Integrated multi-omics analyses reveal the role of PAXX in colorectal cancer progression and the tumor immune microenvironment

Abstract

PAXX is a DNA double-strand break repair factor involved in classical non-homologous end joining. Although elevated PAXX expression has been reported in colon cancer, its functional role and downstream mechanisms in colorectal cancer (CRC) remain incompletely defined. This study investigated the role of PAXX in CRC progression and its association with the tumor immune microenvironment. Public transcriptomic, proteomic, genomic, and single-cell datasets were integrated with clinical sample validation and functional experiments. Stable PAXX knockdown models were used to assess CRC cell proliferation, migration, invasion, and xenograft growth. RNA sequencing, Western blotting, and EGF-mediated rescue experiments were performed to evaluate EMT-related alterations and MAPK/ERK signaling. PAXX was upregulated in CRC tissues and cell lines and was associated with poorer overall survival, although its standalone prognostic discrimination was limited. PAXX knockdown suppressed proliferation, migration, invasion, and xenograft growth and attenuated EMT-related molecular alterations. RNA-seq and enrichment analyses showed coordinated suppression of MAPK signaling and EMT-related transcriptional programs following PAXX depletion. Consistently, p-MEK1/2 and p-ERK1/2 levels were reduced without substantial changes in total MEK1/2 or ERK1/2. EGF-mediated pathway stimulation restored MEK/ERK phosphorylation and partially reversed the inhibitory effects of PAXX depletion on malignant phenotypes and EMT-related alterations. High PAXX expression was also associated with distinct immune and stromal characteristics, while single-cell and CellChat analyses identified heterogeneous PAXX expression and predicted HGF- and VEGF-related intercellular communication. PAXX is associated with CRC progression and unfavorable prognosis. Functional and rescue experiments support MAPK/ERK signaling as a partial mediator of PAXX-associated malignant phenotypes. Immune and intercellular communication findings remain computationally inferred and require further validation.