ETS1, a target gene of the EWSR1::FLI1 fusion oncoprotein, regulates the expression of the focal adhesion protein TENSIN3.

The mechanistic basis for the metastasis of Ewing sarcomas remains poorly understood, as these tumors harbor few mutations beyond the chromosomal translocation that initiates the disease. Instead, the epigenome of Ewing sarcoma (EWS) cells reflects the regulatory state of genes associated with the DNA binding activity of the fusion oncoproteins EWSR1::FLI1 or EWSR1::ERG. In this study, we examined the EWSR1::FLI1/ERG's repression of transcription factor genes, concentrating on those that exhibit a broader range of expression in tumors than in EWS cell lines. Focusing on one of these target genes, ETS1, we detected EWSR1::FLI1 binding and an H3K27me3 repressive mark at this locus. Depletion of EWSR1::FLI1 results in ETS1's binding of promoter regions, substantially altering the transcriptome of EWS cells, including the upregulation of the gene encoding TENSIN3 (TNS3), a focal adhesion protein. EWS cell lines expressing ETS1 (CRISPRa) exhibited increased TNS3 expression and enhanced movement compared to control cells. Visualization of control EWS cells showed a distributed vinculin signal and a network-like organization of F-actin; in contrast, ETS1-activated EWS cells showed an accumulation of vinculin and F-actin towards the plasma membrane. Interestingly, the phenotype of ETS1-activated EWS cell lines depleted of TNS3 resembled the phenotype of the control cells. Critically, these findings have clinical relevance as TNS3 expression in EWS tumors positively correlates with that of ETS1. Implications: ETS1's transcriptional regulation of the gene encoding the focal adhesion protein TENSIN3 in Ewing sarcoma cells promotes cell movement, a critical step in the evolution of metastasis.

Evaluating a Remotely Delivered Cardio-Oncology Rehabilitation Intervention for Patients With Breast Cancer (REMOTE-COR-B): Protocol for a Single-Arm Feasibility Trial.

BACKGROUND: Exercise rehabilitation is a promising strategy for reducing cardiovascular disease risk among patients with breast cancer. However, the evidence is primarily derived from programs based at exercise centers with in-person supervised delivery. Conversely, most patients report a preference for home-based rehabilitation. As such, there is a clear need to explore strategies that can provide real-time supervision and coaching while addressing consumer preferences. Evidence from cardiac rehabilitation has demonstrated the noninferiority of a smartphone-based telerehabilitation approach (REMOTE-CR) to improve cardiorespiratory fitness in people with cardiovascular disease compared to a center-based program. OBJECTIVE: This study aims to assess the feasibility, safety, and preliminary efficacy of the REMOTE-CR program adapted for patients with breast cancer at risk of cardiotoxicity (REMOTE-COR-B). We will also assess the satisfaction and usability of REMOTE-COR-B. METHODS: We will conduct a single-arm feasibility study of the REMOTE-COR-B program among patients with stage I-III breast cancer who are at risk of cardiotoxicity (taking treatment type and dose, as well as other common cardiovascular disease risk factors into account) and who are within 24 months of completing primary definitive treatment. Participants (target sample size of 40) will receive an 8-week smartphone-based telerehabilitation exercise program involving remotely delivered real-time supervision and behavior change support. The platform comprises a smartphone and wearable heart rate monitor, as well as a custom-built smartphone app and web application. Participants will be able to attend remotely monitored exercise sessions during set operating hours each week, scheduled in both the morning and evening. Adherence is the primary outcome of the trial, assessed through the number of remotely monitored exercise sessions attended compared to the trial target (ie, 3 sessions per week). Secondary outcomes include additional trial feasibility indicators (eg, recruitment and retention), safety, satisfaction, and usability, and objective and patient-reported efficacy outcomes (cardiovascular fitness, quality of life, fatigue, self-reported exercise, self-efficacy, habit strength, and motivation). Adherence, feasibility, and safety outcomes will be assessed during the intervention period; intervention satisfaction and usability will be assessed post intervention; and objective and patient-reported efficacy outcomes will be assessed at baseline, post intervention (2-month postbaseline assessment), and at follow-up (5-month postbaseline assessment). RESULTS: Recruitment for this trial commenced in March 2023, and 7 participants had been recruited as of the submission of the manuscript. The estimated completion date for the project is October 2024, with results expected to be published in mid-2025. CONCLUSIONS: The REMOTE-COR-B intervention is a novel and promising approach to providing exercise therapy to patients with breast cancer at risk of cardiotoxicity who have unique needs and heightened safety risks. This project will provide important information on the extent to which this approach is satisfactory to patients with breast cancer, safe, and potentially effective, which is necessary before larger-scale research or clinical projects. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry ACTRN12621001557820; www.anzctr.org.au/ACTRN12621001557820.aspx. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/53301.

