Drosophila Ref1/ALYREF regulates transcription and toxicity associated with ALS/FTD disease etiologies

Axon guidance genes modulate neurotoxicity of ALS-associated UBQLN2

Mutations in the ubiquitin (Ub) chaperone Ubiquilin 2 (UBQLN2) cause X-linked forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) through unknown mechanisms. Here, we show that aggregation-prone, ALS-associated mutants of UBQLN2 (UBQLN2ALS) trigger heat stress-dependent neurodegeneration in Drosophila. A genetic modifier screen implicated endolysosomal and axon guidance genes, including the netrin receptor, Unc-5, as key modulators of UBQLN2 toxicity. Reduced gene dosage of Unc-5 or its coreceptor Dcc/frazzled diminished neurodegenerative phenotypes, including motor dysfunction, neuromuscular junction defects, and shortened lifespan, in flies expressing UBQLN2ALS alleles. Induced pluripotent stem cells (iPSCs) harboring UBQLN2ALS knockin mutations exhibited lysosomal defects while inducible motor neurons (iMNs) expressing UBQLN2ALS alleles exhibited cytosolic UBQLN2 inclusions, reduced neurite complexity, and growth cone defects that were partially reversed by silencing of UNC5B and DCC. The combined findings suggest that altered growth cone dynamics are a conserved pathomechanism in UBQLN2-associated ALS/FTD.

Studies of neurodegenerative diseases using Drosophila and the development of novel approaches for their analysis

The use of Drosophila in neurodegenerative disease research has contributed to the identification of modifier genes for the pathology. The basis for neurodegenerative disease occurrence in Drosophila is the conservation of genes across species and the ability to perform rapid genetic analysis using a compact brain. Genetic findings previously discovered in Drosophila can reveal molecular pathologies involved in human neurological diseases in later years. Disease models using Drosophila began to be generated during the development of genetic engineering. In recent years, results of reverse translational research using Drosophila have been reported. In this review, we discuss research on neurodegenerative diseases; moreover, we introduce various methods for quantifying neurodegeneration in Drosophila.

HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS

A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The exact mechanism resulting in these neurodegenerative diseases remains elusive, but C9 repeat RNA toxicity has been implicated as a gain-of-function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS-linked phenotype. We discovered that the RNA-binding protein heterogeneous nuclear ribonucleoprotein K (HNRNPK) reverses the toxicity of both sense and antisense repeat RNA, which is dependent on its subcellular localization and RNA recognition, and not on C9orf72 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts, induced pluripotent stem cell (iPSC)-derived motor neurons and post-mortem motor cortex and spinal cord, in line with a disrupted HNRNPK function in C9orf72 ALS. In C9orf72 ALS/FTD patient tissue, we discovered an increased nuclear translocation, but reduced expression of ribonucleotide reductase regulatory subunit M2 (RRM2), a downstream target of HNRNPK involved in the DNA damage response. Last but not least, we showed that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9orf72 RNA toxicity zebrafish model. Overall, our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9orf72 ALS and demonstrates its link with an aberrant DNA damage response, opening novel therapeutic avenues for C9orf72 ALS/FTD.

Heat shock protein Grp78/BiP/HspA5 binds directly to TDP-43 and mitigates toxicity associated with disease pathology

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with no cure or effective treatment in which TAR DNA Binding Protein of 43 kDa (TDP-43) abnormally accumulates into misfolded protein aggregates in affected neurons. It is widely accepted that protein misfolding and aggregation promotes proteotoxic stress. The molecular chaperones are a primary line of defense against proteotoxic stress, and there has been long-standing interest in understanding the relationship between chaperones and aggregated protein in ALS. Of particular interest are the heat shock protein of 70 kDa (Hsp70) family of chaperones. However, defining which of the 13 human Hsp70 isoforms is critical for ALS has presented many challenges. To gain insight into the specific Hsp70 that modulates TDP-43, we investigated the relationship between TDP-43 and the Hsp70s using proximity-dependent biotin identification (BioID) and discovered several Hsp70 isoforms associated with TDP-43 in the nucleus, raising the possibility of an interaction with native TDP-43. We further found that HspA5 bound specifically to the RNA-binding domain of TDP-43 using recombinantly expressed proteins. Moreover, in a Drosophila strain that mimics ALS upon TDP-43 expression, the mRNA levels of the HspA5 homologue (Hsc70.3) were significantly increased. Similarly we observed upregulation of HspA5 in prefrontal cortex neurons from human ALS patients. Finally, overexpression of HspA5 in Drosophila rescued TDP-43-induced toxicity, suggesting that upregulation of HspA5 may have a compensatory role in ALS pathobiology.

