Nollen EAA et al. (2004) Proc Natl Acad Sci U S A "Genome-wide RNA interference screen identifies previously undescribed regulators of polyglutamine aggregation."

Plasterk RHA, Garcia SM, Kim S, Nollen EAA, Van Haaften G, Morimoto RI, Chavez A

[Proc Natl Acad Sci U S A, 2004]

Protein misfolding and the formation of aggregates are increasingly recognized components of the pathology of human genetic disease and hallmarks of many neurodegenerative disorders. As exemplified by polyglutamine diseases, the propensity for protein misfolding is associated with the length of polyglutamine expansions and age-dependent changes in protein-folding homeostasis, suggesting a critical role for a protein homeostatic buffer. To identify the complement of protein factors that protects cells against the formation of protein aggregates, we tested transgenic Caenorhabditis elegans strains expressing polyglutamine expansion yellow fluorescent protein fusion proteins at the threshold length associated with the age-dependent appearance of protein aggregation. We used genome-wide RNA interference to identify genes that, when suppressed, resulted in the premature appearance of protein aggregates. Our screen identified 186 genes corresponding to five principal classes of polyglutamine regulators: genes involved in RNA metabolism, protein synthesis, protein folding, and protein degradation; and those involved in protein trafficking. We propose that each of these classes represents a molecular machine collectively comprising the protein homeostatic buffer that responds to the expression of damaged proteins

Koopman M et al. (2019) Methods Mol Biol "C. elegans as a Model for Synucleinopathies and Other Neurodegenerative Diseases: Tools and Techniques."

Seinstra RI, Nollen EAA, Koopman M

[Methods Mol Biol, 2019]

Caenorhabditis elegans is widely used to investigate biological processes related to health and disease. Multiple C. elegans models for human neurodegenerative diseases do exist, including those expressing human -synuclein. Even though these models do not feature all pathological and molecular hallmarks of the disease they mimic, they allow for the identification and dissection of molecular pathways that are involved. In line with this, genetic screens have yielded multiple modifiers of proteotoxicity in C. elegans models for neurodegenerative diseases. Here, we describe a set of common screening approaches and tools that can be used to study synucleinopathies and other neurodegenerative diseases in C. elegans. RNA interference and mutagenesis screens can be used to find genes that affect proteotoxicity, while relatively simple molecular, cellular (fractionation studies), metabolic (respiration studies), and behavioral (thrashing and crawling) readouts can be used to study the effects of disease proteins and modifiers more closely.

Koopman M et al. (2021) BMC Biol "An economical and highly adaptable optogenetics system for individual and population-level manipulation of Caenorhabditis elegans."

Janssen L, Nollen EAA, Koopman M

[BMC Biol, 2021]

BACKGROUND: Optogenetics allows the experimental manipulation of excitable cells by a light stimulus without the need for technically challenging and invasive procedures. The high degree of spatial, temporal, and intensity control that can be achieved with a light stimulus, combined with cell type-specific expression of light-sensitive ion channels, enables highly specific and precise stimulation of excitable cells. Optogenetic tools have therefore revolutionized the study of neuronal circuits in a number of models, including Caenorhabditis elegans. Despite the existence of several optogenetic systems that allow spatial and temporal photoactivation of light-sensitive actuators in C. elegans, their high costs and low flexibility have limited wide access to optogenetics. Here, we developed an inexpensive, easy-to-build, modular, and adjustable optogenetics device for use on different microscopes and worm trackers, which we called the OptoArm. RESULTS: The OptoArm allows for single- and multiple-worm illumination and is adaptable in terms of light intensity, lighting profiles, and light color. We demonstrate OptoArm's power in a population-based multi-parameter study on the contributions of motor circuit cells to age-related motility decline. We found that individual components of the neuromuscular system display different rates of age-dependent deterioration. The functional decline of cholinergic neurons mirrors motor decline, while GABAergic neurons and muscle cells are relatively age-resilient, suggesting that rate-limiting cells exist and determine neuronal circuit ageing. CONCLUSION: We have assembled an economical, reliable, and highly adaptable optogenetics system which can be deployed to address diverse biological questions. We provide a detailed description of the construction as well as technical and biological validation of our set-up. Importantly, use of the OptoArm is not limited to C. elegans and may benefit studies in multiple model organisms, making optogenetics more accessible to the broader research community.

Koopman M et al. (2023) MicroPubl Biol "Neuronal overexpression of hTDP-43 in Caenorhabditis elegans impairs motor function."

Koopman M, Seinstra RI, Nollen EAA, Gungordu L

[MicroPubl Biol, 2023]

Transactive response DNA binding-protein 43 (TDP-43) is a conserved RNA/DNA-binding protein with a role in RNA metabolism and homeostasis. Aberrant TDP-43 functioning has been considered a major culprit in amyotrophic lateral sclerosis (ALS). <i>Caenorhabditis elegans</i> can be used to phenocopy ALS <i>in vivo</i> . Since disrupted locomotion is a strong readout of toxicity, we examined multiple motor phenotypes of a <i>C. elegans</i> model expressing human wild-type <i>TDP-43</i> ( <i>hTDP-43</i> ) pan-neuronally. Our data reveal that impaired locomotion includes more than the common deficits in crawling capacity and the presence of early-onset paralysis. We show that reduced thrashing, abnormal coiling, and decreased pharyngeal pumping are also observed, in a temperature-dependent fashion.

