SF3B4-QKI Splicing Complex Generates Circ-FNDC3B and Mediates Breast Cancer Inhibition

Abstract Circular RNA (circRNA), usually produced through a back-splicing process, is a type of single-stranded RNA that is covalently bonded. Our research indicated that a spliceosome composed of SF3B4 and QKI promoted the back-splicing of FNDC3B, thereby promoting the generation of circRNA FNDC3B (Circ-FNDC3B). Circ-FNDC3B is underexpressed in breast cancer and is characterized by a high metastatic risk. In addition, Circ-FNDC3B expression was reduced in breast cancer with larger tumor diameter, later clinical staging, and lymph node metastasis. The secondary structure of Circ-FNDC3B, specifically the 356 to 425 bp sequence, interacts with the biotin carboxylase domain of pyruvate carboxylase (PC), inhibiting the activity of PC. Low expression of Circ-FNDC3B enhances the activity of PC, thereby facilitating cell proliferation. The underlying mechanism involves the promotion of aspartate synthesis and the acceleration of the citrate-pyruvate cycle. This, in turn, promotes NADPH synthesis, thus alleviating the oxidative damage induced by reactive oxygen species. Furthermore, in human breast cancer organoids and a mouse model of lung metastasis, we have validated that exogenous expression of Circ-FNDC3B can inhibit the activity of PC, thereby suppressing tumor proliferation and promoting tumor cell apoptosis. In general, upregulating the expression of Circ-FNDC3B can impede the progression of breast cancer. Implications: This study reveals significant heterogeneity in the expression of circRNAs commonly used to identify breast cancer metastasis and confirms that circRNAs affect the metabolic state of breast cancer through their binding proteins.