Parkinson's Disease (PD) is a late-onset neurodegenerative disease characterized by progressive motor dysfunction caused by a loss of dopaminergic neurons for which there is no known cure. Among the most common genetic causes of PD are mutations in the leucine-rich repeat kinase 2 gene (LRRK2), encoding a multi-domain protein with kinase activity. The LRRK2 G2019S mutation causes hyperactivity of the kinase domain and is the most frequent LRRK2 mutation in patients with familial PD, though its role in PD pathology remains unclear. Preliminary data from the lab of our collaborator, Dr. David Park, demonstrated through a genetic screen in Drosophila melanogaster that the deletion of rbp9 encoding an RNA-binding protein prevented pathology induced by PD-relevant mutations in the LRRK2 kinase domain. The neuronal homolog of RBP9 in humans is HuD, a member of the Hu family of RNA-binding proteins that regulates the expression of many transcripts involved in neuronal development, plasticity, and survival. In addition, HuD has been shown to modify the age-at-onset or risk of developing PD. Here, we studied the effect of LRRK2 on the post-transcriptional regulation of mRNAs bound by HuD in the context of PD. Our findings showed that HuD is a substrate for LRRK2 phosphorylation in vitro, and that LRRK2 G2019S hyperphosphorylates HuD. We demonstrated that LRRK2 kinase activity is required for the binding of several transcripts by HuD that encode PD-relevant proteins such as α-synuclein and neuronal survival factor BDNF. Our findings in human neuroblastoma cells indicated that LRRK2 regulates the protein levels of HuD mRNA targets α-synuclein and BDNF in a mechanism that can by modified by HuD. Finally, we showed that the combination of HuD knockout with LRRK2 G2019S expression in mice rescues aberrant expression of HuD targets in mice with only the LRRK2 G2019S mutation or the knockout of HuD alone. Together, our findings demonstrate that LRRK2 affects the post-transcriptional regulation of HuD-bound mRNAs, and suggest the use of HuD as a potential therapeutic target in patients with PD caused by the LRRK2 G2019S mutation.

abstract: Exome sequencing was used to identify novel variants linked to amyotrophic lateral sclerosis (ALS), in a family without mutations in genes previously linked to ALS. A F115C mutation in the gene MATR3 was identified, and further examination of other ALS kindreds identified an additional three mutations in MATR3; S85C, P154S and T622A. Matrin 3 is an RNA/DNA binding protein as well as part of the nuclear matrix. Matrin 3 interacts with TDP-43, a protein that is both mutated in some forms of ALS, and found in pathological inclusions in most ALS patients. Matrin 3 pathology, including mislocalization and rare cytoplasmic inclusions, was identified in spinal cord tissue from a patient carrying a mutation in Matrin 3, as well as sporadic ALS patients. In an effort to determine the mechanism of Matrin 3 linked ALS, the protein interactome of wild-type and ALS-linked MATR3 mutations was examined. Immunoprecipitation followed by mass spectrometry experiments were performed using NSC-34 cells expressing human wild-type or mutant Matrin 3. Gene ontology analysis identified a novel role for Matrin 3 in mRNA transport centered on proteins in the TRanscription and EXport (TREX) complex, known to function in mRNA biogenesis and nuclear export. ALS-linked mutations in Matrin 3 led to its re-distribution within the nucleus, decreased co-localization with endogenous Matrin 3 and increased co-localization with specific TREX components. Expression of disease-causing Matrin 3 mutations led to nuclear mRNA export defects of both global mRNA and more specifically the mRNA of TDP-43 and FUS. Our findings identify ALS-causing mutations in the gene MATR3, as well as a potential pathogenic mechanism attributable to MATR3 mutations and further link cellular transport defects to ALS. / Dissertation/Thesis / Doctoral Dissertation Neuroscience 2018

