Overexpression of Ribosomal Protein S6 Kinase A4 (RPS6KA4) Predicts a Poor Prognosis in Hepatocellular Carcinoma Patients: A Study Based on TCGA Samples.

AIM: This study aims to comprehensively analyse the Ribosomal Protein S6 Kinase A4 (RPS6KA4) and determine the prognostic value for hepatocellular carcinoma (HCC). BACKGROUND: Liver cancer is a common type of tumor worldwide, and HCC accounts for about 75 to 85% of all primary liver cancer cases. The Ribosomal S6 protein kinases (RSK) family plays an important regulatory role in cell growth, movement, survival, and proliferation. METHODS: We collected the expression and clinicopathological features of RPS6KA4 in The Cancer Genome Atlas (TCGA) cohort and evaluated the prognostic value of RPS6KA4 in HCC. Gene Ontology (GO)/ Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA) were performed to determine the enrichment pathways of RPS6KA4. Correlation between RPS6KA4 expression and immune infiltration was analyzed. Protein-protein interaction (PPI) network analysis was performed to screen hub genes. RESULTS: RPS6KA4 overexpression is statistically significant in HCC relative to normal tissues (P < 0.001). Increased expression of RPS6KA4 is associated with higher T stage (p=0.021), pathological stage (p=0.006), α-fetoprotein (AFP) value (p=0.026), and vascular invasion (p=0.023) of HCC. Overexpression of RPS6KA4 predicted worse overall survival (OS, P=0.002), disease-specific survival (DSS, P=0.012), and progress-free interval (PFI, P=0.031) for HCC. Univariate/multivariate Cox regression analysis confirmed that RPS6KA4 was an independent risk factor for HCC (P=0.002 in univariate analysis; P=0.014 in multivariate analysis). GO/KEGG analysis and GSEA analysis suggest that RPS6KA4 plays a precancer role in HCC through epigenetics, cell adhesion, tumor-driven GTPase pathways, infection-related carcinogenesis, and adaptive immunity. Immune infiltration analysis confirmed the strong negative relationship between RPS6KA4 and B cells, CD4+ T cells, macrophages, neutrophils, as well as dendritic cells. Protein-protein interactions (PPI) analysis and hub gene identification revealed the cancer-promoting effects of RPS6KA4 related to RSKs, AP-2, clathrin, and MAPK/ ERK pathways. CONCLUSION: RPS6KA4 is a potentially valuable molecule for understanding HCC tumorigenesis. Increased RPS6KA4 might be a promising prognostic factor for low HCC survival.

Single-cell RNA-seq reveals invasive trajectory and determines cancer stem cell-related prognostic genes in pancreatic cancer.

Pancreatic duct adenocarcinoma (PDAC) is an aggressive and lethal malignancy. Pancreatic cancer stem cells (PCSCs) are assumed to contribute to the initiation and invasion of PDAC. In this study, we performed single-cell RNA sequencing (scRNA-seq) analysis of PDAC tumor samples from patients and control pancreas tissues to reveal the transformation process of cancer stem cell (CSC)-like ductal cells into ductal cells with invasive potential and we screened out CSC-related genes (CRGs). Subsequently, we applied LASSO and Cox regression models to identify five CRGs with potential prognostic values and constructed a risk prognostic model using the Cancer Genome Atlas datasets. The risk models were verified using Gene Expression Omnibus datasets. Patients in the high-risk group had a significantly poor overall survival (Pvalue<0.0001), as illustrated by the Kaplan-Meier survival curve, and the area under the curve confirmed the accuracy of predictions by our risk model. Tumor mutation burden variations were used to further explore the differences between the two risk cohorts. In addition, the Human Protein Atlas was used to investigate the protein expression of five hub CRGs. In brief, we utilized scRNA-seq to reveal the invasive trajectory of ductal cells and identified crucial CRGs in PDAC, which may help predict patient survival and provide potential clinical therapeutic targets against CSCs.

The Crosstalk Between Malignant Cells and Tumor-Promoting Immune Cells Relevant to Immunotherapy in Pancreatic Ductal Adenocarcinoma.

Background: Pancreatic ductal adenocarcinoma (PDAC) is dominated by an immunosuppressive microenvironment, which makes immune checkpoint blockade (ICB) often non-responsive. Understanding the mechanisms by which PDAC forms an immunosuppressive microenvironment is important for the development of new effective immunotherapy strategies. Methods: This study comprehensively evaluated the cell-cell communications between malignant cells and immune cells by integrative analyses of single-cell RNA sequencing data and bulk RNA sequencing data of PDAC. A Malignant-Immune cell crosstalk (MIT) score was constructed to predict survival and therapy response in PDAC patients. Immunological characteristics, enriched pathways, and mutations were evaluated in high- and low MIT groups. Results: We found that PDAC had high level of immune cell infiltrations, mainly were tumor-promoting immune cells. Frequent communication between malignant cells and tumor-promoting immune cells were observed. 15 ligand-receptor pairs between malignant cells and tumor-promoting immune cells were identified. We selected genes highly expressed on malignant cells to construct a Malignant-Immune Crosstalk (MIT) score. MIT score was positively correlated with tumor-promoting immune infiltrations. PDAC patients with high MIT score usually had a worse response to immune checkpoint blockade (ICB) immunotherapy. Conclusion: The ligand-receptor pairs identified in this study may provide potential targets for the development of new immunotherapy strategy. MIT score was established to measure tumor-promoting immunocyte infiltration. It can serve as a prognostic indicator for long-term survival of PDAC, and a predictor to ICB immunotherapy response.