Chen X et al. (2019) Phys Rev E "Searching for collective behavior in a small brain."

Bialek W, Leifer AM, Randi F, Chen X

[Phys Rev E, 2019]

In large neuronal networks, it is believed that functions emerge through the collective behavior of many interconnected neurons. Recently, the development of experimental techniques that allow simultaneous recording of calcium concentration from a large fraction of all neurons in Caenorhabditis elegans-a nematode with 302 neurons-creates the opportunity to ask whether such emergence is universal, reaching down to even the smallest brains. Here, we measure the activity of 50+ neurons in C. elegans, and analyze the data by building the maximum entropy model that matches the mean activity and pairwise correlations among these neurons. To capture the graded nature of the cells' responses, we assign each cell multiple states. These models, which are equivalent to a family of Potts glasses, successfully predict higher statistical structure in the network. In addition, these models exhibit signatures of collective behavior: the state of single cells can be predicted from the state of the rest of the network; the network, despite being sparse in a way similar to the structural connectome, distributes its response globally when locally perturbed; the distribution over network states has multiple local maxima, as in models of memory; and the parameters that describe the real network are close to a critical surface in this family of models.

Chen X et al. (2012) Science "Nucleosomes suppress spontaneous mutations base-specifically in eukaryotes."

Chen X, Su Z, Chen Z, Lin F, Shi S, Yang J, He X, Chen H

[Science, 2012]

It is unknown how the composition and structure of DNA within the cell affect spontaneous mutations. Theory suggests that in eukaryotic genomes, nucleosomal DNA undergoes fewer CT mutations because of suppressed cytosine hydrolytic deamination relative to nucleosome-depleted DNA. Comparative genomic analyses and a mutation accumulation experiment showed that nucleosome occupancy nearly eliminated cytosine deamination, resulting in an ~50% decrease of the CT mutation rate in nucleosomal DNA. Furthermore, the rates of GT and AT mutations were also about twofold suppressed by nucleosomes. On the basis of these results, we conclude that nucleosome-dependent mutation spectra affect eukaryotic genome structure and evolution and may have implications for understanding the origin of mutations in cancers and in induced pluripotent stem cells.

Chen X et al. (2014) J Neurosci "Modulation of C. elegans touch sensitivity is integrated at multiple levels."

Chalfie M, Chen X

[J Neurosci, 2014]

Sensory systems can adapt to different environmental signals. Here we identify four conditions that modulate anterior touch sensitivity in Caenorhabditis elegans after several hours and demonstrate that such sensory modulation is integrated at multiple levels to produce a single output. Prolonged vibration involving integrin signaling directly sensitizes the touch receptor neurons (TRNs). In contrast, hypoxia, the dauer state, and high salt reduce touch sensitivity by preventing the release of long-range neuroregulators, including two insulin-like proteins. Integration of these latter inputs occurs at upstream neurohormonal cells and at the insulin signaling cascade within the TRNs. These signals and those from integrin signaling converge to modulate touch sensitivity by regulating AKT kinases and DAF-16/FOXO. Thus, activation of either the integrin or insulin pathways can compensate for defects in the other pathway. This modulatory system integrates conflicting signals from different modalities, and adapts touch sensitivity to both mechanical and non-mechanical conditions.

Chen X et al. (2015) J Neurosci "Regulation of mechanosensation in C. elegans through ubiquitination of the MEC-4 mechanotransduction channel."

Chen X, Chalfie M

[J Neurosci, 2015]

In Caenorhabditis elegans, gentle touch is sensed by the anterior (ALM and AVM) and posterior (PLM) touch receptor neurons. Anterior, but not posterior, touch is affected by several stress conditions via the action of AKT kinases and the DAF-16/FOXO transcription factor. Here we show that a ubiquitination-dependent mechanism mediates such effects. AKT-1/AKT kinase and DAF-16 alter the transcription of mfb-1, which encodes an E3 ubiquitin ligase needed for the ubiquitination of the mechanosensory channel subunit MEC-4. Ubiquitination of MEC-4 reduces the amount of MEC-4 protein in the processes of ALM neurons and, consequently, the mechanoreceptor current. Even under nonstress conditions, differences in the amount of MFB-1 appear to cause the PLM neurons to be less sensitive to touch than the ALM neurons. These studies demonstrate that modulation of surface mechanoreceptors can regulate the sensitivity to mechanical signals.

