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, focusing on the characterization of post-transcriptional networks implicated in 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.
Post-transcriptional regulation in perspective
We have been working on NIH funded projects to characterize RBP target genes and pertinent regulatory sequences genome-wide in human cells. Projects rely on biochemical methods that consist in isolating RNA-protein complexes (RNPs) of interest followed by characterization of the RNA component by CLIP (Cross-linking and Immuno-Precipitation) or RIP (Ribonucleoprotein Immuno-Precipitation) sequencing. We worked initially in the context of the ENCODE program (NHGRI) to characterize a collection of RNA binding proteins involved in translation and mRNA stability. This project has been continued in partnership with Andrew Smith (USC). As result of this study, we developed two computational pipelines: PIRANHA, used to map RBP targets and ZAGROS, used to define the characteristic of RBP binding sites. We have just obtained a new R01 to specifically study translation regulation. Our plan is to develop a new computational pipeline to analyze Ribosomal Profiling data, map novel regulatory elements implicated in translation regulation and examine changes in translation in cancer relevant processes (radiation, cell cycle, drug treatment).
Similar to RBPs, miRNAs control complex networks of genes. Mapping miRNA targets is a basic step towards the understanding of their specific biological functions. We were successful in designing in collaboration with Epicentre a simpler and more effective approach for miRNA target identification. Our high-throughput approach targets Poly A binding protein (PABP), a critical player in miRNA mediated regulation. By measuring in glioblastoma cells changes in PABP association driven by the transfection of the tumor suppressor miR-137, we effectively identified circa 500 mRNA targets and defined a gene network with important players in cell differentiation and cancer development (c-KIT, TGFβ-2, CDC42, CDK6, YBX1, AKT2, CD24, AEG-1 among others).
Figure 1: Model of antagonism between Musashi1 and miR-124,-128 and-137 and possible impact on cell fate decisions and brain tumor development.
The RNA binding protein Musashi1 in neurogenesis
and brain tumor development
We have identified Musashi1 (Msi1) in a genomic study as a potential oncogenic factor in brain tumors (medulloblastoma and glioblastoma). In normal circumstances, Msi1 is expressed exclusively in stem cells where it controls the balance between self-renewal and differentiation. In the cancer scenario, high Msi1 expression has been detected in a variety of solid tumors including breast, lung, colon, ovary, neuroblastoma, medullobastoma and glioblastoma. In the past five years, we have extensively characterized Msi1 in both medulloblastoma and glioblastoma by defining its roles in cancer relevant processes. In medulloblastoma, we showed a correlation between Musashi1 expression levels and survival and diseases free survival; we also determined that Musashi1 is highly expressed in the high risk sub-groups 3 and 4. Msi1 knockdown affects tumor growth and impacts multiple cancer-relevant processes including apoptosis, cell cycle, proliferation, migration, invasion, and adhesion. Msi1 possibly plays as a critical role in GBM and medulloblastoma response to treatment as its levels of expression influence both radio- and chemo-resistance and its function is required for the survival of tumor initiating cells. We further determined that increased Msi1 expression in transgenic mice boosts proliferation of stem cells and induces tumor production. We carried out several genomic analyses (CLIP and RIP) to identify Msi1 targets. The results corroborated Msi1 broad impact on tumorigenesis; Msi1 target genes are preferentially located in several cancer relevant pathways including Focal Adhesion, Wnt, JAK-Stat, p53, MAPK, VEGF and ErbB.
Figure 2: Musashi1 is an important player in medulloblastoma. Musashi1 expression is particularly high in medulloblastoma high-risk groups. Musashi1 high expression is a sing of poor outcome.
miRNAs in neural differentiation and brain tumor development
There is an interesting connection between neural differentiation and brain tumor development, and miRNAs are important components of this crossroad. We have shown that miR-124, miR-128 and miR-137 which are among the top-expressed miRNAs in the brain, act as pro-neurogenic factors. They display parallel increase in expression as cells differentiate, while blockage of their activity by antagomiRs drastically reduces neuronal production. Moreover, 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 to regulate phenotype changes and to modulate gene expression.
We conducted in vivo target mapping of these three miRNAs in the context of neurogenesis and determined that they control highly overlapping and inter-connected gene networks; the most important one is formed by transcription factors. We also determined that miR-124, -128 and -137 share a large number of targets with Musashi1. In addition, we established Musashi1 as a target of both miR-128 and -137. We propose then an antagonist model where Musashi1 and these three miRNAs target a common set of genes but produce distinct impact on their expression (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.
Figure 3: miR-124, -128 and -137 are regulators of neurogenesis. miRNA mimics transfection dramatically increases neuronal production.
Dr. Luiz O. Penalva received his PhD from Universidad Autonoma de Madrid, Spain and worked as a post-doctoral fellow at the European Molecular Biology Laboratories (EMBL-Germany) and Duke University. He has been a principal investigator at Greehey Children's Cancer Research Institute since 2004 and is a member of the Department of Cellular and Structural Biology
RNA biology, genomics, RNA binding proteins, post-transcriptional regulation, brain tumors
- Li W, Wang W, Uren PJ, Penalva LO, Smith AD. Riborex: Fast and flexible identification of differential translation from Ribo-seq data. Bioinformatics. 2017 Jan 31. doi: 10.1093/bioinformatics/btx047.