Sin O et al. (2018) Bio Protoc "Filter Retardation Assay for Detecting and Quantifying Polyglutamine Aggregates Using Caenorhabditis elegans Lysates."

Nollen EAA, Mata-Cabana A, Sin O, Seinstra RI

[Bio Protoc, 2018]

Protein aggregation is a hallmark of several neurodegenerative diseases and is associated with impaired protein homeostasis. This imbalance is caused by the loss of the protein's native conformation, which ultimately results in its aggregation or abnormal localization within the cell. Using a <i>C. elegans</i> model of polyglutamine diseases, we describe in detail the filter retardation assay, a method that captures protein aggregates in a cellulose acetate membrane and allows its detection and quantification by immunoblotting.

Koopman M et al. (2023) MicroPubl Biol "Neuronal overexpression of hTDP-43 in Caenorhabditis elegans impairs different neuronally controlled behaviors and decreases fecundity."

Nollen EAA, Gungordu L, Koopman M, Seinstra RI

[MicroPubl Biol, 2023]

Cytoplasmic inclusions consisting of transactive response DNA-binding protein 43 (TDP-43) are a key hallmark of TDP-43 proteinopathies like amyotrophic lateral sclerosis (ALS). Caenorhabditis elegans is considered a useful model for studying the molecular mechanisms underlying TDP-43 toxicity in vivo . Here, we assessed different neuronal systems through established behavioral assays and extended the phenotypic characterisation of a C. elegans model expressing wildtype human TDP-43 ( hTDP-43 ) pan-neuronally. Our data show that neuronal expression of hTDP-43 in C. elegans disrupts chemotaxis and decreases fecundity. The basal slowing response, on the other hand, appears to be preserved in the presence of hTDP-43.

Koopman M et al. (2023) MicroPubl Biol "Neuronal overexpression of human TDP-43 in Caenorhabditis elegans causes a range of sensorimotor phenotypes."

Seinstra RI, Koopman M, Nollen EAA, Gungordu L

[MicroPubl Biol, 2023]

Mata-Cabana A et al. (2018) Bio Protoc "Nuclear/Cytoplasmic Fractionation of Proteins from Caenorhabditis elegans."

Nollen EAA, Sin O, Mata-Cabana A, Seinstra RI

[Bio Protoc, 2018]

<i>C. elegans</i> is widely used to investigate biological processes related to health and disease. To study protein localization, fluorescently-tagged proteins can be used <i>in vivo</i> or immunohistochemistry can be performed in whole worms. Here, we describe a technique to localize a protein of interest at a subcellular level in <i>C. elegans</i> lysates, which can give insight into the location, function and/or toxicity of proteins.

Koopman M et al. (2023) MicroPubl Biol "Neuronal overexpression of hTDP-43 in Caenorhabditis elegans mimics the cellular pathology commonly observed in TDP-43 proteinopathies."

Nollen EAA, Seinstra RI, Hogewerf W, Koopman M, Gungordu L

[MicroPubl Biol, 2023]

Inclusions consisting of transactive response DNA-binding protein 43 (TDP-43) are a characteristic feature of amyotrophic lateral sclerosis (ALS). <i>Caenorhabditis elegans</i> has been instrumental in studying the underlying mechanisms of TDP-43 pathology. Here, we extend the possibilities of previous studies by examining a <i>C. elegans</i> model expressing human wild-type <i>TDP-43</i> ( <i>hTDP-43</i> ) pan-neuronally. We show that disease-related (hyper)phosphorylation and cytosolic localisation of hTDP-43 are present in hTDP-43 worms and that these features can be enhanced by adjusting the environmental temperature.

Van Haaften G et al. (2004) Proc Natl Acad Sci U S A "Gene interactions in the DNA damage-response pathway identified by genome-wide RNA-interference analysis of synthetic lethality."

Vastenhouw NL, Plasterk RHA, Van Haaften G, Tijsterman M, Nollen EAA

[Proc Natl Acad Sci U S A, 2004]

Here, we describe a systematic search for synthetic gene interactions in a multicellular organism, the nematode Caenorhabditis elegans. We established a high-throughput method to determine synthetic gene interactions by genome-wide RNA interference and identified genes that are required to protect the germ line against DNA double-strand breaks. Besides known DNA-repair proteins such as the C. elegans orthologs of TopBP1, RPA2, and RAD51, eight genes previously unassociated with a double-strand-break response were identified. Knockdown of these genes increased sensitivity to ionizing radiation and camptothecin and resulted in increased chromosomal nondisjunction. All genes have human orthologs that may play a role in human carcinogenesis.