SYNCRIP is the Molecular Brake of APOBEC-driven Mutagenesis, Tumor Heterogeneity and Therapy Resistance

Intratumoral genetic heterogeneity and mutational burden have been suggested to be the fuel and the source of resistance for many molecularly targeted therapies throughout a multitude of cancers. Emerging evidence indicates that tumor cells could hijack the powerful mutagenesis machinery mediated by the DNA deaminase APOBEC family proteins to intensify mutagenesis, promote intratumoral heterogeneity, and foster therapy resistance through a cell-autonomous mechanism. However, this mechanism has yet to be characterized. Utilizing prostate cancer (PCa) as a relevant model, we have identified the Synaptotagmin Binding Cytoplasmic RNA Interacting Protein (SYNCRIP) as a molecular brake for APOBEC-driven mutagenesis, intratumoral heterogeneity, and resistance to Androgen Receptor (AR) targeted therapies. Through a multi-disciplinary approach integrating bulk and single cell RNA-Seq (scRNA-Seq), whole-genome exome-sequencing (WES), and CRISPR library screening, we identified eight mutated resistance driver genes and revealed unparalleled details of how these heterogeneously aberrant subclones fuel the evolution of AR therapy resistance. For the first time, these findings exposed a cell-autonomous mechanism activating APOBEC-driven mutagenesis, consequently fueling mutational burden, genetic heterogeneity, and therapy resistance, and suggested that APOBEC proteins could be the potential therapeutic targets for preventing or overcoming resistance in PCa. Overall design: 1) Examination of transcriptomic changes in LNCaP/AR prostate cancer cell lines with modifications of SYNCRIP genes. There is total 4 different conditions with 3 biological replicates each. 2) Examination of whole gxome changes in LNCaP/AR prostate cancer cell lines with modifications of SYNCRIP genes. There is total 4 different conditions with 3 biological replicates each. 3) Single cell RNA-seq examine the transcrptomic changes in LNCaP/AR prostate cancer cell lines with various shRNAs targeting SYNCRIP and treated with enzalutamide or vehicle. There is total 6 different conditions, with around 6,000 cells being sequenced each. 4) Examination of whole genome changes in LNCaP/AR prostate cancer cell line single clones. There is total 21 single clones. 5) Examination of whole genome changes in LNCaP/AR SREX and NREX cells. There is total 19 cell lines.