Loss of aly/ALYREF suppresses toxicity in both tau and TDP-43 models of neurodegeneration

Neurodegenerative diseases with tau pathology, or tauopathies, include Alzheimer's disease and related dementia disorders. Previous work has shown that loss of the poly(A) RNA-binding protein gene sut-2/MSUT2 strongly suppressed tauopathy in Caenorhabditis elegans, human cell culture, and mouse models of tauopathy. However, the mechanism of suppression is still unclear. Recent work has shown that MSUT2 protein interacts with the THO complex and ALYREF, which are components of the mRNA nuclear export complex. Additionally, previous work showed ALYREF homolog Ref1 modulates TDP-43 and G4C2 toxicity in Drosophila melanogaster models. We used transgenic C. elegans models of tau or TDP-43 toxicity to investigate the effects of loss of ALYREF function on tau and TDP-43 toxicity. In C. elegans, three genes are homologous to human ALYREF: aly-1, aly-2, and aly-3. We found that loss of C. elegans aly gene function, especially loss of both aly-2 and aly-3, suppressed tau-induced toxic phenotypes. Loss of aly-2 and aly-3 was also able to suppress TDP-43-induced locomotor behavior deficits. However, loss of aly-2 and aly-3 had divergent effects on mRNA and protein levels as total tau protein levels were reduced while mRNA levels were increased, but no significant effects were seen on total TDP-43 protein or mRNA levels. Our results suggest that although aly genes modulate both tau and TDP-43-induced toxicity phenotypes, the molecular mechanisms of suppression are different and separated from impacts on mRNA and protein levels. Altogether, this study highlights the importance of elucidating RNA-related mechanisms in both tau and TDP-43-induced toxicity.

A system-wide mislocalization of RNA-binding proteins in motor neurons is a new feature of ALS

Amyotrophic lateral sclerosis (ALS) is a motor neuron disease characterized by progressive degeneration of motor neurons. Mislocalization of TAR DNA-binding protein 43 (TDP-43) is an early event in the formation of cytoplasmic TDP-43-positive inclusions in motor neurons and a hallmark of ALS. However, the underlying mechanism and the pathogenic impact of this mislocalization are relatively unexplored. We previously reported that abnormal AMPK activation mediates TDP-43 mislocalization in motor neurons of humans and mice with ALS. In the present study, we hypothesized that other nuclear proteins are mislocalized in the cytoplasm of motor neurons due to the AMPK-mediated phosphorylation of importin-α1 and subsequently contribute to neuronal degeneration in ALS. To test this hypothesis, we analyzed motor neurons of sporadic ALS patients and found that when AMPK is activated, importin-α1 is abnormally located in the nucleus. Multiple integrative molecular and cellular approaches (including proteomics, immunoprecipitation/western blot analysis, immunohistological evaluations and gradient analysis of preribosomal complexes) were employed to demonstrate that numerous RNA binding proteins are mislocalized in a rodent motor neuron cell line (NSC34) and human motor neurons derived from iPSCs during AMPK activation. We used comparative proteomic analysis of importin-α1 complexes that were immunoprecipitated with a phosphorylation-deficient mutant of importin-α1 (importin-α1-S105A) and a phosphomimetic mutant of importin-α1 (importin-α1-S105D) to identify 194 proteins that have stronger affinity for the unphosphorylated form than the phosphorylated form of importin-α1. Furthermore, GO and STRING analyses suggested that RNA processing and protein translation is the major machinery affected by abnormalities in the AMPK-importin-α1 axis. Consistently, the expression of importin-α1-S105D alters the assembly of preribosomal complexes and increases cell apoptosis. Collectively, we propose that by impairing importin-α1-mediated nuclear import, abnormal AMPK activation in motor neurons alters the cellular distribution of many RNA-binding proteins, which pathogenically affect multiple cellular machineries in motor neurons and contribute to ALS pathogenesis.

