Fadia Ibrahim, PhD

My laboratory is mainly focused on understanding the role of RNA-binding proteins (RBPs) and their contribution to the pathogenesis of amyotrophic lateral sclerosis (ALS), and investigating the mechanistic regulation of mRNA lifecycle in health and disease. ALS is a devastating neurodegenerative disease with no current cure. The major goal of our research program is to identify potential targets for therapeutic intervention. Mutations in genes encoding RBPs including TDP-43 and FUS have emerged as causative agents in the pathogenesis of ALS. Aggregation and nuclear-to-cytoplasmic mislocalization of RBPs are hallmarks of ALS pathogenesis. RBPs are multifunctional proteins that modulate several cellular RNA processes including transcription, splicing, transport, and translation. We aim to investigate how dysregulation of RNA processes mainly decay and translation contributes to ALS pathogenesis, and to address the role of RBPs mutations in neurodegeneration.

With the advent of next-generation sequencing, transcriptome profiling using RNA-Seq has become  a universal tool in biomedical researches. Over the past years, I developed several RNA sequencing methods (-see below-) to better understand regulation of mRNA decay in cells. Employing these methods, I uncovered a novel mRNA decay process that we named "ribothrypsis". We aim to investigate the mechanistic regulation of ribothrypsis in health and disease. We will employ a multidisciplinary approach including molecular biology, biochemistry, computational biology, and novel RNA-Seq methods to understand the regulation of mRNAs and the role of RBPs in neurodegeneration.

Contributions to Science

Development of Novel RNA-Seq Methods and Uncovering a Novel RNA Decay Process

As a Research Investigator at the University of Pennsylvania, I designed and developed multiple RNA-Seq methods for three sequencing platforms; Akron-Seq (Illumina), Akron-SMRT (Pacific Biosciences), and TERA-Seq (Oxford Nanopore Technologies; ONT). I applied Akron-Seq and Akron-SMRT to capture the native 5' and 3' ends of mRNAs, which led to the discovery of ribothrypsis. We find that almost all translated human mRNAs are subjected to co-translational, endonucleolytic cleavage following ribosome stalling. Importantly, we revealed that mRNA fragments are prevalent in cells with important implications for the interpretation of gene profiling experiments that rely on the assumption that mRNAs exist largely as full-length molecules in vivo. These findings offer a new post-transcriptional mechanism by which gene expression could be regulated. TERA-Seq addressed limitations of ONT, which permit more thorough transcriptome characterization providing new insights that challenge the current view of mRNA degradation. We find that deadenylation is not a prerequisite for eukaryotic mRNAs decay. These outcomes opened up an innovative area of research that could have significant impact in the field of RNA biology.

Unravelling New RNA-binding Proteins in ALS

As a Postdoctoral Fellow and in collaboration with several investigators at the University of Pennsylvania, we led efforts to discover two new ALS candidate genes TAF15 and EWSR1, and identified missense mutations of both genes in sporadic ALS cases. These mutations conferred neurodegeneration in Drosophila and aggregation in primary neurons. Coupling CLIP-Seq with RNA-Seq, I then identified the in vivo conserved neuronal RNA targets of TAF15 in human brain and cultured neurons. I uncovered potential targets with essential roles in synaptic activities, providing further evidence for the role of RNA dysregulation in ALS pathogenesis. Findings from these studies will serve as a platform for our future studies to interrogate the link between RNA dysfunction and mutations of RBPs.

Discovery of New Regulatory Mechanisms of the RNA Interference Pathway

My doctoral studies focused primarily on understanding the mechanistic regulation of the RNA interference (RNAi). I led several studies that were at the forefront of several discoveries in the RNAi field. I identified a novel poly(A) polymerase enzyme (MUT68) required for target mRNA degradation through untemplated adenines addition to the 3' ends of the RISC-cleaved 5' fragments stimulating their degradation. I also uncovered a novel quality control mechanism required for clearing dysfunctional miRNAs and siRNAs through the untemplated addition of uridine to their 3' ends. I also identified a role of the Chlamydomonas Vasa intronic gene in small RNAs-mediated translation repression. These studies unraveled new layers of regulation of small RNAs turnover and their cleaved products. We anticipate that understanding these mechanisms will have direct implications for fundamental biology and for applications of RNAi technology.

PhD in Molecular Biology and Microbiology, University of Nebraska-Lincoln - 2009
Certificate in Biotechnology, California State University-East Bay - 2003
MSc in Microbiology, Jordan University of Science and Technology - 2001

Fellowships

Postdoctoral Fellow, Department of Pathology and Laboratory Medicine, University of Pennsylvania, 2010-2015 
Milton E. Mohr Fellowship, University of Nebraska-Lincoln, 2007-2008
Larsen Fellowship, University of Nebraska-Lincoln, 2004-2005