- Patricia Rosa de Araujo, Aparna Gorthi, Acarizia Eduardo da Silva, Sonal S. Tonapi, Dat T. Vo, Suzanne C. Burns, Mei Qiao, Philip J. Uren, Zhi-Min Yuan, Alexander J.R. Bishop, Luiz O.F. Penalva. Musashi1 Impacts Radio-Resistance in Glioblastoma by Controlling DNA-PKcs. American Journal of Pathology
- Uren PJ, Bahrami-Samani E, Araujo P, Vogel C, Burns SC, Qiao M, Smith AD, Penalva LOF. High-throughput analyses of hnRNP H1 dissects its multi-functional aspect. RNA Biology 2016 Apr 2;13(4):400-11. doi: 10.1080/15476286.2015.1138030.
- Ennajdaoui H, Howard JM, Sterne-Weiler T, Jahanbani F, Coyne DJ, Uren PJ, Dargyte M, Katzman S, Draper JM, Wallace A, Cazarez O, Burns SC, Qiao M, Hinck L, Smith AD, Masoud M. Toloue, Benjamin J. Blencowe, Penalva LOF, Sanford JR. IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC. Cell Reports 2016. DOI: http://dx.doi.org/10.1016/j.celrep.2016.04.083.
- Correa BR, de Araujo PR, Qiao M, Burns SC, Chen C, Agarwal S, Galante PAF, Penalva LOF. RNA-binding proteins in perspective: a functional genomics analysis reveals the splicing regulator SNRPB as a potential oncogenic candidate in glioblastoma. Genome Biology 2016 Jun 10;17(1):125
- Santos MC, Tegge AN, Correa BR, Mahesula S, Kohnke LQ, Qiao M, Ferreira MA, Kokovay E, Penalva LO. miR-124, -128, and -137 Orchestrate Neural Differentiation by Acting on Overlapping Gene Sets Containing a Highly Connected Transcription Factor Network. Stem Cells. 2016 Jan;34(1):220-32. doi: 10.1002/stem.2204. Epub 2015 Sep 15. PMID: 26369286
- Cambuli FM, Correa BR, Rezza A, Burns SC, Qiao M, Uren PJ, Kress E, Boussouar A, Galante P, Penalva L, Plateroti M. A mouse model of targeted Musashi1 expression in whole intestinal epithelium suggests regulatory roles in cell cycle and stemness. Stem Cells. 2015 Dec;33(12):3621-34. doi: 10.1002/stem.2202. Epub 2015 Sep 26. PMID: 26303183
- Uren PJ, Vo DT, de Araujo PR, Pötschke R, Burns SC, Bahrami-Samani E, Qiao M, de Sousa Abreu R, Nakaya HI, Correa BR, Kühnöl C, Ule J, Martindale JL, Abdelmohsen K, Gorospe M, Smith AD, Penalva LO. RNA-Binding Protein Musashi1 Is a Central Regulator of Adhesion Pathways in Glioblastoma. Mol Cell Biol. 2015 Sep 1;35(17):2965-78. doi: 10.1128/MCB.00410-15. Epub 2015 Jun 22. PMID: 26100017.
- Bahrami-Samani E, Vo DT, de Araujo PR, Vogel C, Smith AD, Penalva LO, Uren PJ. Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput. Wiley Interdiscip Rev RNA. 2015 May-Jun;6(3):291-310. doi: 10.1002/wrna.1274. Epub 2014 Dec 16. PMID: 25515586
- Bahrami-Samani E, Penalva LO, Smith AD, Uren PJ. Leveraging cross-link modification events in CLIP-seq for motif discovery. Nucleic Acids Res. 2015 Jan;43(1):95-103. doi: 10.1093/nar/gku1288. Epub 2014 Dec 10.
- Tamim S, Vo DT, Uren PJ, Qiao M, Bindewald E, Kasprzak WK, Shapiro BA, Nakaya HI, Burns SC, Araujo PR, Nakano I, Radek AJ, Kuersten S, Smith AD, Penalva LO. Genomic analyses reveal broad impact of miR-137 on genes associated with malignant transformation and neuronal differentiation in glioblastoma cells. PLoS One. 2014 Jan 22;9(1):e85591. doi: 10.1371/journal.pone.0085591. eCollection 2014.
- Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F, Corbett AH, Carstens RP, Frey BJ, Anderson RA, Lynch KW, Penalva LO, Lei EP, Fraser AG, Blencowe BJ, Morris QD, Hughes TR. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 2013 Jul 11;499(7457):172-7. doi: 10.1038/nature12311.
- Wang XY, Yu H, Linnoila RI, Li L, Li D, Mo B, Okano H, Penalva LO, Glazer RI. Musashi1 as a potential therapeutic target and diagnostic marker for lung cancer. Oncotarget. 2013 May;4(5):739-50.
- Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, Hannon GJ, Sanford JR, Penalva LO, Smith AD. Site identification in high-throughput RNA-protein interaction data. Bioinformatics. 2012 Dec 1;28(23):3013-20. doi: 10.1093/bioinformatics/bts569.
- Vo DT, Subramaniam D, Remke M, Burton TL, Uren PJ, Gelfond JA, de Sousa Abreu R, Burns SC, Qiao M, Suresh U, Korshunov 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. 0Am J Pathol. 2012 Nov;181(5):1762-72. doi: 10.1016/j.ajpath.2012.07.031.
- Uren PJ, Burns SC, Ruan J, Singh KK, Smith AD, Penalva LO. Genomic analyses of the RNA-binding protein Hu antigen R (HuR) identify a complex network of target genes and novel characteristics of its binding sites. J Biol Chem. 2011 Oct 28;286(43):37063-6. doi: 10.1074/jbc.C111.266882.
- 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. doi: 10.1038/msb.2010.59