TY - JOUR A1 - Briese, Michael A1 - Saal, Lena A1 - Appenzeller, Silke A1 - Moradi, Mehri A1 - Baluapuri, Apoorva A1 - Sendtner, Michael T1 - Whole transcriptome profiling reveals the RNA content of motor axons JF - Nucleic Acids Research N2 - Most RNAs within polarized cells such as neurons are sorted subcellularly in a coordinated manner. Despite advances in the development of methods for profiling polyadenylated RNAs from small amounts of input RNA, techniques for profiling coding and non-coding RNAs simultaneously are not well established. Here, we optimized a transcriptome profiling method based on double-random priming and applied it to serially diluted total RNA down to 10 pg. Read counts of expressed genes were robustly correlated between replicates, indicating that the method is both reproducible and scalable. Our transcriptome profiling method detected both coding and long non-coding RNAs sized >300 bases. Compared to total RNAseq using a conventional approach our protocol detected 70% more genes due to reduced capture of ribosomal RNAs. We used our method to analyze the RNA composition of compartmentalized motoneurons. The somatodendritic compartment was enriched for transcripts with post-synaptic functions as well as for certain nuclear non-coding RNAs such as 7SK. In axons, transcripts related to translation were enriched including the cytoplasmic non-coding RNA 7SL. Our profiling method can be applied to a wide range of investigations including perturbations of subcellular transcriptomes in neurodegenerative diseases and investigations of microdissected tissue samples such as anatomically defined fiber tracts. KW - RNA KW - motor axons Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-126800 ER - TY - THES A1 - Saal, Lena T1 - Whole transcriptome profiling of compartmentalized motoneurons T1 - Globale Transkriptomanalyse von kompartimentierten Motoneuronen N2 - Spinal muscular atrophy and amyotrophic lateral sclerosis are the two most common devastating motoneuron diseases. The mechanisms leading to motoneuron degeneration are not resolved so far, although different hypotheses have been built on existing data. One possible mechanism is disturbed axonal transport of RNAs in the affected motoneurons. The underlying question of this study was therefore to characterize changes in transcript levels of distinct RNAs in cell culture models of spinal muscular atrophy and amyotrophic lateral sclerosis, especially in the axonal compartment of primary motoneurons. To investigate this in detail we first established compartmentalized cultures of Primary mouse motoneurons. Subsequently, total RNA of both compartments was extracted separately and either linearly amplified and subjected to microarray profiling or whole transcriptome amplification followed by RNA-Sequencing was performed. To make the whole transcriptome amplification method suitable for compartmentalized cultures, we adapted a double-random priming strategy. First, we applied this method for initial optimization onto serial dilutions of spinal cord RNA and later on to the compartmentalized motoneurons. Analysis of the data obtained from wildtype cultures already revealed interesting results. First, the RNA composition of axons turned out to be highly similar to the somatodendritic compartment. Second, axons seem to be particularly enriched for transcripts related to protein synthesis and energy production. In a next step we repeated the experiments by using knockdown cultures. The proteins depleted hereby are Smn, Tdp-43 and hnRNP R. Another experiment was performed by knocking down the non-coding RNA 7SK, the main interacting RNA of hnRNP R. Depletion of Smn led to a vast number of deregulated transcripts in the axonal and somatodendritic compartment. Transcripts downregulated in the axons upon Smn depletion were especially enriched for GOterms related to RNA processing and encode proteins located in neuron projections including axons and growth cones. Strinkingly, among the upregulated transcripts in the somatodendritic compartment we mainly found MHC class I transcripts suggesting a potential neuroprotective role. In contrast, although knockdown of Tdp-43 also revealed a large number of downregulated transcripts in the axonal compartment, these transcripts were mainly associated with functions in transcriptional regulation and RNA splicing. For the hnRNP R knockdown our results were again different. Here, we observed downregulated transcripts in the axonal compartment mainly associated with regulation of synaptic transmission