Identifying PSIP1 as a critical R-loop regulator in osteosarcoma via machine-learning and multi-omics analysis

Area of Science:

• Oncology
• Molecular Biology
• Genomics

Background:

• Dysregulation of R-loops is linked to cancer development and the tumor immune microenvironment (TME).
• The specific roles of R-loops in osteosarcoma (OS) pathogenesis are not well understood.
• Understanding R-loop involvement is crucial for developing novel therapeutic strategies in OS.

Purpose of the Study:

• To develop a prognostic model for osteosarcoma based on R-loop-related genes.
• To investigate the association between R-loop gene expression and the tumor immune microenvironment (TME) in OS.
• To identify key R-loop-associated genes influencing OS progression and validate their functional roles.

Main Methods:

• Construction of an R-loop Gene Prognostic Score Model (RGPSM) using RNA-sequencing (RNA-seq) data.
• Analysis of the correlation between RGPSM scores and TME characteristics.
• Utilizing single-cell RNA sequencing (scRNA-seq) to identify key R-loop genes in OS progression, followed by in vitro and in vivo experimental validation.
• Investigating the role of PC4 and SRSF1 Interacting Protein 1 (PSIP1) in R-loop dynamics and DNA damage.

Main Results:

• High RGPSM scores were associated with poorer prognosis, lower Huvos grades, and a more suppressive TME in osteosarcoma patients.
• A higher proportion of malignant cells was observed in patients with high RGPSM scores.
• PC4 and SRSF1 Interacting Protein 1 (PSIP1) was identified as highly expressed in proliferative OS cells and linked to poor prognosis.
• PSIP1 knockdown inhibited OS progression, increased R-loop accumulation and DNA damage, while PSIP1 overexpression promoted R-loop resolution.

Conclusions:

• The developed RGPSM is a valuable tool for predicting osteosarcoma patient outcomes.
• PSIP1 plays a critical role in osteosarcoma progression by modulating R-loop accumulation and DNA damage.
• Targeting PSIP1 may represent a potential therapeutic strategy for osteosarcoma.