Decoding phase separation and tumor-associated macrophage-related co-expression molecular patterns in progression of stomach adenocarcinoma

Abstract Background Phase separation and tumor-associated macrophage contribute to tumorigenesis. However, Phase separation in modulation tumor-associated macrophage activity in stomach adenocarcinoma(STAD) has not yet been elucidated. Objective Our study aims to investigate phase separation-associated pathogenic patterns by regulating tumor-associated macrophage in STAD. Methods We identified phase separation and tumor-associated macrophage (PTAM)-related hub oncogenic indicator and prognostic model for STAD patients by cross-performed WGCNA and systemic with explainable machine learning models on multi-center public STAD bulk profiles. Next, we also examined molecular and immune profiles of PTAM-related hub indicator in diverse public tumor database. Significantly, by applying advanced single-cell analytical frameworks, such as bayes-prism and scTenifoldKnk, we investigated tumor-associated macrophage and hub indicator oncogenic patterns in a temporal and spatial manner. Subsequently, 10X high-resolution spatial transcriptome profiling, immunohistochemistry (IHC) samples of STAD patients, and in vitro assays of STAD were performed for multi-dimensional validation of aforementioned in silico results. Besides, drug sensitivity analysis and in vitro assays enriched potential reproposing framework for the treatment of STAD by targeting hub indicator. Results PTAM-associated gene signature can be recognized as molecular overall survival(OS) predictive framework for STAD patients, and RUVBL1 can be considered as potential up-regulated PTAM-associated oncogenic indicator involved in STAD metastasis. Gemcitabine sensitivity is associated with RUVBL1 expression, suggesting that gemcitabine may exert its effect through RUVBL1-related pathways. Conclusion This study provides an initial characterization of PTAM-associated molecular profiles in STAD, potentially suggesting RUVBL1 as a candidate prognostic and therapeutic target for STAD patients for further investigation.