Gomez Saldivar, Georgina et al. (2021) International Worm Meeting "Tissue-specific transcription footprinting in C. elegans using RNA PoI DamID (RAPID) and Nanopore sequencing"

Meister, Peter, Glauser, Dominique A., Gomez Saldivar, Georgina

[International Worm Meeting, 2021]

Differential gene expression across cell types is a major determinant of multicellular organism development and physiology. In C. elegans, it is notoriously difficult to characterize individual cell types due to the difficulty to obtain comprehensive tissue-specific gene transcription data. Available methods require tissue dissociation and cell sorting from large worm populations or the use of transgenic approaches to purify transcripts from the target cell type. This can be challenging when the considered cell type is hard to separate from surrounding cells or is a rare cell type. Here, we present the RNA Pol DamID (RAPID) approach, in which the Dam methyltransferase is fused to a ubiquitous RNA polymerase subunit in order to create transcriptional footprints via methyl marks on the DNA of transcribed genes. We implemented a Cre-lox recombination system to target specific tissue and 3rd generation sequencing (Oxford Nanopore Technologies) to eliminate the need for an external sequencing facility and streamline data acquisition to achieve analyses from DNA extraction to sequencing results in less than a week. To validate the method, we determined the polymerase footprints in whole animals and in different tissues from intact young adults. We obtained meaningful transcriptional footprints in line with RNA-seq studies in whole animals, muscle and intestine. To challenge the sensitivity of RAPID and demonstrate its utility to determine novel tissue-specific transcriptional profiles, we determined the transcriptional footprints of the pair of XXX cells, representing 0.2% of the somatic cell content of the animals. We identified 2362 genes potentially transcribed in XXX cells, among which the few known XXX markers, such as daf-9 and sdf-9. Using transcriptional reporters for a subset of new hits, we confirmed that the majority of them were indeed expressed in XXX. Interestingly, results of a gene ontology analysis on a refined list of 275 genes, whose expression is strongly enriched in XXX cells as compared to other profiled tissues, are in line with the endocrine function of these cells, with implications in signalling and dauer formation. A transcription factor predictive tool also revealed an association with specific transcription factors playing a role in dauer formation. Taken together, our work establishes RAPID as a valid method for the determination of polymerase footprints in specific tissues of C. elegans without the need for cell sorting or RNA tagging.

Jordan, Aurore et al. (2021) International Worm Meeting "Human pain gene ortholog screen in C. elegans"

Lia, Andrei-Stefan, Glauser, Dominique A., Jordan, Aurore

[International Worm Meeting, 2021]

Chronic pain affects up to 30% of the population and can be caused by different factors such as injuries or genetic mutations. Chronic pain can take various forms like migraines, different musculoskeletal conditions (low back pain, fibromyalgia), neuropathic pain disorders triggered by cancer or diabetes, as well as visceral pain disorders. Available drugs are not always effective and could trigger many undesirable side effects. In the recent years, genes responsible for those pathologies have been screened in the population with methods, such as linkage analysis and genome wide association studies. Those approaches have revealed a plethora of new candidates but, for the majority of them, we know nothing about their function in the pain pathway. Because studies on pain in human are very limited, we propose C. elegans as a complementary model organism to study conserved nociception genes. In the present study, we first determined a list of C. elegans orthologs for candidate human pain genes reported in the literature and recovered available mutants (109 mutants). We then screened these mutants for alterations in noxious heat-evoked reversals using as high-throughput, computer-assisted behavior analysis pipeline. Using different heat intensities and comparing naive animals with animals repeatedly stimulated with heat, we obtained a set of measures reflecting baseline sensitivity profiles, and the ability to adapt (desensitize) in response to repeated stimuli. Twenty-two mutants displayed significant alterations and could be clustered in different categories, including fast-adapting mutants, non-adapting mutants, and mutants with exacerbated naive sensitivity. As a whole, our study suggests that C. elegans represent a promising model to tackle the function of recently identified human pain-associated genes and set the bases for additional studies on specific candidates. Topics: neurobiology, behavior Keywords: noxious heat avoidance; sensory plasticity; pain modelling

Driesschaert, Brecht et al. (2022) MicroPubl Biol

Driesschaert, Brecht, Temmerman, Liesbet

[MicroPubl Biol, 2022]