Endogenous EWSR1 Exists in Two Visual Modalities That Reflect Its Associations with Nucleic Acids and Concentration at Sites of Active Transcription.

EWSR1 is a member of the FET family of nucleic acid binding proteins that includes FUS and TAF15. Here, we report the systematic analysis of endogenous EWSR1's cellular organization in human cells. We demonstrate that EWSR1, which contains low complexity and nucleic acid binding domains, is present in cells in faster and slower-recovering fractions, indicative of a protein undergoing both rapid exchange and longer-term interactions. The employment of complementary high-resolution imaging approaches shows EWSR1 exists in two visual modalities, a distributed state which is present throughout the nucleoplasm, and a concentrated state consistent with the formation of foci. Both EWSR1 visual modalities localize with nascent RNA. EWSR1 foci concentrate in regions of euchromatin, adjacent to protein markers of transcriptional activation, and significantly colocalize with phosphorylated RNA polymerase II. Our results contribute to bridging the gap between our understanding of the biophysical and biochemical properties of FET proteins, including EWSR1, their functions as transcriptional regulators, and the participation of these proteins in tumorigenesis and neurodegenerative disease.

Behavior Change Techniques for the Maintenance of Physical Activity in Cancer.

Ester et al report the findings from a 2-arm cluster randomized controlled trial nested within a hybrid effectiveness-implementation study, which involved a 12-week exercise and behavior change program for rural and remote Canadians (Exercise for Cancer to Enhance Living Well [EXCEL]). The addition of 23 weeks of app-based physical activity monitoring to the EXCEL program did not result in significant between-group differences in physical activity at 6 months. While several behavior change techniques were included in the initial 12-week intervention, additional techniques were embedded within the mobile app. However, there is currently a lack of evidence regarding how many and which behavior change techniques are the most effective for people with cancer and if these differ based on individual characteristics. Potentially, the use of the mobile app was not required in addition to the behavior change support delivered to both groups as part of the EXCEL program. Further research should involve participants who may be in most need of behavioral support, for example, those with lower levels of self-efficacy. Suggestions for future research to tailor behavior change support for people with cancer are discussed.

Self-efficacy, motivation, and habits: psychological correlates of exercise among women with breast cancer.

PURPOSE: The purpose of this analysis was to explore associations between exercise behaviour among breast cancer survivors and three behavioural constructs from distinct theories: self-efficacy from social cognitive theory, motivation from self-determination theory, and habits from habit theory. METHODS: Breast cancer survivors (n = 204) completed a cross-sectional survey that collected demographic and disease characteristics, exercise levels, and self-efficacy, motivation, and habits. Multivariable linear regression models were used to identify constructs associated with total activity and resistance training. RESULTS: Participants were a mean (SD) age of 57.3 (10.8) years and most were diagnosed with early-stage disease (72%) and engaged in sufficient levels of total activity (94%), though only 45% completed ≥ 2 resistance training sessions/week. Identified motivation (ꞵ[95% CI] = 7.6 [3.9-11.3]) and habits (ꞵ[95% CI] = 4.4 [1.4-7.4]) were significantly associated with total activity (as were body mass index and disease stage), whilst identified motivation (ꞵ[95% CI] = 0.6 [0.3-0.9]) and coping self-efficacy (ꞵ[95% CI] = 0.02 [< 0.01-0.03]) were significantly associated with resistance training. The models explained 27% and 16% of variance in total activity and resistance training behaviour, respectively. CONCLUSION: Results suggest that incorporating strategies that support identified motivation, habits, and coping self-efficacy in future interventions could promote increased exercise behaviour among breast cancer populations. Future longitudinal research should examine associations with exercise in a more representative, population-based sample.

EWSR1's visual modalities are defined by its association with nucleic acids and RNA polymerase II.

