Bioinformatics and Experimental Analysis of the Prognostic and Predictive Value of the CHPF Gene on Breast Cancer

Abstract

BackgroundRecent studies in the United States have shown that breast cancer accounts for 30% of all new cancer diagnoses in women and has become the leading cause of cancer deaths in women worldwide. Chondroitin Polymerizing Factor (CHPF), is an enzyme involved in chondroitin sulfate (CS) elongation and a novel key molecule in the poor prognosis of many cancers. However, its role in the development and progression of breast cancer remains unclear.MethodsThe transcript expression of CHPF in the Cancer Genome Atlas-Breast Cancer (TCGA-BRCA), Gene Expression Omnibus (GEO) database was analyzed separately using the limma package of R software, and the relationship between CHPF transcriptional expression and CHPF DNA methylation was investigated in TCGA-BRCA. Kaplan-Meier curves were plotted using the Survival package to further assess the prognostic impact of CHPF DNA methylation/expression. The association between CHPF transcript expression/DNA methylation and cancer immune infiltration and immune markers was investigated using the TIMER and TISIDB databases. We also performed gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis with the clusterProfiler package. Western blotting and RT-PCR were used to verify the protein level and mRNA level of CHPF in breast tissue and cell lines, respectively. Small interfering plasmids and lentiviral plasmids were constructed for transient and stable transfection of breast cancer cell lines MCF-7 and SUM1315, respectively, followed by proliferation-related functional assays, such as CCK8, EDU, clone formation assays; migration and invasion-related functional assays, such as wound healing assay and transwell assays. We also conducted a preliminary study of the mechanism.ResultsWe observed that CHPF was significantly upregulated in breast cancer tissues and correlated with poor prognosis. CHPF gene transcriptional expression and methylation are associated with immune infiltration immune markers. CHPF promotes proliferation, migration, invasion of the breast cancer cell lines MCF-7 and SUM1315, and is significantly enriched in pathways associated with the ECM-receptor interaction and PI3K-AKT pathway.ConclusionCHPF transcriptional expression and DNA methylation correlate with immune infiltration and immune markers. Upregulation of CHPF in breast cancer promotes malignant behavior of cancer cells and is associated with poorer survival in breast cancer, possibly through ECM-receptor interactions and the PI3K-AKT pathway.

ENST00000535926 is an unfavorable prognosis-related and tumor-promoting transcript of the CHPF gene in luminal A and B breast cancer

“…CHPF promotes triple-negative breast cancer cell growth, metastasis, and accumulation of myeloid-derived suppressor cells (MDSCs) (Liao et al, 2021). Its prognostic significance in breast cancer was also confirmed by a recent bioinformatic analysis (Li et al, 2022).…”

“…Alternative splicing of CHPF and the functional differences of the isoforms have been reported in normal human neurons (Kuroda et al, 2012). The link between total CHPF expression and unfavorable survival of breast cancer patients was also observed (Li et al, 2022;Liao et al, 2021). However, it is not confirmed whether the link is transcript specific.…”

MiR‐214‐3p overexpression‐triggered chondroitin polymerizing factor (CHPF) inhibition modulates the ferroptosis and metabolism in colon cancer

“…T A B L E 1 Association of the CHPF expression levels with clinicopathologic characteristics in colon cancer. Extensive evidence has demonstrated that CHPF is highly expressed and serves as an oncogene in tumors, such as gastric cancer, 10 breast cancer, 9,21,23 lung cancer, 15,22 malignant melanoma, 11 cholangiocarcinoma, 13 hepatocellular carcinoma, 12 and glioma. 14 In accordance with the previous report, 16 we also found CHPF level was increased in both colon cancer tissues and cells, which indicated that CHPF might be a biomarker of diagnosis and treatment for colon cancer.…”

Tandem mass tag (TMT) quantitative protein analysis‐based proteomics and parallel reaction monitoring (PRM) validation revealed that MST4 accelerates osteosarcoma proliferation by increasing MRC2 activity

“…Li et al reported that upregulation of CHPF in breast cancer promotes the malignant behavior of cancer cells, possibly through ECM-receptor interactions and the PI3K-AKT pathway. 23 In the cell adhesion pathway, upregulated cell adhesion molecules promote apoptosis and inhibit malignant proliferation in tumor cells. 24 Based on these results, we hypothesize that the ECM-receptor response and cell adhesion pathway are also critical pathways in the promotion of OS proliferation by MST4.…”

“…The GO and KEGG enrichment analyses suggested that the role of MST4 in OS may be related to the regulation of fibronectin binding and ECM‐receptor interactions. Li et al reported that upregulation of CHPF in breast cancer promotes the malignant behavior of cancer cells, possibly through ECM‐receptor interactions and the PI3K‐AKT pathway 23 . In the cell adhesion pathway, upregulated cell adhesion molecules promote apoptosis and inhibit malignant proliferation in tumor cells 24 .…”