Integrated Pan-Cancer Profiling and Breast Cancer Validation Identify BEND3 as a Potential Prognostic and Immune Biomarker

Yuting Gou,1,* Yongxiang Li,1,* Yiyang Wang,1,* Haotian Ma,1 Haocong Li,2 Reyima Geni,2 Dilimulati Ismtula,1 Chenming Guo1,3 1Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, People’s Republic of China; 2Department of Clinical Medicine, Xinjiang Medical University, Urumqi, People’s Republic of China; 3State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, People’s Republic of China*These authors contributed equally to this workCorrespondence: Chenming Guo; Dilimulati Ismtula, Email [email protected]; [email protected]: BEND3 is implicated in various physiological processes, including chromatin regulation, cell cycle regulation, etc.; nonetheless, its function in cancer is not well comprehended.Methods: Using public databases including UCSC Xena, TCGA, GTEx, and GEO, we conducted a comprehensive pan-cancer analysis to evaluate the clinical relevance of BEND3 across 33 cancer types. We analyzed genetic alterations, copy number variations (CNVs), and methylation profiles of BEND3, and explored its associations with tumor mutational burden (TMB), microsatellite instability (MSI), immune checkpoint molecules, and the tumor immune microenvironment. A protein-protein interaction (PPI) network and functional enrichment analysis were performed to investigate potential molecular mechanisms. In vitro, BEND3 expression was assessed by immunohistochemistry (IHC), Western blot (WB), and qRT-PCR. Cell Counting Kit-8 (CCK-8), colony formation, and wound healing assays were performed to validate BEND3’s oncogenic role in breast cancer cell lines.Results: Our results show that BEND3 is frequently overexpressed in multiple cancers, including breast, liver, lung, thyroid, and gastric cancers, among others, and is associated with poor prognosis. Its expression correlates with TMB, MSI, immune checkpoint molecules, and immunoinfiltration, suggesting a role in tumor immunity. Functional analysis indicates involvement in key cancer-related pathways. In breast cancer, BEND3 was upregulated in clinical tissues and cell lines, and in vitro experiments demonstrated that BEND3 overexpression promoted the proliferation, migration, and invasion of breast cancer cells, whereas its knockdown suppressed these phenotypes.Conclusion: Our findings suggest BEND3 is a potential prognostic and immune-related cancer biomarker. Its overexpression in multiple cancers, association with poor survival, and role in tumor immunity support its oncogenic function. Functional analysis indicates it may regulate key cancer pathways. Importantly, in vitro experiments confirm its tumor-promoting effects in breast cancer, providing a foundation for further study of BEND3’s mechanisms and therapeutic implications.Keywords: BEND3, pan-cancer, prognosis, tumor immunity, methylation