In many diseases, molecularly targeted therapies have improved outcomes and decreased treatment-related toxic effects. In oncology, examples such as ERBB2-positive breast cancer¹ and EGFR-mutant lung cancer² have led to excitement about the promise of precision cancer medicine. These and other similar treatment advances typically occurred after years of investigation during which (1) a genomic alteration was identified in a reasonable proportion of patients with a particular diagnosis; (2) the alteration was validated to be a central oncogenic event; (3) the activity of targeted therapy was studied in preclinical models and then in early-phase trials; and (4) clinical trials demonstrated activity of the targeted agent only in cancer subtypes with specific molecular alterations. The essential nature of most pathogenic variants has, therefore, been established only in the context of specific disease subsets. Nevertheless, some oncologists have adopted a precision medicine approach for their patients with recurrent or refractory cancers based on the premise that receipt of matched targeted therapy will have superior clinical activity, regardless of diagnosis or patient characteristics.

Alternative splicing of mRNA precursors represents a key gene expression regulatory step and permits the generation of distinct protein products with diverse functions. In a genome-scale expression screen for inducers of the epithelial-to-mesenchymal transition (EMT), we found a striking enrichment of RNA-binding proteins. We validated that QKI and RBFOX1 were necessary and sufficient to induce an intermediate mesenchymal cell state and increased tumorigenicity. Using RNA-seq and eCLIP analysis, we found that QKI and RBFOX1 coordinately regulated the splicing and function of the actin-binding protein FLNB, which plays a causal role in the regulation of EMT. Specifically, the skipping of FLNB exon 30 induced EMT by releasing the FOXC1 transcription factor. Moreover, skipping of FLNB exon 30 is strongly associated with EMT gene signatures in basal-like breast cancer patient samples. These observations identify a specific dysregulation of splicing, which regulates tumor cell plasticity and is frequently observed in human cancer.

ABCB1, also known as MDR1, is a gene that encodes P-glycoprotein (P-gp), a membrane-associated ATP-dependent transporter. P-gp is widely expressed in many healthy tissues—in the gastrointestinal tract, liver, kidney, and at the blood–brain barrier. P-gp works to pump xenobiotics such as toxins and drugs out of cells. P-gp is also commonly upregulated across multiple cancer types such as ovarian, breast, and lung. Overexpression of ABCB1 has been linked to the development of chemotherapy resistance across these cancers. In vitro work across a wide range of drug-sensitive and -resistant cancer cell lines has shown that upon treatment with chemotherapeutic agents such as doxorubicin, cisplatin, and paclitaxel, ABCB1 is upregulated. This upregulation is caused in part by a variety of genetic and epigenetic mechanisms. This includes single-nucleotide variants that lead to enhanced P-gp ATPase activity without increasing ABCB1 RNA and protein levels. In this review, we summarize current knowledge of genetic and epigenetic mechanisms leading to ABCB1 upregulation and P-gp-enhanced ATPase activity in the setting of chemotherapy resistance across a variety of cancers.