Fly for ALS: Drosophila modeling on the route to amyotrophic lateral sclerosis modifiers

Amyotrophic lateral sclerosis (ALS) is a rare, devastating disease, causing movement impairment, respiratory failure and ultimate death. A plethora of genetic, cellular and molecular mechanisms are involved in ALS signature, although the initiating causes and progressive pathological events are far from being understood. Drosophila research has produced seminal discoveries for more than a century and has been successfully used in the past 25 years to untangle the process of ALS pathogenesis, and recognize potential markers and novel strategies for therapeutic solutions. This review will provide an updated view of several ALS modifiers validated in C9ORF72, SOD1, FUS, TDP-43 and Ataxin-2 Drosophila models. We will discuss basic and preclinical findings, illustrating recent developments and novel breakthroughs, also depicting unsettled challenges and limitations in the Drosophila-ALS field. We intend to stimulate a renewed debate on Drosophila as a screening route to identify more successful disease modifiers and neuroprotective agents.

Exploring the alternative: Fish, flies and worms as preclinical models for ALS

Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disorder characterized by the loss of upper and lower motor neurons. In general, patients succumb to respiratory insufficiency due to respiratory muscle weakness. Despite many promising therapeutic strategies primarily identified in rodent models, patient trials remain rather unsuccessful. There is a clear need for alternative approaches, which could provide directions towards the justified use of rodents and which increase the likelihood to identify new promising clinical candidates. In the last decades, the use of fast genetic approaches and the development of high-throughput screening platforms in the nematode Caenorhabditis elegans, in the fruit fly (Drosophila melanogaster) and in zebrafish (Danio rerio) have contributed to new insights into ALS pathomechanisms, disease modifiers and therapeutic targets. In this mini-review, we provide an overview of these alternative small animal studies, modeling the most common ALS genes and discuss the most recent preclinical discoveries. We conclude that small animal models will not replace rodent models, yet they clearly represent an important asset for preclinical studies.

Triad of TDP43 control in neurodegeneration: autoregulation, localization and aggregation

Cytoplasmic aggregation of TAR DNA-binding protein 43 (TDP43; also known as TARDBP or TDP-43) is a key pathological feature of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). TDP43 typically resides in the nucleus but can shuttle between the nucleus and the cytoplasm to exert its multiple functions, which include regulation of the splicing, trafficking and stabilization of RNA. Cytoplasmic mislocalization and nuclear loss of TDP43 have both been associated with ALS and FTD, suggesting that calibrated levels and correct localization of TDP43 - achieved through an autoregulatory loop and tightly controlled nucleocytoplasmic transport - safeguard its normal function. Furthermore, TDP43 can undergo phase transitions, including its dispersion into liquid droplets and its accumulation into irreversible cytoplasmic aggregates. Thus, autoregulation, nucleocytoplasmic transport and phase transition are all part of an intrinsic control system regulating the physiological levels and localization of TDP43, and together are essential for the cellular homeostasis that is affected in neurodegenerative disease.

RNA dependent suppression of C9orf72 ALS/FTD associated neurodegeneration by Matrin-3

The most common genetic cause of amyotrophic lateral sclerosis (ALS) is a GGGGCC (G4C2) hexanucleotide repeat expansions in first intron of the C9orf72 gene. The accumulation of repetitive RNA sequences can mediate toxicity potentially through the formation of intranuclear RNA foci that sequester key RNA-binding proteins (RBPs), and non-ATG mediated translation into toxic dipeptide protein repeats. However, the contribution of RBP sequestration to the mechanisms underlying RNA-mediated toxicity remain unknown. Here we show that the ALS-associated RNA-binding protein, Matrin-3 (MATR3), colocalizes with G4C2 RNA foci in patient tissues as well as iPSC-derived motor neurons harboring the C9orf72 mutation. Hyperexpansion of C9 repeats perturbed subcellular distribution and levels of endogenous MATR3 in C9-ALS patient-derived motor neurons. Interestingly, we observed that ectopic expression of human MATR3 strongly mitigates G4C2-mediated neurodegeneration in vivo. MATR3-mediated suppression of C9 toxicity was dependent on the RNA-binding domain of MATR3. Importantly, we found that expression of MATR3 reduced the levels of RAN-translation products in mammalian cells in an RNA-dependent manner. Finally, we have shown that knocking down endogenous MATR3 in C9-ALS patient-derived iPSC neurons decreased the presence of G4C2 RNA foci in the nucleus. Overall, these studies suggest that MATR3 genetically modifies the neuropathological and the pathobiology of C9orf72 ALS through modulating the RNA foci and RAN translation.