Spinal muscular atrophy is an autosomal recessive genetic disease that results from the loss and/or degeneration of alpha motor neurons in the lower part of the spinal cord. With ~ 1 in 6000 live births per year being affected, this disease is the second leading cause of infant death and is caused by the loss or decrease of the Survival of Motor Neuron protein (SMN). While a lot is known about the role that SMN plays in the cytoplasmic assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs), it remains a crucial question in the field to gain a better understanding of what specific/distinct function(s) SMN might have in motor neurons. We have identified novel interactions between SMN and two RNA-binding proteins (RBPs) known to be components of axonal RNA granules. More specifically, we demonstrated that SMN interacts with HuD and SERBP1 in a direct fashion in foci-like structures along neurites of motor neuron-derived cells. We have also demonstrated that the SMN/HuD interaction is required for the localization of HuD into RNA granules in neurites of motor neuron-derived cells. Furthermore, I have shown that SERBP1 is down-regulated in the absence of normal levels of SMN and, most importantly, that over-expression of SERBP1 can rescue SMA-like neuronal defects using a cell culture model of the disease. These findings may help shed light on the non-canonical molecular pathway(s) involving SMN and RBPs in motor neurons and underscores the possible therapeutic benefits of targeting these RBPs in the treatment of SMA.

La protéine de liaison aux ARN MEX-3 est un régulateur essentiel du développement embryonnaire chez le nématode Caenorhabditis elegans. Une famille de quatre gènes homologues à hMex-3 (dénommés hMex-3A, 3B, 3C et 3D) a été identifiée chez les mammifères par notre équipe. Afin de mieux comprendre la fonction physiologique in vivo des protéines Mex-3, nous avons invalidé le gène Mex-3B chez la souris. Cette approche expérimentale a révélé que Mex-3B est un acteur majeur de la spermatogenèse. Les souris mâles nullizygotes présentent une obstruction des tubes séminifères conduisant à une réduction importante du nombre des spermatozoïdes produits. L’ablation de Mex-3B ciblée à la cellule de Sertoli, cellule somatique essentielle à la fonction de l’épithélium séminifère, a permis d’établir que le phénotype testiculaire a pour origine une perturbation des propriétés biologiques de cette cellule. En effet, les cellules de Sertoli déficientes pour Mex-3B présentent des défauts de la phagocytose qui conduisent à une élimination défectueuse des corps résiduels au cours de la spemiogenèse. L’exploration des mécanismes moléculaires impliqués a montré que Mex-3B contrôle la phagocytose via la régulation de l’activité et de la localisation membranaire de Rap1GAP, une protéine qui régule négativement la petite protéine G Rap1. En accord avec ces données, l’absence de Mex-3B provoque une déstabilisation de la barrière hémato-testiculaire due à un défaut de localisation à la membrane plasmique des molécules de jonction connexine 43 et N-Cadhérine, protéines dont la translocation et la stabilité dépendent de Rap1. En conclusion, mes travaux de thèse ont permis de mettre en évidence un rôle clé de Mex-3B dans le contrôle spatial de la voie de signalisation Rap1 au cours de la spermatogenèse / The RNA binding-protein MEX-3 is a post-transcriptional regulator involved in early embryogenesis of the nematode Caenorhabditis elegans. We have recently reported the characterization of a novel family of four mammalian genes homologous to hMex-3 (called hMex-3A, 3B, 3C and 3D). To gain insight into the biological functions of these proteins in vivo, we disrupted the Mex-3B gene in mice. Using this experimental approach, we found that Mex-3B is as a major regulator of spermatogenesis. We observed that male Mex-3B null mice hypofertile and present an obstruction of seminiferous epithelium. Phagocytic properties of Sertoli cells were impaired, thus impeding the clearance of residual bodies released during spermiogenesis. Exploration of the underlying molecular mechanisms revealed that Mex-3B regulates phagocytosis through the activation and the transport at the peripheral membrane of Rap1GAP, a protein that downregulates the small G protein Rap1. Consistently, the Rap1-dependent recruitment of the junction proteins, connexin 43 and N-Cadherin at the cell surface was compromised in Mex-3B deficient mice. In conclusion, my work highlights a key role gor Mex-3B in the spatial control of Rap1 signaling during spermatogenesis