Chen X et al. (2023) Aging Cell "Impaired mitophagosome-lysosome fusion mediates olanzapine-induced aging."

Dang X, Yu Y, Zheng P, Xie Y, Chen X, Dongol A, Zheng M, Ge X, Nagaratnam N, Wang Z, Seyhan ZB, Huang XF

[Aging Cell, 2023]

The lifespan of schizophrenia patients is significantly shorter than the general population. Olanzapine is one of the most commonly used antipsychotic drugs (APDs) for treating patients with psychosis, including schizophrenia and bipolar disorder. Despite their effectiveness in treating positive and negative symptoms, prolonged exposure to APDs may lead to accelerated aging and cognitive decline, among other side effects. Here we report that dysfunctional mitophagy is a fundamental mechanism underlying accelerated aging induced by olanzapine, using in vitro and in vivo (Caenorhabditis elegans) models. We showed that the aberrant mitophagy caused by olanzapine was via blocking mitophagosome-lysosome fusion. Furthermore, olanzapine can induce mitochondrial damage and hyperfragmentation of the mitochondrial network. The mitophagosome-lysosome fusion in olanzapine-induced aging models can be restored by a mitophagy inducer, urolithin A, which alleviates defective mitophagy, mitochondrial damage, and fragmentation of the mitochondrial network. Moreover, the mitophagy inducer ameliorated behavioral changes induced by olanzapine, including shortened lifespan, and impaired health span, learning, and memory. These data indicate that olanzapine impairs mitophagy, leading to the shortened lifespan, impaired health span, and cognitive deficits. Furthermore, this study suggests the potential application of mitophagy inducers as therapeutic strategies to reverse APD-induced adverse effects associated with accelerated aging.

Chen X et al. (2024) Nat Commun "Germ granule compartments coordinate specialized small RNA production."

Yan YH, Xu D, Feng X, Mufti FUD, Jin Q, Huang X, Shi Y, Wang K, Dong MQ, Zeng C, Guang S, Chen X, Zhu C, Kennedy S

[Nat Commun, 2024]

Germ granules are biomolecular condensates present in most animal germ cells. One function of germ granules is to help maintain germ cell totipotency by organizing mRNA regulatory machinery, including small RNA-based gene regulatory pathways. The C. elegans germ granule is compartmentalized into multiple subcompartments whose biological functions are largely unknown. Here, we identify an uncharted subcompartment of the C. elegans germ granule, which we term the E granule. The E granule is nonrandomly positioned within the germ granule. We identify five proteins that localize to the E granule, including the RNA-dependent RNA polymerase (RdRP) EGO-1, the Dicer-related helicase DRH-3, the Tudor domain-containing protein EKL-1, and two intrinsically disordered proteins, EGC-1 and ELLI-1. Localization of EGO-1 to the E granule enables synthesis of a specialized class of 22G RNAs, which derive exclusively from 5' regions of a subset of germline-expressed mRNAs. Defects in E granule assembly elicit disordered production of endogenous siRNAs, which disturbs fertility and the RNAi response. Our results define a distinct subcompartment of the C. elegans germ granule and suggest that one function of germ granule compartmentalization is to facilitate the localized production of specialized classes of small regulatory RNAs.

Chen X et al. (2015) Genetics "Targeted Chromosomal Translocations and Essential Gene Knockout Using CRISPR/Cas9 Technology in Caenorhabditis elegans."

Li M, Feng X, Chen X, Guang S

[Genetics, 2015]

Many genes play essential roles in development and fertility; their disruption leads to growth arrest or sterility. Genetic balancers have been widely used to study essential genes in many organisms. However, it is technically challenging and laborious to generate and maintain the loss-of-function mutations of essential genes. The CRISPR/Cas9 technology has been successfully applied for gene editing and chromosome engineering. Here, we have developed a method to induce chromosomal translocations and produce genetic balancers using the CRISPR/Cas9 technology and have applied this approach to edit essential genes in Caenorhabditis elegans. The co-injection of dual small guide RNA targeting genes on different chromosomes resulted in reciprocal translocation between nonhomologous chromosomes. These animals with chromosomal translocations were subsequently crossed with animals that contain normal sets of chromosomes. The F1 progeny were subjected to a second round of Cas9-mediated gene editing. Through this method, we successfully produced nematode strains with specified chromosomal translocations and generated a number of loss-of-function alleles of two essential genes (csr-1 and mes-6). Therefore, our method provides an easy and efficient approach to generate and maintain loss-of-function alleles of essential genes with detailed genetic background information.