and nerve impulses. Interestingly, a comparison between deregulated transcripts in the axonal compartment of both hnRNP R and 7SK knockdown presented a significant overlap of several transcripts suggesting some common mechanism for both knockdowns. Thus, our data indicate that a loss of disease-associated proteins involved in axonal RNA transport causes distinct transcriptome alterations in motor axons. N2 - Spinale Muskelatrophie und Amyotrophe Lateralsklerose zählen zu den beiden häufigsten und schwersten Motoneuronerkrankungen. Der zugrunde liegende Mechanismus beider Krankheiten ist bis heute nicht geklärt, dennoch werden verschiedene Theorien diskutiert. Ein möglicher Grund ist ein gestörter axonaler Transport von RNAs in den betroffenen Motoneuronen. Daraus folgernd ergab sich die zugrunde liegende Frage dieser Arbeit, ob Veränderungen in den Transkriptleveln bestimmter RNAs unter krankheitsähnlichen Bedingungen vor allem im axonalen Kompartiment von primären Maus-Motoneuronen beobachtet werden können. Um die Fragestellung genauer zu untersuchen, etablierten wir zuerst kompartimentierte Kulturen von primären Motoneuronen. Darauffolgend haben wir die totale RNA aus beiden Kompartimenten separat extrahiert und entweder diese linear amplifiziert und zur Microarrayanalyse gegeben oder wir führten eine Amplifikation des kompletten Transkriptoms mit anschließender RNA-Sequenzierung durch. Um die Amplifikation des kompletten Transkriptoms auch für die kompartimentierten Kulturen geeignet zu machen, verwendeten wir eine doublerandom priming Strategie und haben diese entsprechend angepasst. Zuerst wendeten wir die Methode an Serienverdünnungen von RNA aus dem Rückenmark an, um die Methode zu optimisieren. Später benutzten wir die Methode ebenfalls für kompartimentierte Motoneurone. Schon die Analyse der Wildtyp-Daten lieferte interessante Ergebnisse. Erstens, die Zusammensetzung der RNA in Axonen war höchst ähnlich zu der im somatodendritischen Kompartiment. Zweitens, in Axonen scheinen speziell Transkripte angereichert zu sein, welche mit Proteinsynthese und Energieproduktion in Verbindung stehen. In einem nächsten Schritt wurden dann die Experimente unter Verwendung von Knockdown-Kulturen wiederholt. Die Proteine, die dabei vermindert wurden waren Smn, Tdp-43 und hnRNP R. Ein weiteres Experiment wurde durchgeführt indem die nicht-codierende RNA 7SK verringert wurde. Die Depletion von Smn führte zu einer hohen Anzahl an deregulierten Transkripten sowohl im axonalen, als auch im somatodendritischen Kompartiment. Transkripte, die im axonalen Kompartiment nach Smn Depletion verringert waren, waren überwiegend für GOTerms angereichert, welche mit RNA Prozessierung in Verbindung stehen oder welche Proteine codieren, die in neuronalen Fortsätzen, einschließlich Axon und Wachstumskegel lokalisiert sind. Bemerkenswert ist, dass wir unter den hochregulierten Transkripten im somatodendritischen Kompartiment überwiegend MHC Klasse I Transkripte gefunden haben. Dies könnte eine mögliche neuroprotektive Rolle dieser Transkripte annehmen lassen. Im Gegensatz zu den Ergebnissen beim Smn Knockdown fanden wir beim Tdp-43 Knockdown ebenfalls eine große Anzahl an herunterregulierten Transkripten im axonalen Kompartiment, diese sind allerdings überwiegend mit Funktionen in der Transkriptionsregulierung und beim RNA Splicing assoziiert. Die Ergebnisse des hnRNP R Knockdowns waren ebenfalls unterschiedlich. Bei diesem fanden wir die herunteregulierten Transkripte im axonalen Kompartiment überwiegend mit einer Regulierung der synaptischen Übertragung sowie mit Nervenimpulsen assoziiert. Interessanterweise zeigte ein Vergleich der deregulierten Transkripte sowohl im axonalen Kompartiment vom hnRNP R Knockdown, als auch vom 7SK Knockdown eine signifikante Übereinstimmung mehrerer Transkripte. Dies lässt einen teilweise gemeinsamen Mechanismus für beide Genprodukte vermuten. Somit deuten unsere Daten darauf hin, dass ein Verlust von krankheitsassoziierten Proteinen, die eine Rolle beim axonalen RNA-Transport spielen, zu verschiedenen Transkriptomveränderungen in Axonen von Motoneuronen führt. KW - Axon KW - Motoneuron KW - Spinale Muskelatrophie KW - amyotrophic lateral sclerosis Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-140006 ER - TY - JOUR A1 - Briese, Michael A1 - Saal-Bauernschubert, Lena A1 - Lüningschrör, Patrick A1 - Moradi, Mehri A1 - Dombert, Benjamin A1 - Surrey, Verena A1 - Appenzeller, Silke A1 - Deng, Chunchu A1 - Jablonka, Sibylle A1 - Sendtner, Michael T1 - Loss of Tdp-43 disrupts the