Trypanosomatid parasites such as Trypanosoma brucei have unusual mechanisms of gene expression including polycistronic transcription, mitochondrial RNA editing and trans-splicing. Additionally, these protists rely mainly on post-transcriptional regulation where RNA-binding proteins (RBP) have shown to play a major role. RBP6 and RBP10 are two examples of RBPs that play crucial roles in procyclic and bloodstream form parasites differentiation respectively, by post-transcriptional regulation. Over-expression of RBP6 is enough to promote differentiation into metacyclic trypomastigotes that are infective to mice. However, continuous expression is required, and this pattern does not reflect the natural expression in the tsetse fly or the influence of other RNA-binding proteins. RBP5 is a RBP with a single RNA-recognition motif similar to RBP6 and RBP10, whose expression is upregulated during the life stages within the salivary glands of tsetse flies. We hypothesize the RBP5 facilitates metacyclogenesis in the tsetse fly. To evaluate possible contributions to T. brucei differentiation, we will over-express RBP5 in procyclic cells alone and in combination with RBP6. Initial screening of cells over-expressing PTP-tagged RBP5 resulted in parasites with a moderate growing defect, and the scoring of nuclei and kinetoplasts in fixed cells showed a progressive accumulation of cells with 2 nuclei and 2 kinetoplasts (2N2K) and appearance of multinucleated cells. On the other hand, over-expression of non-tagged RBP5 generated a more severe growing defect, starting immediately after the first day of induction. The scoring of nuclei and kinetoplasts resulted in a drastic increase of 2N2K cells and a greater appearance of multinucleated cells, which suggests an irregular cell cycle progression. When developing the dual over-expression system, our cells over-expressing RBP6 were not able to differentiate into any stage, and when over-expressing RBP5 and RBP6 coordinately, no differentiation process was observed either. Together these data suggest that RBP5 might be a regulator of genes involved in the initiation of cytokinesis in T. brucei parasites, however a role in metacyclogenesis cannot be discarded since we were not able to obtain metacyclic parasites. This study helped us to get a better understanding of the post-transcriptional regulatory mechanisms that repress and regulate T. brucei cell cycle progression.

No description available.

Within hours after its initiation, the severe systemic inflammatory response of sepsis shifts to an adaptive anti-inflammatory state with coincident immunosuppression. This anti-inflammatory phenotype is characterized by diminished proinflammatory cytokine gene expression in response to toll-like receptor (TLR) stimulation with bacterial endotoxin/lipopolysaccharide (LPS), also known as endotoxin tolerance/adaptation. Our and other studies have established that gene-specific reprogramming following TLR4 responses independently represses transcription and translation of proinflammatory genes such as tumor necrosis factor alpha (TNFα). We also previously demonstrated that TNFα and interleukin (IL)-6 mRNA translation is repressed in endotoxin-adapted THP-1 human monocytes by an miRNA-based mechanism involving the argonaute family protein argonaute 2 (Ago2). Here, we further define the molecular nature of reprogramming translation by showing that TLR4-induced microRNA-146 promotes a feed-forward loop that modifies the subcellular localization of the RNA-binding protein RBM4 (RNA-binding motif protein 4) and promotes its interaction with Ago2. This interaction results in the assembly of a translation-repressor complex that disrupts TNFα and IL-6 cytokine synthesis in endotoxin-adapted THP-1 monocytes. This novel molecular path prevents the phosphorylation of RBM4 on serine-309 by p38 MAPK (mitogen-activated protein kinase), which leads to RBM4 accumulation in the cytosol and interaction with Ago2. We further find that microRNA-146a knockdown by antagomirs or protein phosphatase inhibition by okadaic acid increases p38 MAPK phosphorylation and results in RBM4 serine-309 phosphorylation and nuclear relocalization, which disrupts RBM4 and Ago2 interactions and restores TLR4-dependent synthesis of TNFα and IL-6. We conclude that miR-146a has a diverse and critical role in limiting an excessive acute inflammatory reaction.