We report systematic analysis of endogenous EWSR1's cellular organization. We demonstrate that EWSR1, which contains low complexity and nucleic acid binding domains, is present in cells in faster and slower-recovering fractions, indicative of a protein undergoing both rapid exchange and longer-term interactions. The employment of complementary high-resolution imaging approaches shows EWSR1 exists in in two visual modalities, a distributed state which is present throughout the nucleoplasm, and a concentrated state consistent with the formation of foci. Both EWSR1 visual modalities localize with nascent RNA. EWSR1 foci concentrate in regions of euchromatin, adjacent to protein markers of transcriptional activation, and significantly colocalize with phosphorylated RNA polymerase II. Interestingly, EWSR1 and FUS, another FET protein, exhibit distinct spatial organizations. Our results contribute to bridging the gap between our understanding of the biophysical and biochemical properties of FET proteins, including EWSR1, their functions as transcriptional regulators, and the participation of these proteins in tumorigenesis and neurodegenerative disease.

The safety, feasibility, and efficacy of an 18-week exercise intervention for adults with primary brain cancer - the BRACE study.

PURPOSE: To determine the safety, feasibility, and potential effect of an 18-week exercise intervention for adults with primary brain cancer. MATERIALS AND METHODS: Eligible patients were 12-26-weeks post-radiotherapy for brain cancer. The individually-prescribed weekly exercise was ≥150-minutes of moderate-intensity exercise, including two resistance-training sessions. The intervention was deemed "safe" if exercise-related, serious adverse events (SAE) were experienced by <10% of participants, and feasible if recruitment, retention, and adherence rates were ≥75%, and ≥75% compliance rates were achieved in ≥75% of weeks. Patient-reported and objectively-measured outcomes were assessed at baseline, mid-intervention, end-intervention, and 6-month follow-up, using generalized estimating equations. RESULTS: Twelve participants enrolled (51 ± 19.5 years, 5 females). There were no exercise-related SAEs. The intervention was feasible (recruitment:80%, retention:92%, adherence:83%). Participants completed a median of 172.8 (min:77.5, max:560.8) minutes of physical activity per week. 17% met the compliance outcome threshold for ≥75% of the intervention. Improvements in quality of life (mean change (95% CI): 7.9 units (1.9, 13.8)), functional well-being (4.3 units (1.4, 7.2)), depression (-2.0 units (-3.8, -0.2)), activity (112.8 min (42.1, 183.4)), fitness (56.4 meters (20.4, 92.5)), balance (4.9 s (0.9, 9.0)), and lower-body strength (15.2 kg (9.3, 21.1)) were observed end-intervention. CONCLUSION: Preliminary evidence support that exercise is safe and beneficial to the quality of life and functional outcomes for people with brain cancer.Registration: ACTRN12617001577303.

The BRAin Cancer and Exercise (BRACE) study highlights the need for regular monitoring of disease- and treatment-related side effects which may present as barriers to exercise.Exercise prescription should be modified according to the presence and severity of disease- and treatment-related barriers.Adverse events observed, such as dizziness, highlight the importance of supervised exercise for people with brain cancer.If supervision is not possible, then exercise modes with low risk of harm from falls are recommended (e.g., walking, machine-based resistance training).

Barriers, facilitators, perceptions and preferences influencing physical activity participation, and the similarities and differences between cancer types and treatment stages - A systematic rapid review.

The aim of this systematic rapid review was to explore barriers, facilitators, perceptions and preferences of physical activity for people diagnosed with cancer, by cancer type and treatment stage. The search strategy, implemented through four databases, included terms relating to cancer, physical activity, barriers, facilitators, perceptions and preferences, and relevant study designs. Studies reporting the outcomes of interests for adults diagnosed with cancer and living in Western countries were included and grouped according to the Social-Ecological Model and the Health Belief Model, and pragmatically. A total of 118 studies, involving 15 cancers were included. Outcomes were most commonly explored within samples involving mixed cancers (32 studies) and breast cancer (31 studies), and at the post-treatment phase (52 studies). Across all cancers and during- and post-treatment, treatment- and disease-related side-effects were the most commonly identified barrier, social support and guidance was the most commonly identified facilitator, and promoting health and recovery was the most commonly identified perception of benefit of physical activity. Notable differences were identified in barriers, facilitators and perceptions across cancer types and treatment stages, with specific examples including: comorbidities were inconsistently reported as a barrier across cancers; time pressure was more commonly reported as a barrier post-treatment; and women with breast cancer reported inaccessibility of appropriate services more commonly during-treatment than post-treatment. Preference findings varied widely across cancer types and treatment phases. These findings can be used to aid efforts to improve physical activity levels post-cancer by providing healthcare professionals with information to facilitate individualised advice and services.