Quality-control mechanisms targeting translationally stalled and C-terminally extended poly(GR) associated with ALS/FTD

Maintaining the fidelity of nascent peptide chain (NP) synthesis is essential for proteome integrity and cellular health. Ribosome-associated quality control (RQC) serves to resolve stalled translation, during which untemplated Ala/Thr residues are added C terminally to stalled peptide, as shown during C-terminal Ala and Thr addition (CAT-tailing) in yeast. The mechanism and biological effects of CAT-tailing-like activity in metazoans remain unclear. Here we show that CAT-tailing-like modification of poly(GR), a dipeptide repeat derived from amyotrophic lateral sclerosis with frontotemporal dementia (ALS/FTD)-associated GGGGCC (G4C2) repeat expansion in C9ORF72, contributes to disease. We find that poly(GR) can act as a mitochondria-targeting signal, causing some poly(GR) to be cotranslationally imported into mitochondria. However, poly(GR) translation on mitochondrial surface is frequently stalled, triggering RQC and CAT-tailing-like C-terminal extension (CTE). CTE promotes poly(GR) stabilization, aggregation, and toxicity. Our genetic studies in Drosophila uncovered an important role of the mitochondrial protease YME1L in clearing poly(GR), revealing mitochondria as major sites of poly(GR) metabolism. Moreover, the mitochondria-associated noncanonical Notch signaling pathway impinges on the RQC machinery to restrain poly(GR) accumulation, at least in part through the AKT/VCP axis. The conserved actions of YME1L and noncanonical Notch signaling in animal models and patient cells support their fundamental involvement in ALS/FTD.

Altered MICOS Morphology and Mitochondrial Ion Homeostasis Contribute to Poly(GR) Toxicity Associated with C9-ALS/FTD

Amyotrophic lateral sclerosis (ALS) manifests pathological changes in motor neurons and various other cell types. Compared to motor neurons, the contribution of the other cell types to the ALS phenotypes is understudied. G4C2 repeat expansion in C9ORF72 is the most common genetic cause of ALS along with frontotemporal dementia (C9-ALS/FTD), with increasing evidence supporting repeat-encoded poly(GR) in disease pathogenesis. Here, we show in Drosophila muscle that poly(GR) enters mitochondria and interacts with components of the Mitochondrial Contact Site and Cristae Organizing System (MICOS), altering MICOS dynamics and intra-subunit interactions. This impairs mitochondrial inner membrane structure, ion homeostasis, mitochondrial metabolism, and muscle integrity. Similar mitochondrial defects are observed in patient fibroblasts. Genetic manipulation of MICOS components or pharmacological restoration of ion homeostasis with nigericin effectively rescue the mitochondrial pathology and disease phenotypes in both systems. These results implicate MICOS-regulated ion homeostasis in C9-ALS pathogenesis and suggest potential new therapeutic strategies.

Alcohol Causes Lasting Differential Transcription in Drosophila Mushroom Body Neurons

Repeated alcohol experiences can produce long-lasting memories for sensory cues associated with intoxication. These memories can problematically trigger relapse in individuals recovering from alcohol use disorder (AUD). The molecular mechanisms by which ethanol changes memories to become long-lasting and inflexible remain unclear. New methods to analyze gene expression within precise neuronal cell types can provide further insight toward AUD prevention and treatment. Here, we used genetic tools in Drosophila melanogaster to investigate the lasting consequences of ethanol on transcription in memory-encoding neurons. Drosophila rely on mushroom body (MB) neurons to make associative memories, including memories of ethanol-associated sensory cues. Differential expression analyses revealed that distinct transcripts, but not genes, in the MB were associated with experiencing ethanol alone compared to forming a memory of an odor cue associated with ethanol. Adult MB-specific knockdown of spliceosome-associated proteins demonstrated the necessity of RNA-processing in ethanol memory formation. These findings highlight the dynamic, context-specific regulation of transcription in cue-encoding neurons, and the lasting effect of ethanol on transcript usage during memory formation.

