CRC using immunohistochemistry (IHC).

Results

NLRC4 and CASP1 were expressed low in CRC tissues and CRC cell lines. The expression of NLRC4 was significantly related to the patient’s gender and lymph node metastasis. NLRC4 and CASP1 down-regulated expression was observably correlated with poor survival and diverse immune cells infiltration in CRC patients. NLRC4 and CASP1 have a gene mutation alteration. NLRC4 and CASP1 had a significant positive correlation in CRC.

Conclusion

This study will provide new ideas for the prognosis and treatment in CRC. NLRC4 and CASP1 are expected to be novel biomarkers and potential immunotherapy targets in CRC patients.