Abstract PL02-02: Spliceomics: Alternative RNA splicing as a source of ancestry-related molecular targets in precision oncology and cancer disparities
Authors: Patierno Steven R. 
Published: August 2019

Genomic profiling of human tumors has had a major impact on translational and clinical research and clinical practice by providing important molecular information to researchers, health care providers and patients. Most studies have focused on mutations and aggregate gene expression in patients of European ancestry, resulting in potential missed drivers of cancer heterogeneity among patients of different ancestries. This underscores the importance of conducting further translational and clinical research on additional oncogenic molecular mechanisms in diverse populations to aid in development of new diagnostic and therapeutic interventions.

Cancer disparities are the result of a complex interplay among social, structural (health system), lifestyle and biological determinants of health. Biological determinants of health vary between populations as a function of the human diaspora and the dynamic interplay between genome and environment over time, resulting in both genotypic and phenotypic diversity. An important driver of both organismal and cellular biological heterogeneity is Alternative RNA Splicing (ARS), a key step in gene expression and protein diversification in higher eukaryotes. Consistent with its role in driving evolutionary biological diversity, ARS is increasingly implicated as a major driver of tumor-related biological diversity, yet it is often overlooked in translational and clinical cancer research. Genetic variation in cis-acting splicing elements, differential expression of trans-acting splicing factors, mutation in genes encoding components of the RNA splicing machinery and aberrant and ARS events can all contribute to cancer.

Work from our laboratory and others highlights the importance of ancestry-related ARS in cancer biology and cancer disparities, and demonstrates that dysregulation of ARS is a principal feature differentiating cancers from their host tissues of origin. Extensive race-related differences in expression of RNA splice variants between prostate cancer (PCa) in self-identified African American (AA) and white (W) patients were observed, and approximately one-third of the variants enriched in PCa in AA patients were also present in patient-matched normal prostate specimens, indicating potential germline origin and clinical significance as biomarkers. Ancestry-specific PCa cell lines and xenografts were used to demonstrate the functional significance of these AA-enriched RNA splice variants in driving ancestry-related PCa aggressiveness and influencing drug response to corresponding targeted therapeutics.

This approach has revealed novel molecular targets that are being studied further pre-clinically in population-specific PCa cell lines and mouse trials, at the population-level using diverse human PCa specimens and controls and in first-ever clinical trials in PCa patients stratified by both biomarker and ancestry. We have also developed an algorithm to enable analysis of race-related ARS using annotated publicly available RNA Seq data. Using this algorithm and data from The Cancer Genome Atlas, we have identified additional race-related ARS events between PCa from AA and W patients. The majority of these events involve exon skipping. Genes that undergo race-related ARS do not overlap with genes that exhibit race-related aggregate gene expression in the same specimens; however, a significant number of the Gene Ontology terms corresponding to the genes exhibiting race-related aggregate gene expression or ARS do overlap, indicating that, despite these two distinct mechanisms of regulation (transcription and RNA splicing), both differentially regulate common pathways in PCa between AA and W patients. We have also identified 10 trans-acting splicing factors, whose aggregate gene expression significantly differed between PCa from AA and W patients, suggesting a potential mechanistic relationship between these factors and the identified race-related ARS events. In addition, analysis of race-related ARS in PCa tissue stratified by Gleason grade 6, 7, &gt;8 from AA and white patients has revealed additional novel ARS events now under preclinical evaluation, and a subset of genes exhibiting race-related ARS that are common among prostate, lung, breast and liver cancer. Finally, we have computationally identified associations between single nucleotide polymorphisms predicted to regulate RNA splicing and disparities in PCa risk, PCa aggressiveness and PCa survival, and we are currently investigating the significance of such single nucleotide polymorphisms in mechanistic and functional biology.

Our laboratory is also engaged in developing therapeutic approaches to manipulate ARS, correct aberrant RNA splicing or produce novel RNA splice variants. These include splice-switching oligonucleotides (SSOs) that can modulate pre-mRNA splicing by binding to target pre-mRNAs and blocking access of the RNA splicing machinery to a particular splice site, thereby simultaneously limiting production of pathogenic RNA splice variants and maintaining/inducing expression of RNA splice variants with therapeutic value. In addition, we are using phenotypic readouts and RNA splicing-specific reporters to conduct high-throughput screens of small molecules and have identified novel potential modulators of RNA splicing.

Despite the significance of ARS to cancer, most profiling of tumor heterogeneity and clinically-oriented studies of cancer biomarkers and therapeutics overlook its importance. We are only now starting to appreciate the translational importance of ARS in cancer, including its emerging role in generating novel immunogenic neoantigens, predicting clinical responses to therapy and in dysregulating major tumor suppressor genes and oncogenes affecting virtually every hallmark of cancer. Also under-appreciated are its contributions to ancestry-related tumor aggressiveness, heterogeneity of tumor and host cell stress responses, and therapeutic target potential. Increased collaborations among bioinformaticians, cancer biologists and clinicians are needed to identify, analyze, and develop ARS into precision oncology.

This work is supported by a DoD Prostate Cancer Research Program Health Disparity Research Award PC131972, a NIH Feasibility Studies to Build Collaborative Partnerships in Cancer Research P20 Award 1P20-CA202925-01A1 to, a NIH Basic Research in Cancer Health Disparities R01 Award R01CA220314 and a Prostate Cancer Foundation 2018 Challenge Award.

Citation Format: Steven R. Patierno. Spliceomics: Alternative RNA splicing as a source of ancestry-related molecular targets in precision oncology and cancer disparities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr PL02-02.