SF3B1 mutations induce proteome remodeling, metabolic reprogramming, and a novel kind of tumor surface antigen in human cells

Mutations in the SF3B1 gene occur in multiple cancers, creating a neomorphic spliceosome protein that induces aberrant mRNA splicing in thousands of genes. Little is known about the downstream oncogenic or therapeutic consequences of this missplicing. To study this, we engineered knockins of SF3B1 mutation in untransformed breast epithelial cells, as well as “reverse” knockins in which SF3B1-mutant uveal melanoma cells were corrected to wild type. Transcriptomic analysis of these isogenic pairs showed cryptic splicing induced by mutant SF3B1, and SILAC proteomics demonstrated a broad reshaping of the proteome dominated by downregulation of misspliced genes. Interestingly, pathway analysis revealed a suppression of proteins involved in energy metabolism. This included mitochondrial complex III, which rescue experiments showed was downregulated through missplicing of its assembly factor UQCC1, and PHGDH, a serine synthesis enzyme likewise misspliced and downregulated. Metabolomic analysis also showed evidence of metabolic reprogramming by mutant SF3B1, including suppression of serine, glycine, and aspartate levels. Because serine and glycine (SG) starvation can have anticancer activity in vivo—and because PHGDH expression modulates this effect—we tested SG starvation on SF3B1-mutant cells. Growth of our SF3B1-mutant isogenic cells was differentially suppressed by SG starvation, and two independent AML cell lines with endogenous SF3B1 mutation demonstrated significant cell death upon SG starvation, in contrast to multiple AML cell lines wild type for SF3B1. These data suggest impaired serine synthesis may be a therapeutic vulnerability in SF3B1-mutant cancers. In addition to downregulation of genes induced by mutant SF3B1, our proteomic data also revealed a novel cryptic protein that was highly enriched in SF3B1-mutant cells. This protein, CD98, is a surface membrane protein, and the cryptic peptide change occurred in its extracellular domain. Additional transcriptome analysis revealed eleven more candidate surface proteins with mutant SF3B1-induced cryptic isoforms containing in-frame peptide changes in extracellular domains, and overexpression studies demonstrated at least two of these cryptic proteins can traffic to the cell surface. We have named these putative proteins MASAs, for Missplicing-Associated Surface Antigens, and we believe they represent a novel kind of tumor surface antigen that may be targetable with antibody-based immunotherapeutics. In summary, our data provide evidence that SF3B1 mutations induce proteome alterations, metabolic reprogramming, and a new kind of tumor surface antigen in human cells. Citation Format: William B. Dalton, Daniel Shinn, Noel Walsh, Eric Christenson, Taylor Groginski, Dhanashree Kelkar, Anil Magugundu, Arun Patil, Daniel Zabransky, Arielle Medford, Justin Lee, Alex Cole, Josh Donaldson, Amy DeZern, Karen Cravero, David Chu, Natasha Hunter, Akhilesh Pandey, Josh Lauring, Ben Park. SF3B1 mutations induce proteome remodeling, metabolic reprogramming, and a novel kind of tumor surface antigen in human cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1408.