RNA binding proteins (RBPs) and miRNAs play major roles in gene expression by controlling all stages of mRNA processing, its transport, localization, decay and translation. My laboratory studies these two regulators from a global perspective. We use a combination of genomics, systems biology, biochemistry, bioinformatics and molecular biology to investigate the networks formed by RNA binding proteins, miRNAs and their target genes and evaluate their impact on biological processes, cancer and disease states. I am particularly interested in the neuronal tissue and the analysis of gene regulators implicated in both differentiation and brain tumor development.
Major components of my research program include:
- Screening and characterization of RBPs and miRNAs implicated in neuronal stem cell function and brain tumors.
- Construction of regulatory maps for neuronal differentiation and brain tumor development.
- Development and improvement of computational and functional methods for miRNA/RBP target identification and functional outcome.
- Development of RNA based approaches for therapy.
Musashi1 in brain tumor development
Our lab is interested in RNA-binding proteins acting at the intersection neurogenesis-brain tumor development. For the last ten years, the major highlight of our work has been the stem cell protein Musashi1 (Msi1) and its participation in medulloblastoma and glioblastoma. We showed that Musashi1 is highly expressed in the high risk medulloblastoma sub-groups 3 and 4 and linked to poor prognosis. We have established that Msi1 regulates multiple cancer-relevant processes including apoptosis, cell cycle, proliferation, migration, invasion and adhesion via a complex network of target genes. Msi1 expression levels influence both radio- and chemo-resistance and its function is required for the survival of tumor initiating cells. Convinced that Msi1 is a critical oncogenic factor, we have recently developed an inhibitor that blocks Msi1 RNA binding domains. We are currently working to improve its structure and drug properties, aiming its future use in cancer therapy.
miRNAs in neurogenesis and brain tumor development
miRNAs function as important regulatory switches, influencing cell fate decisions and tumor development. miR-124, miR-128 and miR-137 are among the top-expressed miRNAs in the brain. They display parallel increase in expression as cells differentiate and their function is absolutely required for neuronal production. These three miRNAs are often repressed in glioblastoma and suggested to work as tumor suppressors. Our results indicate that miR-124, -128 and -137 act synergistically and control highly overlapping target sets. Interestingly, we also determined that miR-124, -128 and -137 share a large number of targets with Musashi1. In the antagonist model we propose to establish, Musashi1 and these three miRNAs have opposite impact on the expression of shared targets (activation by Musashi1 vs. repression by miR-124, -128 and -137). The concentration of each regulator would ultimately influence this network and neural stem cell fate with the options of self-renewal, differentiation or tumor development.
Alternative splicing regulation in brain tumor development
Analysis of several hundred glioblastoma samples compiled by the TCGA (The Cancer Genome Atlas) produced an extensive transcriptomic map, identified prevalent chromosomal alterations and defined important driver mutations. However, as of today, clinical trials based on these results have not delivered an improvement on outcome. Therefore, we decided to characterize other regulatory routes known for playing a role in tumor relapse and response to treatment. We selected splicing regulation for the following reasons: 1) Alternative splicing affects 90% of the transcriptome and is an important source for transcript variation and gene regulation; 2) Numerous genes involved in apoptosis, proliferation, migration and DNA repair display cancer specific splicing isoforms with functions distinct from the ones in normal tissue; 3) Mutations and alterations in splicing factors are highly prevalent in multiple cancers and can act as tumor drivers; 4) Genomic instability, a common characteristic of cancer, can be induced by splicing defects; 5) The splicing machinery is targetable: there are numerous examples of drugs that either inhibit splicing factors or promote changes in splicing; 6) Importantly, no comprehensive studies have been performed to study splicing regulation in GBM.
Using resources from TCGA (The Cancer Genome Atlas) and GTex (Genotype-Tissue Expression), we have analyzed the expression profile of splicing regulators in normal and brain tumor tissues and produced detailed maps of splicing alterations in cancer cells. Our current plans are to link splicing regulators to oncogenic signals required for transformation, identify critical splicing isoforms and evaluate their contribution to gliomagenesis.
Understanding the dynamics of translation regulation
Genome-scale knowledge of translational regulation has lagged behind that of transcription, despite a central role determining cell phenotype, and major implications for numerous diseases and cancer. The assay of choice for global gene expression profiling is RNA-seq, which makes sense for understanding transcriptional control. But levels of mRNA in a cell explain only a fraction of observed protein levels, and much of the remainder is due to translational control. Ribosome profiling (RP) or Ribo-seq is a novel genomic approach that delivers quantitative information on the number and behavior of ribosomes, and gives profiles of gene expression much more closely linked to actual protein levels. We are using Ribo-seq aligned with computational tools to identify alterations in translation regulation in cancer cells and study its behavior upon drug and radiation treatments. We are also interested in examining the role of aberrantly expressed ribosomal proteins in tumor development and determine if they affect translation in specific fashions.
Saleh T, Vo DT, Uren PJ, Bindewald E, Wojciech KK, Shapiro BA, Qiao M,
Nakaya HI, Burns SC, Nakano I, Kuersten S, Smith AD, Penalva LOF.
High-throughput analysis of miR-137 in glioblastoma cells reveals a
complex network of targets associated with malignant transformation and
neuronal differentiation. PLoS ONE 2014 Jan 22;9(1):e85591. doi:
A, Dubuc AM, Northcott
PA, Smith AD, Pfister SM, Taylor MD, Janga SC, Anant S, Vogel C, Penalva
LO. The RNA-binding protein Musashi1 affects medulloblastoma growth via a network of cancer-related genes and is an indicator of poor prognosis. Am J Pathol. 2012 Nov;181(5):1762-72.
Vo DT, Abdelmohsen K, Martindale JL, Qiao M, Tominaga K, Burton TL,
Gelfond JA, Brenner AJ, Patel V, Trageser D, Scheffler B, Gorospe M,
Penalva LO. The oncogenic RNA-binding protein Musashi1 is regulated by HuR via mRNA translation and stability in glioblastoma cells. Mol Cancer Res. 2012 Jan;10(1):143-55.
Vo DT, Qiao M, Smith AD, Burns SC, Brenner AJ, Penalva LO. The oncogenic RNA-binding protein Musashi1 is regulated by tumor suppressor miRNAs. RNA Biol. 2011 Sep-Oct;8(5):817-28.
Vogel C, Abreu Rde S, Ko D, Le SY, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol. 2010 Aug 24;6:400.
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