The Q system is a genetic tool developed to deliver spatiotemporal control over gene expression (Giles et al. 1991; Potter et al. 2010; Wei et al. 2012). Although it has already been adapted for use in C. elegans by Wei et al. in 2012, to date, the Q system has not been applied extensively in this nematode. In the relatively few available reports, it is mainly used to constitutively restrict gene expression in a spatial manner (e.g. Schild et al. 2014; Schild and Glauser 2015; Jee et al. 2016; Tolstenkov et al. 2018; Chiyoda et al. 2021), while but a handful of studies also explore the temporal aspect of the system (Matus et al. 2015; Yuan et al. 2016; Cottee et al. 2017; Hoang and Miller 2017). We aimed to apply this tool in the C. elegans nervous system to gain both spatial and temporal control over expression of a gene encoding a reporter protein that is targeted to the secretory pathway. Despite our efforts, we here report that in our hands, the Q system is not suitable for application in the neurons due to a lack of dynamic range.

Quartey MO et al. (2021) Sci Rep "The A(1-38) peptide is a negative regulator of the A(1-42) peptide implicated in Alzheimer disease progression."

Pennington PR, Heistad RM, Nyarko JNK, Barnes JR, Bolanos MAC, Parsons MP, Knudsen KJ, De Carvalho CE, Leary SC, Mousseau DD, Buttigieg J, Maley JM, Quartey MO

[Sci Rep, 2021]

The pool of -Amyloid (A) length variants detected in preclinical and clinical Alzheimer disease (AD) samples suggests a diversity of roles for A peptides. We examined how a naturally occurring variant, e.g. A(1-38), interacts with the AD-related variant, A(1-42), and the predominant physiological variant, A(1-40). Atomic force microscopy, Thioflavin T fluorescence, circular dichroism, dynamic light scattering, and surface plasmon resonance reveal that A(1-38) interacts differently with A(1-40) and A(1-42) and, in general, A(1-38) interferes with the conversion of A(1-42) to a -sheet-rich aggregate. Functionally, A(1-38) reverses the negative impact of A(1-42) on long-term potentiation in acute hippocampal slices and on membrane conductance in primary neurons, and mitigates an A(1-42) phenotype in Caenorhabditis elegans. A(1-38) also reverses any loss of MTT conversion induced by A(1-40) and A(1-42) in HT-22 hippocampal neurons and APOE 4-positive human fibroblasts, although the combination of A(1-38) and A(1-42) inhibits MTT conversion in APOE 4-negative fibroblasts. A greater ratio of soluble A(1-42)/A(1-38) [and A(1-42)/A(1-40)] in autopsied brain extracts correlates with an earlier age-at-death in males (but not females) with a diagnosis of AD. These results suggest that A(1-38) is capable of physically counteracting, potentially in a sex-dependent manner, the neuropathological effects of the AD-relevant A(1-42).

Danielle Thierry-Mieg et al. (2003) Worm Breeder's Gazette "www.wormgenes.org , a new gene centered database"

Vahan Simonyan, Michel Potdevin, Mark Sienkiewicz, Yuji KOHARA, Jean Thierry-Mieg, Danielle Thierry-Mieg, Tadasu SHIN-I

[Worm Breeder's Gazette, 2003]

Wormgenes is a new resource for C.elegans offering a detailed summary about each gene and a powerful query system.

Cao M et al. (2018) MicroPubl Biol "Application of the red-shifted channelrhodopsin Chrimson for the Caenorhabditis elegans cGAL bipartite system"

Cao M, Liu J, Chai C, Sternberg PW

[MicroPubl Biol, 2018]

