Binding of the nuclear ribonucleoprotein family member FUS to RNA prevents R-loop RNA:DNA hybrid structures

The protein FUS (FUSed in sarcoma) is a metazoan RNA-binding protein that influences RNA production by all three nuclear polymerases. FUS also binds nascent transcripts, RNA processing factors, RNA polymerases, and transcription machinery. Here, we explored the role of FUS binding interactions for activity during transcription. In vitro run-off transcription assays revealed FUS-enhanced RNA produced by a non-eukaryote polymerase. The activity also reduced the formation of R-loops between RNA products and their DNA template. Analysis by domain mutation and deletion indicated RNA-binding was required for activity. We interpret that FUS binds and sequesters nascent transcripts to prevent R-loops from forming with nearby DNA. DRIP-seq analysis showed that a knockdown of FUS increased R-loop enrichment near expressed genes. Prevention of R-loops by FUS binding to nascent transcripts has the potential to affect transcription by any RNA polymerase, highlighting the broad impact FUS can have on RNA metabolism in cells and disease.

Fusion protein EWS-FLI1 is incorporated into a protein granule in cells

Ewing sarcoma is driven by fusion proteins containing a low complexity (LC) domain that is intrinsically disordered and a powerful transcriptional regulator. The most common fusion protein found in Ewing sarcoma, EWS-FLI1, takes its LC domain from the RNA-binding protein EWSR1 (Ewing Sarcoma RNA-binding protein 1) and a DNA-binding domain from the transcription factor FLI1 (Friend Leukemia Virus Integration 1). EWS-FLI1 can bind RNA polymerase II (RNA Pol II) and self-assemble through its low-complexity (LC) domain. The ability of RNA-binding proteins like EWSR1 to self-assemble or phase separate in cells has raised questions about the contribution of this process to EWS-FLI1 activity. We examined EWSR1 and EWS-FLI1 activity in Ewing sarcoma cells by siRNA-mediated knockdown and RNA-seq analysis. More transcripts were affected by the EWSR1 knockdown than expected and these included many EWS-FLI1 regulated genes. We reevaluated physical interactions between EWS-FLI1, EWSR1, and RNA Pol II, and employed a cross-linking based strategy to investigate protein assemblies associated with the proteins. The LC domain of EWS-FLI1 was required for the assemblies observed to form in cells. These results offer new insights into a protein assembly that may enable EWS-FLI1 to bind its wide network of protein partners and contribute to regulation of gene expression in Ewing sarcoma.

Abstract 5137: Tryptophan catabolism in ovarian cancer

Serous epithelial ovarian cancer metastasizes by direct seeding to form disseminated tumors within the peritoneal cavity and has an extremely poor clinical outcome with a 46.5% five-year survival rate. Resistance to anoikis (detachment-induced cell death) is a critical factor in the progression of this disease. We previously demonstrated that triple-negative breast cancer (TNBC) upregulates tryptophan-2,3-dioxygenase (TDO2), a rate limiting enzyme in tryptophan catabolism, under anchorage-independent conditions or by stimulation with an NFκB stimulating cocktail (IL1-β, TNFα). Indoleamine-pyrrole 2,3-dioxygenase (IDO1) is also a rate-limiting enzyme in the tryptophan catabolism pathway, & both TDO2 and ID01 can be expressed by tumors. Kynurenine, a metabolite of tryptophan catabolism acts in an autocrine fashion through the aryl hydrocarbon receptor to provide anti-apoptotic signals that enhance survival under anchorage independent conditions. Through paracrine action, kynurenine can suppress anti-tumor cytotoxic T-cell function. We hypothesize that tryptophan catabolism promotes ovarian cancer progression through these two mechanisms, primarily through TDO2. We mined the publically available Tothill Ovarian Cancer patient cohort (n=293) for correlations between TDO2 or IDO1 & ovarian cancer outcomes. The anoikis resistant serous ovarian cancer cell lines HEY, OV-1847, OVCA-420 & OVCA-433 were used to test levels of enzymes involved in tryptophan catabolism in vitro at baseline, in attached versus suspended conditions & following NFκB stimulation with IL1-β and TNFα. Three enzymes in the pathway; TDO2, IDO1 & Kynureninase (KYNU) were quantified by qRT-PCR & immunohistochemistry. Using a cytokine/chemokine array and follow-up ELISA, we also analyzed factors secreted by ovarian cancer cells surviving in suspension culture as compared to attached. In the ovarian cancer patient cohort, high TDO2 significantly correlated with higher stage disease (p=0.0033), increased recurrence rates (p<0.0001) & lower survival rates (p=0.0034), whereas IDO1 did not show significant correlations. The expression of tryptophan catabolizing enzymes was significantly increased in the suspended condition when compared to attached & following NFκB stimulation. Ovarian cancer cell lines in suspension have increased levels of IL-1α, G-CSF, MIF and IL-6 on arrays, & IL-6 was confirmed by ELISA. Data mining of patient specimens indicates that TDO2 may be the more relevant enzyme responsible for tryptophan metabolism in ovarian cancer since high TDO2 is correlated with higher clinical stage, disease progression & in recurrent disease, suggesting that TDO2 may facilitate disease progression. Tryptophan catabolizing enzymes are elevated in ovarian cancer cells under anchorage independent condition or inflammatory stimuli. Based on these findings, we believe that clinical trials targeting TDO2 in addition to IDO may be warranted for serous ovarian cancer.

Citation Format: Lynelle P. Smith, Lucas M. Harrell, Jessica L. Christenson, Benjamin Bitler, Jill Slansky, Jennifer K. Richer. Tryptophan catabolism in ovarian cancer [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 5137.

Development of an instrument to assess stress levels and quality of life in children with asthma

The purpose of this study was to develop and evaluate a new instrument, About My Asthma (AMA), to assess stressors affecting quality of life in children with asthma. The AMA is a 55-item, 4-point Likert-type scale. Concurrent validity was established by comparing the AMA with the Pediatric Asthma Quality of Life Questionnaire (PAQLQ). Increased levels of stress measured by the AMA correlated with a decreased quality of life measured by the PAQLQ. We conclude that the AMA is a valid and reliable instrument to measure the quantity and type of stressors experienced by children who have asthma.