Chen X et al. (2014) Sci Rep "Dual sgRNA-directed gene knockout using CRISPR/Cas9 technology in Caenorhabditis elegans."

Ji J, Xu F, Chen X, Feng X, Guang S, Zhu C, Zhou X

[Sci Rep, 2014]

The CRISPR RNA-guided Cas9 nuclease gene-targeting system has been successfully used for genome editing in a variety of organisms. Here, we report the use of dual sgRNA-guided Cas9 nuclease to generate knockout mutants of protein coding genes, noncoding genes, and repetitive sequences in C. elegans. Co-injection of C. elegans with dual sgRNAs results in the removal of the interval between two sgRNAs and the loss-of-function phenotype of targeted genes. We sought to determine how large an interval can be eliminated and found that at least a 24 kb chromosome segment can be deleted using this dual sgRNA/Cas9 strategy. The deletion of large chromosome segments facilitates mutant screening by PCR and agarose electrophoresis. Thus, the use of the CRISPR/Cas9 system in combination with dual sgRNAs provides a powerful platform with which to easily generate gene knockout mutants in C. elegans. Our data also suggest that encoding multiple sgRNA sequences into a single CRISPR array to simultaneously edit several sites within the genome may cause the off-target deletion of chromosome sequences.

Chen X et al. (2015) Mol Neurodegener "Ethosuximide ameliorates neurodegenerative disease phenotypes by modulating DAF-16/FOXO target gene expression."

Burgoyne RD, Kashyap SS, Chen X, Barclay JW, McCueF HV, Kraemer BC, Morgan A, Wong SQ

[Mol Neurodegener, 2015]

BACKGROUND: Many neurodegenerative diseases are associated with protein misfolding/aggregation. Treatments mitigating the effects of such common pathological processes, rather than disease-specific symptoms, therefore have general therapeutic potential. RESULTS: Here we report that the anti-epileptic drug ethosuximide rescues the short lifespan and chemosensory defects exhibited by C. elegans null mutants of dnj-14, the worm orthologue of the DNAJC5 gene mutated in autosomal-dominant adult-onset neuronal ceroid lipofuscinosis. It also ameliorates the locomotion impairment and short lifespan of worms expressing a human Tau mutant that causes frontotemporal dementia. Transcriptomic analysis revealed a highly significant up-regulation of DAF-16/FOXO target genes in response to ethosuximide; and indeed RNAi knockdown of daf-16 abolished the therapeutic effect of ethosuximide in the worm dnj-14 model. Importantly, ethosuximide also increased the expression of classical FOXO target genes and reduced protein aggregation in mammalian neuronal cells. CONCLUSIONS: We have revealed a conserved neuroprotective mechanism of action of ethosuximide from worms to mammalian neurons. Future experiments in mouse neurodegeneration models will be important to confirm the repurposing potential of this well-established anti-epileptic drug for treatment of human neurodegenerative diseases.

Chen X et al. (2018) Elife "Rap2 and TNIK control Plexin-dependent tiled synaptic innervation in C. elegans."

MacVicar BA, Mizumoto K, Chen X, Weilinger NL, Shibata AC, Murakoshi H, Kurashina M, Hendi A, Fortes E

[Elife, 2018]

During development, neurons form synapses with their fate-determined targets. While we begin to elucidate the mechanisms by which extracellular ligand-receptor interactions enhance synapse specificity by inhibiting synaptogenesis, our knowledge about their intracellular mechanisms remains limited. Here we show that Rap2 GTPase (<i>rap-2</i>) and its effector, TNIK (<i>mig-15</i>), act genetically downstream of Plexin (<i>plx-1</i>) to restrict presynaptic assembly and to form tiled synaptic innervation in <i>C. elegans</i>. Both constitutively GTP- and GDP-forms of <i>rap-2</i> mutants exhibit synaptic tiling defects as <i>plx-1</i> mutants, suggesting that cycling of the RAP-2 nucleotide state is critical for synapse inhibition. Consistently, PLX-1 suppresses local RAP-2 activity. Excessive ectopic synapse formation in <i>mig-15</i> mutants causes a severe synaptic tiling defect. Conversely, overexpression of <i>mig-15</i> strongly inhibited synapse formation, suggesting that <i>mig-15</i> is a negative regulator of synapse formation. These results reveal that subcellular regulation of small GTPase activity by Plexin shapes proper synapse patterning in vivo.