Channelrhodopsins are light-gated ion channels that serve as photoreceptors in photosynthetic microbes and have been applied as crucial optogenetic tools in genetic model organisms. When expressed in animals, they enable light-inducible control of ionic membrane permeability, which directly manipulates the activity of neurons expressing the protein. The application of channelrhodopsin-based optogenetics is particularly powerful when used in conjugation with the cGAL (GAL4-UAS) bipartite system (Wang et al., 2017). The mating of neuron-specific GAL4 driver lines to new channelrhodopsin effector lines could expand the genetic toolkit to perturb and manipulate neural circuits in the organism. Blue light-gated channelrhodopsins have been widely used in Caenorhabditis elegans neurobiology but often have to be performed in lite-1(ce314) mutant backgrounds because short-wavelength blue light is an aversive cue in wild-type animals and directly affects C. elegans neuronal physiology. Previously, a red light-gated variant of channelrhodopsin, termed Chrimson, has been successfully applied in fruit fly and mice, and has recently been codon-optimized for use in C. elegans (Klapoetke et al., 2014; Schild and Glauser, 2015). Here, we constructed a Chrimson (15xUAS::chrimson::gfp) cGAL effector line. We introduced the UAS::chrimson::gfp effector DNA construct as an extrachromosomal array into a previously published cGAL pan-neuronal driver line (PS6961 syIs334) and generated integrants on chromosome II (PS8023, syIs503) and chromosome V (PS8024, syIs504) (Table 1) via standard X-ray irradiation. We showed Chrimson-GFP expression in the C. elegans head and tail neurons (Fig. 1A-1D). We also showed that red light could induce a seizure-like motility phenotype in C. elegans expressing Chrimson-GFP in a pan-neuronal manner (videos), while the negative controls expressing only the effector, or without light induction showed regular motility as expected (Table 2). The body curvature maps from normal and seizure-like motilities showed distinct patterns (Fig. 1E and 1F). We report the effector construct of red-light-gated channelrhodopsin Chrimson as an addition to our cGAL toolkit, which could be widely used in future research to overcome the technical restrictions of blue light-gated channelrhodopsins in C. elegans.

Tangrodchanapong T et al. (2020) Front Pharmacol "Frondoside A Attenuates Amyloid- Proteotoxicity in Transgenic Caenorhabditis elegans by Suppressing Its Formation."

Tangrodchanapong T, Sobhon P, Meemon K

[Front Pharmacol, 2020]

Oligomeric assembly of Amyloid- (A) is the main toxic species that contribute to early cognitive impairment in Alzheimer's patients. Therefore, drugs that reduce the formation of A oligomers could halt the disease progression. In this study, by using transgenic <i>Caenorhabditis elegans</i> model of Alzheimer's disease, we investigated the effects of frondoside A, a well-known sea cucumber <i>Cucumaria frondosa</i> saponin with anti-cancer activity, on A aggregation and proteotoxicity. The results showed that frondoside A at a low concentration of 1 M significantly delayed the worm paralysis caused by A aggregation as compared with control group. In addition, the number of A plaque deposits in transgenic worm tissues was significantly decreased. Frondoside A was more effective in these activities than ginsenoside-Rg3, a comparable ginseng saponin. Immunoblot analysis revealed that the level of small oligomers as well as various high molecular weights of A species in the transgenic <i>C. elegans</i> were significantly reduced upon treatment with frondoside A, whereas the level of A monomers was not altered. This suggested that frondoside A may primarily reduce the level of small oligomeric forms, the most toxic species of A. Frondoside A also protected the worms from oxidative stress and rescued chemotaxis dysfunction in a transgenic strain whose neurons express A. Taken together, these data suggested that low dose of frondoside A could protect against A-induced toxicity by primarily suppressing the formation of A oligomers. Thus, the molecular mechanism of how frondoside A exerts its anti-A aggregation should be studied and elucidated in the future.

Hodgkin JA (1998) International Journal of Developmental Biology "Seven types of pleiotropy."

Hodgkin JA

[International Journal of Developmental Biology, 1998]

Pleiotropy , a situation in which a single gene influences multiple phenotypic tra its, can arise in a variety of ways. This paper discusses possible underlying mechanisms and proposes a classification of the various phenomena involved.

Tuck S (2011) Curr Biol "Extracellular vesicles: budding regulated by a phosphatidylethanolamine translocase."

Tuck S

[Curr Biol, 2011]

Recent work on a Caenorhabditis elegans transmembrane ATPase reveals a central role for the aminophospholipid phosphatidylethanolamine in the production of a class of extracellular vesicles.

Viney ME et al. (2004) Naturwissenschaften "Is dauer pheromone of Caenorhabditis elegans really a pheromone?"

Viney ME, Franks NR

[Naturwissenschaften, 2004]

Animals respond to signals and cues in their environment. The difference between a signal (e.g. a pheromone) and a cue (e.g. a waste product) is that the information content of a signal is subject to natural selection, whereas that of a cue is not. The model free-living nematode Caenorhabditis elegans forms an alternative developmental morph (the dauer larva) in response to a so-called 'dauer pheromone', produced by all worms. We suggest that the production of 'dauer pheromone' has no fitness advantage for an individual worm and therefore we propose that 'dauer pheromone' is not a signal, but a cue. Thus, it should not be called a pheromone.