Modeling Neurodegenerative Disorders in Drosophila melanogaster

Drosophila melanogaster provides a powerful genetic model system in which to investigate the molecular mechanisms underlying neurodegenerative diseases. In this review, we discuss recent progress in Drosophila modeling Alzheimer's Disease, Parkinson's Disease, Amyotrophic Lateral Sclerosis (ALS), Huntington's Disease, Ataxia Telangiectasia, and neurodegeneration related to mitochondrial dysfunction or traumatic brain injury. We close by discussing recent progress using Drosophila models of neural regeneration and how these are likely to provide critical insights into future treatments for neurodegenerative disorders.

The Role of Lozenge in Drosophila Hematopoiesis

Drosophila hematopoiesis is comparable to mammalian differentiation of myeloid lineages, and therefore, has been a useful model organism in illustrating the molecular and genetic basis for hematopoiesis. Multiple novel regulators and signals have been uncovered using the tools of Drosophila genetics. A Runt domain protein, lozenge, is one of the first players recognized and closely studied in the hematopoietic lineage specification. Here, we explore the role of lozenge in determination of prohemocytes into a special class of hemocyte, namely the crystal cell, and discuss molecules and signals controlling the lozenge function and its implication in immunity and stress response. Given the highly conserved nature of Runt domain in both invertebrates and vertebrates, studies in Drosophila will enlighten our perspectives on Runx-mediated development and pathologies.

Genome wide analysis reveals heparan sulfate epimerase modulates TDP-43 proteinopathy

Pathological phosphorylated TDP-43 protein (pTDP) deposition drives neurodegeneration in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-TDP). However, the cellular and genetic mechanisms at work in pathological TDP-43 toxicity are not fully elucidated. To identify genetic modifiers of TDP-43 neurotoxicity, we utilized a Caenorhabditis elegans model of TDP-43 proteinopathy expressing human mutant TDP-43 pan-neuronally (TDP-43 tg). In TDP-43 tg C. elegans, we conducted a genome-wide RNAi screen covering 16,767 C. elegans genes for loss of function genetic suppressors of TDP-43-driven motor dysfunction. We identified 46 candidate genes that when knocked down partially ameliorate TDP-43 related phenotypes; 24 of these candidate genes have conserved homologs in the human genome. To rigorously validate the RNAi findings, we crossed the TDP-43 transgene into the background of homozygous strong genetic loss of function mutations. We have confirmed 9 of the 24 candidate genes significantly modulate TDP-43 transgenic phenotypes. Among the validated genes we focused on, one of the most consistent genetic modifier genes protecting against pTDP accumulation and motor deficits was the heparan sulfate-modifying enzyme hse-5, the C. elegans homolog of glucuronic acid epimerase (GLCE). We found that knockdown of human GLCE in cultured human cells protects against oxidative stress induced pTDP accumulation. Furthermore, expression of glucuronic acid epimerase is significantly decreased in the brains of FTLD-TDP cases relative to normal controls, demonstrating the potential disease relevance of the candidate genes identified. Taken together these findings nominate glucuronic acid epimerase as a novel candidate therapeutic target for TDP-43 proteinopathies including ALS and FTLD-TDP.

The protein TDP-43 forms aggregates in disease-affected neurons in patients with ALS and FTLD-TDP. In addition, mutations in the human gene coding for TDP-43 can cause inherited ALS. By expressing human mutant TDP-43 protein in C. elegans neurons, we have modelled aspects of ALS pathobiology. This animal model exhibits severe motor dysfunction, progressive neurodegeneration, and accumulation of abnormally modified TDP-43 protein. To identify genes controlling TDP-43 neurotoxicity in C. elegans, we have conducted a genome-wide reverse genetic screen and found 46 genes that participate in TDP-43 neurotoxicity. We demonstrated that one of them, glucuronic acid epimerase, is decreased in patients with FTLD-TDP suggesting inhibitors of glucuronic acid epimerase could have therapeutic value for ALS and FTLD.