Using photovoice to explore young women's experiences of behaviour change techniques in physical activity mobile apps.

BACKGROUND: Research shows that inactive young women are attracted to using mobile phone applications (apps) to increase physical activity. Apps can promote physical activity by delivering a range of behaviour change techniques to influence determinants of user behaviour. Previous qualitative research has examined user experiences with techniques in physical activity apps, however there is little research specifically among young women. This study aimed to explore young women's experiences using commercial physical activity apps to change their behaviour. METHODS: Young women were recruited online to use a randomly assigned app for two weeks to achieve a personal goal. Using photovoice, a qualitative participatory research method, participants generated insights about their experiences through photographs and semi-structured interviews. Thematic analysis was conducted on photograph and interview data. RESULTS: Thirty-two female participants, aged 18-24 years, completed the study. Behaviour change techniques tended to cluster around four key themes: logging and monitoring physical activity; reminders and prompts; workout videos and written instructions; and social features. Social support also strongly influenced participants' experiences. CONCLUSIONS: Results suggest that behaviour change techniques influenced physical activity in line with social cognitive models, and these models are useful to understand how apps can target user behaviour for young women. The findings identified factors important for young women that seemed to moderate their experiences, such as social norms about women's appearance, which should be further explored within the context of behaviour change models and app design.

ETS1, a target gene of the EWSR1::FLI1 fusion oncoprotein, regulates the expression of the focal adhesion protein TENSIN3.

The mechanistic basis for the metastasis of Ewing sarcomas remains poorly understood, as these tumors harbor few mutations beyond the chromosomal translocation that initiates the disease. Instead, the epigenome of Ewing sarcoma (EWS) cells reflects the regulatory state of genes associated with the DNA binding activity of the fusion oncoproteins EWSR1::FLI1 or EWSR1::ERG. In this study, we examined the EWSR1::FLI1/ERG's repression of transcription factor genes, concentrating on those that exhibit a broader range of expression in tumors than in EWS cell lines. Focusing on one of these target genes, ETS1, we detected EWSR1::FLI1 binding and an H3K27me3 repressive mark at this locus. Depletion of EWSR1::FLI1 results in ETS1's binding of promoter regions, substantially altering the transcriptome of EWS cells, including the upregulation of the gene encoding TENSIN3 (TNS3), a focal adhesion protein. EWS cell lines expressing ETS1 (CRISPRa) exhibited increased TNS3 expression and enhanced movement compared to control cells. The cytoskeleton of control cells and ETS1-activated EWS cell lines also differed. Specifically, control cells exhibited a distributed vinculin signal and a network-like organization of F-actin. In contrast, ETS1-activated EWS cells showed an accumulation of vinculin and F-actin towards the plasma membrane. Interestingly, the phenotype of ETS1-activated EWS cell lines depleted of TNS3 resembled the phenotype of the control cells. Critically, these findings have clinical relevance as TNS3 expression in EWS tumors positively correlates with that of ETS1.

HNRNPH1 destabilizes the G-quadruplex structures formed by G-rich RNA sequences that regulate the alternative splicing of an oncogenic fusion transcript.

In the presence of physiological monovalent cations, thousands of RNA G-rich sequences can form parallel G-quadruplexes (G4s) unless RNA-binding proteins inhibit, destabilize, or resolve the formation of such secondary RNA structures. Here, we have used a disease-relevant model system to investigate the biophysical properties of the RNA-binding protein HNRNPH1's interaction with G-rich sequences. We demonstrate the importance of two EWSR1-exon 8 G-rich regions in mediating the exclusion of this exon from the oncogenic EWS-FLI1 transcripts expressed in a subset of Ewing sarcomas, using complementary analysis of tumor data, long-read sequencing, and minigene studies. We determined that HNRNPH1 binds the EWSR1-exon 8 G-rich sequences with low nM affinities irrespective of whether in a non-G4 or G4 state but exhibits different kinetics depending on RNA structure. Specifically, HNRNPH1 associates and dissociates from G4-folded RNA faster than the identical sequences in a non-G4 state. Importantly, we demonstrate using gel shift and spectroscopic assays that HNRNPH1, particularly the qRRM1-qRRM2 domains, destabilizes the G4s formed by the EWSR1-exon 8 G-rich sequences in a non-catalytic fashion. Our results indicate that HNRNPH1's binding of G-rich sequences favors the accumulation of RNA in a non-G4 state and that this contributes to its regulation of RNA processing.