Within hours after its initiation, the severe systemic inflammatory response of sepsis shifts to an adaptive anti-inflammatory state with coincident immunosuppression. This anti-inflammatory phenotype is characterized by diminished proinflammatory cytokine gene expression in response to toll-like receptor (TLR) stimulation with bacterial endotoxin/lipopolysaccharide (LPS), also known as endotoxin tolerance/adaptation. Our and other studies have established that gene-specific reprogramming following TLR4 responses independently represses transcription and translation of proinflammatory genes such as tumor necrosis factor alpha (TNFα). We also previously demonstrated that TNFα and interleukin (IL)-6 mRNA translation is repressed in endotoxin-adapted THP-1 human monocytes by an miRNA-based mechanism involving the argonaute family protein argonaute 2 (Ago2). Here, we further define the molecular nature of reprogramming translation by showing that TLR4-induced microRNA-146 promotes a feed-forward loop that modifies the subcellular localization of the RNA-binding protein RBM4 (RNA-binding motif protein 4) and promotes its interaction with Ago2. This interaction results in the assembly of a translation-repressor complex that disrupts TNFα and IL-6 cytokine synthesis in endotoxin-adapted THP-1 monocytes. This novel molecular path prevents the phosphorylation of RBM4 on serine-309 by p38 MAPK (mitogen-activated protein kinase), which leads to RBM4 accumulation in the cytosol and interaction with Ago2. We further find that microRNA-146a knockdown by antagomirs or protein phosphatase inhibition by okadaic acid increases p38 MAPK phosphorylation and results in RBM4 serine-309 phosphorylation and nuclear relocalization, which disrupts RBM4 and Ago2 interactions and restores TLR4-dependent synthesis of TNFα and IL-6. We conclude that miR-146a has a diverse and critical role in limiting an excessive acute inflammatory reaction.

Nucleocytoplasmic transport (NCT) declines during aging and in the context of age-dependent neurodegenerative diseases. However, the mechanisms underlying NCT decline in the disease are poorly understood. FUS is an RNA binding protein that shuttles between the nucleus and cytoplasm and is actively involved in NCT. Mutations in FUS cause amyotrophic lateral sclerosis (ALS), a fatal and incurable motor neuron disorder. We sought to understand the disease mechanism underlying FUS-induced NCT decline in ALS. Here, I uncovered NCT-related defects in motor neurons derived from human induced pluripotent stem cells (iPSCs) harboring an ALS-linked FUS mutation. Importantly, these NCT defects were rescued by genetically correcting the FUS mutation in iPSCs. To gain insight into how expression of mutant FUS causes nuclear pore defects, I demonstrated an altered localization where FUS and nucleoporins (Nups) interact in situ within patient-derived human neurons. Moreover, FUS became aggregation-prone when interacting with Nup62 in vitro, and RNA further alleviated their aggregation propensity. Importantly, NCT-related defects and neuronal toxicity induced by ALS-FUS were ameliorated by modulating Nup expression in vivo. Collectively, these findings implicate aberrant Nup interactions in the pathogenic mechanism of ALS-FUS, and direct targeting the gain-of-function protein interactions could be therapeutic for multiple causes of neurodegeneration.

Indiana University-Purdue University Indianapolis (IUPUI) / Animals depend on inheriting non-genetic information early in life to grow and develop naturally. This inherited, non-genetic information was previously thought to be limited to DNA modifications and DNA binding proteins. But recent studies have expanded our understanding of inheritance to include RNA and RNA binding proteins. We currently lack methods to identify and enrich for RNA binding proteins that might be involved in providing non-genetic information from mother to daughter cells. Others have developed a method using modified enzyme tags to pulse-label proteins with small molecule fluorescent ligands and follow these proteins as they are inherited by cells. Here I characterized and tested the application of a fluorescent small molecule targeting antibody to enrich for these labeled proteins. I first tested the ability of this antibody to bind to fluorescent ligand-labeled enzymes. I determined that the antibody can efficiently bind to at least one of the labeled enzymes. Second, I determined crystallization conditions for the ligand binding antibody fragment. This thesis sets the stage for structure determination and to test whether this antibody can work in vivo to enrich for RNA binding proteins involved in the delivery of non-genetic information to cells.