Electrostatic Interactions between CSTF2 and pre-mRNA Drive Cleavage and Polyadenylation

RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA Interactions

We present RNAproDB (https://rnaprodb.usc.edu/), a new webserver, analysis pipeline, database, and highly interactive visualization tool, designed for protein-RNA complexes, and applicable to all forms of nucleic acid containing structures. RNAproDB computes several mapping schemes to place nucleic acid components and present protein-RNA interactions appropriately. Various structural annotations are computed including non-canonical base-pairing geometries, hydrogen bonds, and protein-RNA and RNA-RNA water-mediated interactions. This information is presented through integrated visualization and data tools. Subgraph selection facilitates studying smaller components of the interface. Molecular surface electrostatic potential can be visualized. RNAproDB enables analyzing and exploring experimentally determined, predicted, and designed protein-nucleic acid complexes. We present a quantitative analysis of pre-analyzed protein-RNA structures in RNAproDB revealing statistical patterns of molecular binding and recognition.

Expression of CSTF2 in oral squamous cell carcinoma and its relationship with immune infiltration and poor prognosis

Background

Oral squamous cell carcinoma (OSCC) is a prevalent and devastating malignancy of the oral cavity that profoundly affects patient survival and quality of life (QOL). Cleavage Stimulation Factor Subunit 2 (CSTF2) is known to influence tumor development across multiple cancer types. However, its specific association with patient prognosis and immune cell infiltration in OSCC remains insufficiently understood.

Methods

To assess the expression levels and prognostic implications of CSTF2 in OSCC, comprehensive data were acquired from The Cancer Genome Atlas (TCGA) and subsequently normalized. Immunohistochemical staining of tissue microarrays was performed to analyze CSTF2 expression in the OSCC samples. Differences in CSTF2 expression between OSCC and adjacent non-cancerous samples were evaluated using the Wilcoxon rank-sum test. Functional enrichment analyses have been performed to identify biological pathways and functions associated with CSTF2. The relationship between the infiltration of various immune cells and CSTF2 expression levels was assessed using single-sample gene set enrichment analysis (ssGSEA). Ultimately, the prognostic significance of CSTF2 was evaluated through Kaplan-Meier survival analysis, in conjunction with univariate and multivariate Cox regression analyses, as well as receiver operating characteristic (ROC) curves.

Results

High CSTF2 expression was observed in OSCC and associated with unfavorable clinicopathological variables, including histological grade and lymphnode neck dissection. Functional enrichment analysis indicated that CSTF2 plays a role in epidermal development and differentiation, immunoglobulin complexes, peptidases and endopeptidase inhibitor activity, and cytochrome P450 metabolic processes. Additionally, the overexpression of CSTF2 exhibited a negative correlation with the infiltration of immature dendritic cells (iDCs), cytotoxic cells, and plasmacytoid dendritic cells (pDCs). Notably, elevated CSTF2 expression is significantly associated with reduced patient outcomes.

Conclusion

Elevated CSTF2 expression in OSCC is associated with poor prognostic outcomes, highlighting its capacity to function as an innovative prognostic biomarker and a target for therapeutic interventions.

Human CSTF2 RNA Recognition Motif Domain Binds to a U-Rich RNA Sequence through a Multistep Binding Process

The RNA recognition motif (RRM) is a conserved and ubiquitous RNA-binding domain that plays essential roles in mRNA splicing, polyadenylation, transport, and stability. RRM domains exhibit remarkable diversity in binding partners, interacting with various sequences of single- and double-stranded RNA, despite their small size and compact fold. During pre-mRNA cleavage and polyadenylation, the RRM domain from CSTF2 recognizes U- or G/U-rich RNA sequences downstream from the cleavage and polyadenylation site to regulate the process. Given the importance of alternative cleavage and polyadenylation in increasing the diversity of mRNAs, the exact mechanism of binding of RNA to the RRM of CSTF2 remains unclear, particularly in the absence of a structure of this RRM bound to a native RNA substrate. Here, we performed a series of NMR titration and spin relaxation experiments, which were complemented by paramagnetic relaxation enhancement measurements and rigid-body docking, to characterize the interactions of the CSTF2 RRM with a U-rich ligand. Our results reveal a multistep binding process involving differences in ps-ns time scale dynamics and potential structural changes, particularly in the C-terminalα-helix. These results provide insights into how the CSTF2 RRM domain binds to U-rich RNA ligands and offer a greater understanding for the molecular basis of the regulation of pre-mRNA cleavage and polyadenylation.

The role of CSTF2 in cancer: from technology to clinical application

A protein called cleavage-stimulating factor subunit 2 (CSTF2, additionally called CSTF-64) binds RNA and is needed for the cleavage and polyadenylation of mRNA. CSTF2 is an important component subunit of the cleavage stimulating factor (CSTF), which is located on the X chromosome and encodes 557 amino acids. There is compelling evidence linking elevated CSTF2 expression to the pathological advancement of cancer and on its impact on the clinical aspects of the disease. The progression of cancers, including hepatocellular carcinoma, melanoma, prostate cancer, breast cancer, and pancreatic cancer, is correlated with the upregulation of CSTF2 expression. This review provides a fresh perspective on the investigation of the associations between CSTF2 and various malignancies and highlights current studies on the regulation of CSTF2. In particular, the mechanism of action and potential clinical applications of CSTF2 in cancer suggest that CSTF2 can serve as a new biomarker and individualized treatment target for a variety of cancer types.