axonal transcriptome of motoneurons accompanied by impaired axonal translation and mitochondria function JF - Acta Neuropathologica Communications N2 - Protein inclusions containing the RNA-binding protein TDP-43 are a pathological hallmark of amyotrophic lateral sclerosis and other neurodegenerative disorders. The loss of TDP-43 function that is associated with these inclusions affects post-transcriptional processing of RNAs in multiple ways including pre-mRNA splicing, nucleocytoplasmic transport, modulation of mRNA stability and translation. In contrast, less is known about the role of TDP-43 in axonal RNA metabolism in motoneurons. Here we show that depletion of Tdp-43 in primary motoneurons affects axon growth. This defect is accompanied by subcellular transcriptome alterations in the axonal and somatodendritic compartment. The axonal localization of transcripts encoding components of the cytoskeleton, the translational machinery and transcripts involved in mitochondrial energy metabolism were particularly affected by loss of Tdp-43. Accordingly, we observed reduced protein synthesis and disturbed mitochondrial functions in axons of Tdp-43-depleted motoneurons. Treatment with nicotinamide rescued the axon growth defect associated with loss of Tdp-43. These results show that Tdp-43 depletion in motoneurons affects several pathways integral to axon health indicating that loss of TDP-43 function could thus make a major contribution to axonal pathomechanisms in ALS. KW - amyotrophic lateral sclerosis KW - Tdp-43 KW - axonal transcriptome KW - nicotinamide Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-230322 VL - 8 ER - TY - JOUR A1 - Dombert, Benjamin A1 - Balk, Stefanie A1 - Lüningschrör, Patrick A1 - Moradi, Mehri A1 - Sivadasan, Rajeeve A1 - Saal-Bauernschubert, Lena A1 - Jablonka, Sibylle T1 - BDNF/trkB induction of calcium transients through Ca\(_{v}\)2.2 calcium channels in motoneurons corresponds to F-actin assembly and growth cone formation on β2-chain laminin (221) JF - Frontiers in Molecular Neuroscience N2 - Spontaneous Ca\(^{2+}\) transients and actin dynamics in primary motoneurons correspond to cellular differentiation such as axon elongation and growth cone formation. Brain-derived neurotrophic factor (BDNF) and its receptor trkB support both motoneuron survival and synaptic differentiation. However, in motoneurons effects of BDNF/trkB signaling on spontaneous Ca\(^{2+}\) influx and actin dynamics at axonal growth cones are not fully unraveled. In our study we addressed the question how neurotrophic factor signaling corresponds to cell autonomous excitability and growth cone formation. Primary motoneurons from mouse embryos were cultured on the synapse specific, β2-chain containing laminin isoform (221) regulating axon elongation through spontaneous Ca\(^{2+}\) transients that are in turn induced by enhanced clustering of N-type specific voltage-gated Ca\(^{2+}\) channels (Ca\(_{v}\)2.2) in axonal growth cones. TrkB-deficient (trkBTK\(^{-/-}\)) mouse motoneurons which express no full-length trkB receptor and wildtype motoneurons cultured without BDNF exhibited reduced spontaneous Ca\(^{2+}\) transients that corresponded to altered axon elongation and defects in growth cone morphology which was accompanied by changes in the local actin cytoskeleton. Vice versa, the acute application of BDNF resulted in the induction of spontaneous Ca\(^{2+}\) transients and Ca\(_{v}\)2.2 clustering in motor growth cones, as well as the activation of trkB downstream signaling cascades which promoted the stabilization of β-actin via the LIM kinase pathway and phosphorylation of profilin at Tyr129. Finally, we identified a mutual regulation of neuronal excitability and actin dynamics in axonal growth cones of embryonic motoneurons cultured on laminin-221/211. Impaired excitability resulted in dysregulated axon extension and local actin cytoskeleton, whereas upon β-actin knockdown Ca\(_{v}\)2.2 clustering was affected. We conclude from our data that in embryonic motoneurons BDNF/trkB signaling contributes to axon elongation and growth cone formation through changes in the local actin cytoskeleton accompanied by increased Ca\(_{v}\)2.2 clustering and local calcium transients. These findings may help to explore cellular mechanisms which might be dysregulated during maturation of embryonic motoneurons leading to motoneuron disease. KW - growth cone KW - BDNF KW - trkB KW - Ca\(_{v}\)2.2 KW - F-actin KW - motor axon Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-159094 VL - 10 IS - 346 ER -