Practical suggestions for harms reporting in exercise oncology: the Exercise Harms Reporting Method (ExHaRM).

The volume of high-quality evidence supporting exercise as beneficial to cancer survivors has grown exponentially; however, the potential harms of exercise remain understudied. Consequently, the trade-off between desirable and undesirable outcomes of engaging in exercise remains unclear to clinicians and people with cancer. Practical guidance on collecting and reporting harms in exercise oncology is lacking. We present a harms reporting protocol developed and refined through exercise oncology trials since 2015.Development of the Exercise Harms Reporting Method (ExHaRM) was informed by national and international guidelines for harms reporting in clinical trials involving therapeutic goods or medical devices, with adaptations to enhance applicability to exercise. The protocol has been adjusted via an iterative process of implementation and adjustment through use in multiple exercise oncology trials involving varied cancer diagnoses (types: breast, brain, gynaecological; stages at diagnosis I-IV; primary/recurrent), and heterogeneous exercise intervention characteristics (face to face/telehealth delivery; supervised/unsupervised exercise). It has also involved the development of terms (such as, adverse outcomes, which capture all undesirable physical, psychological, social and economic outcomes) that facilitate the harms assessment process in exercise.ExHaRM involves: step 1: Monitor occurrence of adverse outcomes through systematic and non-systematic surveillance; step 2: Assess and record adverse outcomes, including severity, causality, impact on intervention and type; step 3: Review of causality by harms panel (and revise as necessary); and step 4: Analyse and report frequencies, rates and clinically meaningful details of all-cause and exercise-related adverse outcomes.ExHaRM provides guidance to improve the quality of harms assessment and reporting immediately, while concurrently providing a framework for future refinement. Future directions include, but are not limited to, standardising exercise-specific nomenclature and methods of assessing causality.

Physical activity and exercise in adults diagnosed with primary brain cancer: a systematic review.

PURPOSE: The aims of this systematic review were to: (1) describe physical activity (PA) levels following diagnosis of primary brain cancer, (2) determine the relationship between PA levels and health outcomes, and (3) assess the effect of participating in an exercise intervention on health outcomes following a diagnosis of brain cancer. METHODS: PubMed, EMBASE, Scopus and CINAHL were searched for relevant articles published prior to May 1, 2020. Studies reporting levels of PA, the relationship between PA and health outcomes, and exercise interventions conducted in adults with brain cancer were eligible. The search strategy included terms relating to primary brain cancer, physical activity, and exercise. Two independent reviewers assessed articles for eligibility and methodological quality (according to Joanna Briggs Institute Critical Appraisal Tools). Descriptive statistics were used to present relevant data and outcomes. RESULTS: 15 studies were eligible for inclusion. Most adults with brain cancer were insufficiently active from diagnosis through to post-treatment. Higher levels of PA were associated with lower severity of brain cancer specific concerns and higher quality of life. Preliminary evidence suggests that exercise is safe, feasible and potentially beneficial to brain cancer symptom severity and interference, aerobic capacity, body composition and PA levels. However, the level of evidence to support these findings is graded as weak. CONCLUSIONS: Evidence suggests that it is likely appropriate to promote those with brain cancer to be as physically active as possible. The need or ability of those with brain cancer to meet current PA guidelines promoted to all people with cancer remains unclear.

Supporting Those With the Most to Gain: The Potential of Exercise in oncology.

OBJECTIVE: The purpose of this commentary is to summarize the evidence of the feasibility and benefits of exercise for cancer patients with complex health profiles. Case studies are used to describe the therapeutic approach taken by exercise professionals. The information presented will assist the cancer care team in understanding their role in supporting these patients to move more. DATA SOURCES: Professional organizations, peer-reviewed manuscripts, and expert clinical opinion. CONCLUSION: Individually-tailored exercise is safe and feasible in the presence of complex health profiles, and all patients can benefit through exercise, regardless of individual circumstance or disease burden. However, to ensure patients benefit through physical activity, including exercise, a multidisciplinary approach, whereby all members of the health care team promote and encourage physical activity is needed. IMPLICATIONS FOR NURSING PRACTICE: There is a clear need for collaboration between the oncology team and exercise professionals, particularly when dealing with patients with complex health profiles. These patients are more likely to engage in exercise when they are advised and supported by their oncology team to do so. As such, promotion of physical activity and, when relevant, referral to an exercise professional is the responsibility of all members of the cancer team.

