Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis.

Alternative splicing plays important regulatory roles during periods of physiological change. During development, a large number of genes coordinately express protein isoform transitions regulated by alternative splicing; however, the mechanisms that coordinate splicing and the functional integration of the resultant tissue-specific protein isoforms are typically unknown. Here we show that the conserved Rbfox2 RNA binding protein regulates 30% of the splicing transitions observed during myogenesis and is required for the specific step of myoblast fusion. Integration of Rbfox2-dependent splicing outcomes from RNA-seq with Rbfox2 iCLIP data identified Mef2d and Rock2 as Rbfox2 splicing targets. Restored activities of Mef2d and Rock2 rescued myoblast fusion in Rbfox2-depleted cultures, demonstrating functional cooperation of protein isoforms generated by coordinated alterative splicing. The results demonstrate that coordinated alternative splicing by a single RNA binding protein modulates transcription (Mef2d) and cell signaling (Rock2) programs to drive tissue-specific functions (cell fusion) to promote a developmental transition.

The spliceosome is a therapeutic vulnerability in MYC-driven cancer.

MYC (also known as c-MYC) overexpression or hyperactivation is one of the most common drivers of human cancer. Despite intensive study, the MYC oncogene remains recalcitrant to therapeutic inhibition. MYC is a transcription factor, and many of its pro-tumorigenic functions have been attributed to its ability to regulate gene expression programs. Notably, oncogenic MYC activation has also been shown to increase total RNA and protein production in many tissue and disease contexts. While such increases in RNA and protein production may endow cancer cells with pro-tumour hallmarks, this increase in synthesis may also generate new or heightened burden on MYC-driven cancer cells to process these macromolecules properly. Here we discover that the spliceosome is a new target of oncogenic stress in MYC-driven cancers. We identify BUD31 as a MYC-synthetic lethal gene in human mammary epithelial cells, and demonstrate that BUD31 is a component of the core spliceosome required for its assembly and catalytic activity. Core spliceosomal factors (such as SF3B1 and U2AF1) associated with BUD31 are also required to tolerate oncogenic MYC. Notably, MYC hyperactivation induces an increase in total precursor messenger RNA synthesis, suggesting an increased burden on the core spliceosome to process pre-mRNA. In contrast to normal cells, partial inhibition of the spliceosome in MYC-hyperactivated cells leads to global intron retention, widespread defects in pre-mRNA maturation, and deregulation of many essential cell processes. Notably, genetic or pharmacological inhibition of the spliceosome in vivo impairs survival, tumorigenicity and metastatic proclivity of MYC-dependent breast cancers. Collectively, these data suggest that oncogenic MYC confers a collateral stress on splicing, and that components of the spliceosome may be therapeutic entry points for aggressive MYC-driven cancers.

The pINDUCER lentiviral toolkit for inducible RNA interference in vitro and in vivo.

The discovery of RNAi has revolutionized loss-of-function genetic studies in mammalian systems. However, significant challenges still remain to fully exploit RNAi for mammalian genetics. For instance, genetic screens and in vivo studies could be broadly improved by methods that allow inducible and uniform gene expression control. To achieve this, we built the lentiviral pINDUCER series of expression vehicles for inducible RNAi in vivo. Using a multicistronic design, pINDUCER vehicles enable tracking of viral transduction and shRNA or cDNA induction in a broad spectrum of mammalian cell types in vivo. They achieve this uniform temporal, dose-dependent, and reversible control of gene expression across heterogenous cell populations via fluorescence-based quantification of reverse tet-transactivator expression. This feature allows isolation of cell populations that exhibit a potent, inducible target knockdown in vitro and in vivo that can be used in human xenotransplantation models to examine cancer drug targets.

Novel hormone therapy and coordination of care in high-risk biochemically recurrent prostate cancer.

Biochemical recurrence (BCR) occurs in 20-50% of patients with prostate cancer (PCa) undergoing primary definitive treatment. Patients with high-risk BCR have an increased risk of metastatic progression and subsequent PCa-specific mortality, and thus could benefit from treatment intensification. Given the increasing complexity of diagnostic and therapeutic modalities, multidisciplinary care (MDC) can play a crucial role in the individualized management of this patient population. This review explores the role for MDC when evaluating the clinical evidence for the evolving definition of high-risk BCR and the emerging therapeutic strategies, especially with novel hormone therapies (NHTs), for patients with either high-risk BCR or oligometastatic PCa. Clinical studies have used different characteristics to define high-risk BCR and there is no consensus regarding the definition of high-risk BCR nor for management strategies. Next-generation imaging and multigene panels offer potential enhanced patient identification and precision-based decision-making, respectively. Treatment intensification with NHTs, either alone or combined with radiotherapy or metastasis-directed therapy, has been promising in clinical trials in patients with high-risk BCR or oligometastases. As novel risk-stratification and treatment options as well as evidence-based literature evolve, it is important to involve a multidisciplinary team to identify patients with high-risk features at an earlier stage, and make informed decisions on the treatments that could optimize their care and long-term outcomes. Nevertheless, MDC data are scarce in the BCR or oligometastatic setting. Efforts to integrate MDC into the standard management of this patient population are needed, and will likely improve outcomes across this heterogeneous PCa patient population.

