Pancreatic ductal adenocarcinomas from Mexican patients present a distinct genomic mutational pattern

Subtype-WGME enables whole-genome-wide multi-omics cancer subtyping

We present an innovative strategy for integrating whole-genome-wide multi-omics data, which facilitates adaptive amalgamation by leveraging hidden layer features derived from high-dimensional omics data through a multi-task encoder. Empirical evaluations on eight benchmark cancer datasets substantiated that our proposed framework outstripped the comparative algorithms in cancer subtyping, delivering superior subtyping outcomes. Building upon these subtyping results, we establish a robust pipeline for identifying whole-genome-wide biomarkers, unearthing 195 significant biomarkers. Furthermore, we conduct an exhaustive analysis to assess the importance of each omic and non-coding region features at the whole-genome-wide level during cancer subtyping. Our investigation shows that both omics and non-coding region features substantially impact cancer development and survival prognosis. This study emphasizes the potential and practical implications of integrating genome-wide data in cancer research, demonstrating the potency of comprehensive genomic characterization. Additionally, our findings offer insightful perspectives for multi-omics analysis employing deep learning methodologies.

SKP2 promotes the metastasis of pancreatic ductal adenocarcinoma by suppressing TRIM21-mediated PSPC1 degradation

Despite significant advances in diagnostic techniques and treatment approaches, the prognosis of pancreatic ductal adenocarcinoma (PDAC) is still poor. Previous studies have reported that S-phase kinase-associated protein 2 (SKP2), a subunit of the SCF E3 ubiquitin ligase complex, is engaged in the malignant biological behavior of some tumor entities. However, SKP2 has not been fully investigated in PDAC. In the present study, it was observed that high expression of SKP2 significantly correlates with decreased survival time. Further experiments suggested that SKP2 promotes metastasis by interacting with the putative transcription factor paraspeckle component 1 (PSPC1). According to the results of coimmunoprecipitation and ubiquitination assays, SKP2 depletion resulted in the polyubiquitination of PSPC1, followed by its degradation. Furthermore, the SKP2-mediated ubiquitination of PSPC1 partially depended on the activity of the E3 ligase TRIM21. In addition, inhibition of the SKP2/PSPC1 axis by SMIP004, a traditional inhibitor of SKP2, impaired the migration of PDAC cells. In summary, this study provides novel insight into the mechanisms involved in PDAC malignant progression. Targeting the SKP2/PSPC1 axis is a promising strategy for the treatment of PDAC.

The high expression of FOXE1 in colorectal cancer predicts a promising prognosis: a retrospective study

Purpose Forkhead box (FOX) family proteins regulate transcription and DNA repair and are involved in cell growth, differentiation, embryogenesis, and lifespan. The transcription factor FOXE1 is a member of the FOX family. The relationship between the expression level of FOXE1 and colorectal cancer (CRC) prognosis remains controversial. It is vital to verify the relationship between FOXE1 expression and the prognosis of patients with CRC. Methods We constructed a tissue microarray containing 879 primary colorectal cancer tissues and 203 normal mucosa samples. The tumor and normal mucosa tissues were stained with FOXE1 by immunohistochemistry, and the staining results were divided into two groups: high expression group and low expression group. Chi-square test was performed for the classification variable of the difference between FOXE1 expression levels and clinicopathological parameters. The survival curve was calculated according to the Kaplan-Meier method and the logarithmic rank test. The Cox proportional risk regression model was used for multivariate analysis of prognostic factors in patients with CRC.Results The expression level of FOXE1 in colorectal cancer was higher than that in the normal mucosa adjacent to cancer, although the difference was not significant. However, the expression of FOXE1 was correlated with tumor size, T stage, N stage, M stage, and pTNM stage. Univariate and multivariate analyses suggested that FOXE1 could be used as an independent prognostic factor in patients with CRC. Conclusions FOXE1 may be a potential independent prognostic factor for colorectal cancer patients.

The Role of lncRNAs in the Stem Phenotype of Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma is one of the deadliest tumors. This neoplasia is characterized by an important cellular and phenotypic heterogeneity. In particular, it has been shown that at least two subtypes can be found: basal-like, which presents stem-like properties, and classical. Cancer stem cells have been isolated and characterized from these tumors, showing their dependance on general and tissue-specific stem transcription factors and signaling pathways. Nevertheless, little is known about their tissue microenvironment and cell non-autonomous regulators, such as long-non-coding RNAs. (lncRNAs). In this review, we summarize the current knowledge about the positive and negative effects of lncRNAs in the stemness phenotype of pancreatic ductal adenocarcinoma cancer (PDAC).