Cancer biology functional genomics: From small RNAs to big dreams.

The year 2021 marks the 20th anniversary of the first publications reporting the discovery of the gene silencing mechanism, RNA interference (RNAi) in mammalian cells. Along with the many studies that delineated the proteins and substrates that form the RNAi pathway, this finding changed our understanding of the posttranscriptional regulation of mammalian gene expression. Furthermore, the development of methods that exploited the RNAi pathway began the technological revolution that eventually enabled the interrogation of mammalian gene function-from a single gene to the whole genome-in only a few days. The needs of the cancer research community have driven much of this progress. In this perspective, we highlight milestones in the development and application of RNAi-based methods to study carcinogenesis. We discuss how RNAi-based functional genetic analysis of exemplar tumor suppressors and oncogenes furthered our understanding of cancer initiation and progression and explore how such studies formed the basis of genome-wide scale efforts to identify cancer or cancer-type specific vulnerabilities, including studies conducted in vivo. Furthermore, we examine how RNAi technologies have revealed new cancer-relevant molecular targets and the implications for cancer of the first RNAi-based drugs. Finally, we discuss the future of functional genetic analysis, highlighting the increasing availability of complementary approaches to analyze cancer gene function.

Physical activity and exercise in women with ovarian cancer: A systematic review.

OBJECTIVE: A consistent body of evidence supports participating in physical activity (PA) post-cancer diagnosis as beneficial to function, quality-of-life and potentially survival. However, diagnosis of late stage disease, poor prognosis, receipt of high doses of adjuvant therapy and presence of severe acute and persistent treatment-related side-effects may alter how these findings translate to women with ovarian cancer. Therefore, the objectives of this review were to (I) describe PA levels post-diagnosis of ovarian cancer, (II) explore the relationship between PA levels and health outcomes, and (III) evaluate the effect of exercise interventions for women with ovarian cancer. METHODS: PubMed, EMBASE, Scopus and CINAHL were systematically searched to December 31, 2019. Two independent reviewers assessed articles for eligibility. Studies were eligible if they evaluated the relationship between PA levels or an exercise intervention and health outcomes following ovarian cancer. Methodological quality was assessed by two independent reviewers using the Joanna Briggs Institute Critical Appraisal Tools. Descriptive statistics were used to collate relevant data. RESULTS: 34 articles were eligible for inclusion. Results demonstrated that most women decrease PA from pre- to post-diagnosis and remain insufficiently active following diagnosis. Higher levels of PA were associated with higher health-related quality-of-life (HRQOL), and lower levels of anxiety and depression. Exercise appears safe and feasible during and following treatment and leads to improvements in HRQOL, fatigue and additional physical and psychological outcomes. CONCLUSIONS: Findings suggest that PA is relevant to health outcomes for women with ovarian cancer. Interventions that aid women to stay or become sufficiently active, including through exercise interventions during or following treatment have potential to improve the lives of those with ovarian cancer. Future work evaluating targeted interventions that can accommodate disease-specific challenges is now required to ensure scientific findings can translate into improved ovarian cancer care.

Functional Genomic Screening Reveals Splicing of the EWS-FLI1 Fusion Transcript as a Vulnerability in Ewing Sarcoma.

Ewing sarcoma cells depend on the EWS-FLI1 fusion transcription factor for cell survival. Using an assay of EWS-FLI1 activity and genome-wide RNAi screening, we have identified proteins required for the processing of the EWS-FLI1 pre-mRNA. We show that Ewing sarcoma cells harboring a genomic breakpoint that retains exon 8 of EWSR1 require the RNA-binding protein HNRNPH1 to express in-frame EWS-FLI1. We also demonstrate the sensitivity of EWS-FLI1 fusion transcripts to the loss of function of the U2 snRNP component, SF3B1. Disrupted splicing of the EWS-FLI1 transcript alters EWS-FLI1 protein expression and EWS-FLI1-driven expression. Our results show that the processing of the EWS-FLI1 fusion RNA is a potentially targetable vulnerability in Ewing sarcoma cells.