Artificial INtelligence to Support Informed DEcision-making (INSIDE) for Improved Literature Analysis in Oncology.

BACKGROUND: Defining optimal therapeutic sequencing strategies in prostate cancer (PC) is challenging and may be assisted by artificial intelligence (AI)-based tools for an analysis of the medical literature. OBJECTIVE: To demonstrate that INSIDE PC can help clinicians query the literature on therapeutic sequencing in PC and to develop previously unestablished practices for evaluating the outputs of AI-based support platforms. DESIGN, SETTING, AND PARTICIPANTS: INSIDE PC was developed by customizing PubMed Bidirectional Encoder Representations from Transformers. Publications were ranked and aggregated for relevance using data visualization and analytics. Publications returned by INSIDE PC and PubMed were given normalized discounted cumulative gain (nDCG) scores by PC experts reflecting ranking and relevance. INTERVENTION: INSIDE PC for AI-based semantic literature analysis. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: INSIDE PC was evaluated for relevance and accuracy for three test questions on the efficacy of therapeutic sequencing of systemic therapies in PC. RESULTS AND LIMITATIONS: In this initial evaluation, INSIDE PC outperformed PubMed for question 1 (novel hormonal therapy [NHT] followed by NHT) for the top five, ten, and 20 publications (nDCG score, +43, +33, and +30 percentage points [pps], respectively). For question 2 (NHT followed by poly [adenosine diphosphate ribose] polymerase inhibitors [PARPi]), INSIDE PC and PubMed performed similarly. For question 3 (NHT or PARPi followed by 177Lu-prostate-specific membrane antigen-617), INSIDE PC outperformed PubMed for the top five, ten, and 20 publications (+16, +4, and +5 pps, respectively). CONCLUSIONS: We applied INSIDE PC to develop standards for evaluating the performance of AI-based tools for literature extraction. INSIDE PC performed competitively with PubMed and can assist clinicians with therapeutic sequencing in PC. PATIENT SUMMARY: The medical literature is often very difficult for doctors and patients to search. In this report, we describe INSIDE PC-an artificial intelligence (AI) system created to help search articles published in medical journals and determine the best order of treatments for advanced prostate cancer in a much better time frame. We found that INSIDE PC works as well as another search tool, PubMed, a widely used resource for searching and retrieving articles published in medical journals. Our work with INSIDE PC shows new ways in which AI can be used to search published articles in medical journals and how these systems might be evaluated to support shared decision-making.

Micromanaging alternative splicing during muscle differentiation.

A recent report in Genes & Development by Boutz et al. (2007) demonstrates that muscle specific microRNAs (miRNAs) downregulate the alternative splicing regulator nPTB during skeletal muscle differentiation to control a potential network of splicing transitions. The results illustrate how two modes of posttranscriptional regulation combine to direct skeletal muscle development.

Global regulation of alternative splicing during myogenic differentiation.

Recent genome-wide analyses have elucidated the extent of alternative splicing (AS) in mammals, often focusing on comparisons of splice isoforms between differentiated tissues. However, regulated splicing changes are likely to be important in biological transitions such as cellular differentiation, or response to environmental stimuli. To assess the extent and significance of AS in myogenesis, we used splicing-sensitive microarray analysis of differentiating C2C12 myoblasts. We identified 95 AS events that undergo robust splicing transitions during C2C12 differentiation. More than half of the splicing transitions are conserved during differentiation of avian myoblasts, suggesting the products and timing of transitions are functionally significant. The majority of splicing transitions during C2C12 differentiation fall into four temporal patterns and were dependent on the myogenic program, suggesting that they are integral components of myogenic differentiation. Computational analyses revealed enrichment of many sequence motifs within the upstream and downstream intronic regions near the alternatively spliced regions corresponding to binding sites of splicing regulators. Western analyses demonstrated that several splicing regulators undergo dynamic changes in nuclear abundance during differentiation. These findings show that within a developmental context, AS is a highly regulated and conserved process, suggesting a major role for AS regulation in myogenic differentiation.

Mycobacterial ecology of the Rio Grande.

This is the first study to characterize the environmental conditions which contribute to the presence and proliferation of environmental mycobacteria in a major freshwater river. Over 20 different species of environmental mycobacteria were isolated, including the pathogenic M. avium and M. kansasii. Species of the rapidly growing M. fortuitum complex were the most commonly isolated mycobacteria, and one-third of all isolates were not identified at the species level, even by 16S sequencing. PCR restriction analysis of the hsp65 gene was more accurate and rapid than biochemical tests and as accurate as yet less expensive than 16S sequencing, showing great promise as a new tool for species identification of environmentally isolated mycobacteria. Total environmental mycobacteria counts positively correlated with coliform and Escherichia coli counts and negatively correlated with chemical toxicity and water temperature. Environmental mycobacteria can survive in the alkaline conditions of the river despite previous reports that especially acidic conditions favor their presence. A representative river isolate (M. fortuitum) survived better than E. coli O157:H7 at pHs below 7 and above 8 in nutrient broth. The river strain also retained viability at 8 ppm of free chlorine, while E. coli was eliminated at 2 ppm and above. Thus, in vitro studies support environmental observations that a variety of extreme conditions favor the hardy environmental mycobacteria.