Loss-of-function RNAi screens in breast cancer cells identify AURKB, PLK1, PIK3R1, MAPK12, PRKD2, and PTK6 as sensitizing targets of rapamycin activity.

The use of molecularly targeted drugs as single agents has shown limited utility in many tumor types, largely due to the complex and redundant nature of oncogenic signaling networks. Targeting of the PI3K/AKT/mTOR pathway through inhibition of mTOR in combination with aromatase inhibitors has seen success in particular sub-types of breast cancer and there is a need to identify additional synergistic combinations to maximize the clinical potential of mTOR inhibitors. We have used loss-of-function RNAi screens of the mTOR inhibitor rapamycin to identify sensitizers of mTOR inhibition. RNAi screens conducted in combination with rapamycin in multiple breast cancer cell lines identified six genes, AURKB, PLK1, PIK3R1, MAPK12, PRKD2, and PTK6 that when silenced, each enhanced the sensitivity of multiple breast cancer lines to rapamycin. Using selective pharmacological agents we confirmed that inhibition of AURKB or PLK1 synergizes with rapamycin. Compound-associated gene expression data suggested histone deacetylation (HDAC) inhibition as a strategy for reducing the expression of several of the rapamycin-sensitizing genes, and we tested and validated this using the HDAC inhibitor entinostat in vitro and in vivo. Our findings indicate new approaches for enhancing the efficacy of rapamycin including the use of combining its application with HDAC inhibition.

Genetic amplification of the NOTCH modulator LNX2 upregulates the WNT/ß-catenin pathway in colorectal cancer.

Chromosomal copy number alterations (aneuploidy) define the genomic landscape of most cancer cells, but identification of the oncogenic drivers behind these imbalances remains an unfinished task. In this study, we conducted a systematic analysis of colorectal carcinomas that integrated genomic copy number changes and gene expression profiles. This analysis revealed 44 highly overexpressed genes mapping to localized amplicons on chromosome 13, gains of which occur often in colorectal cancers (CRC). RNA interference (RNAi)-mediated silencing identified eight candidates whose loss-of-function reduced cell viability 20% or more in CRC cell lines. The functional space of the genes NUPL1, LNX2, POLR1D, POMP, SLC7A1, DIS3, KLF5, and GPR180 was established by global expression profiling after RNAi exposure. One candidate, LNX2, not previously known as an oncogene, was involved in regulating NOTCH signaling. Silencing LNX2 reduced NOTCH levels but also downregulated the transcription factor TCF7L2 and markedly reduced WNT signaling. LNX2 overexpression and chromosome 13 amplification therefore constitutively activates the WNT pathway, offering evidence of an aberrant NOTCH-WNT axis in CRC.

Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells.

BACKGROUND: Colorectal carcinomas (CRC) carry massive genetic and transcriptional alterations that influence multiple cellular pathways. The study of proteins whose loss-of-function (LOF) alters the growth of CRC cells can be used to further understand the cellular processes cancer cells depend upon for survival. RESULTS: A small-scale RNAi screen of ~400 genes conducted in SW480 CRC cells identified several candidate genes as required for the viability of CRC cells, most prominently CASP8AP2/FLASH. To understand the function of this gene in maintaining the viability of CRC cells in an unbiased manner, we generated gene specific expression profiles following RNAi. Silencing of CASP8AP2/FLASH resulted in altered expression of over 2500 genes enriched for genes associated with cellular growth and proliferation. Loss of CASP8AP2/FLASH function was significantly associated with altered transcription of the genes encoding the replication-dependent histone proteins as a result of the expression of the non-canonical polyA variants of these transcripts. Silencing of CASP8AP2/FLASH also mediated enrichment of changes in the expression of targets of the NFκB and MYC transcription factors. These findings were confirmed by whole transcriptome analysis of CASP8AP2/FLASH silenced cells at multiple time points. Finally, we identified and validated that CASP8AP2/FLASH LOF increases the expression of neurofilament heavy polypeptide (NEFH), a protein recently linked to regulation of the AKT1/ß-catenin pathway. CONCLUSIONS: We have used unbiased RNAi based approaches to identify and characterize the function of CASP8AP2/FLASH, a protein not previously reported as required for cell survival. This study further defines the role CASP8AP2/FLASH plays in the regulating expression of the replication-dependent histones and shows that its LOF results in broad and reproducible effects on the transcriptome of colorectal cancer cells including the induction of expression of the recently described tumor suppressor gene NEFH.