Wang Z (2024) Methods Mol Biol "Caenorhabditis elegans as an In Vivo Model Organism to Elucidate Teratogenic Effects."

Wang Z

[Methods Mol Biol, 2024]

Exogenous teratogens contribute to approximately 10% of the human abnormality with exposure occurrence during the prenatal and fetal period. However, the assessment methods and underlying mechanism remain unclear. The nematode Caenorhabditis elegans has been recognized as one of the ideal model animals for toxicologic research as convenient culture, low cost, and complete phenotypes and genomic profiling. This chapter describes the protocols about the estimations on the teratogenic effects using nematodes as model organisms, including the growth, development, behavior, reproduction, energy balance, and transgenes.

Wang Z et al. (2010) BMC Genomics "Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation."

Martin J, Wang Z, Hawdon J, Mitreva M, Wilson RK, Abubucker S

[BMC Genomics, 2010]

BACKGROUND: Hookworm infection is one of the most important neglected diseases in developing countries, with approximately 1 billion people infected worldwide. To better understand hookworm biology and nematode parasitism, the present study generated a near complete transcriptome of the canine hookworm Ancylostoma caninum to a very high coverage using high throughput technology, and compared it to those of the free-living nematode Caenorhabditis elegans and the parasite Brugia malayi. RESULTS: The generated transcripts from four developmental stages, infective L3, serum stimulated L3, adult male and adult female, covered 93% of the A. caninum transcriptome. The broad diversity among nematode transcriptomes was confirmed, and an impact of parasitic adaptation on transcriptome diversity was inferred. Intra-population analysis showed that A. caninum has higher coding sequence diversity than humans. Examining the developmental expression profiles of A. caninum revealed major transitions in gene expression from larval stages to adult. Adult males expressed the highest number of selectively expressed genes, but adult female expressed the highest number of selective parasitism-related genes. Genes related to parasitism adaptation and A. caninum specific genes exhibited more expression selectivity while those conserved in nematodes tend to be consistently expressed. Parasitism related genes were expressed more selectively in adult male and female worms. The comprehensive analysis of digital expression profiles along with transcriptome comparisons enabled identification of a set of parasitism genes encoding secretory proteins in animal parasitic nematode. CONCLUSIONS: This study validated the usage of deep sequencing for gene expression profiling. Parasitic adaptation of the canine hookworm is related to its diversity and developmental dynamics. This comprehensive comparative genomic and expression study substantially improves our understanding of the basic biology and parasitism of hookworms and, is expected, in the long run, to accelerate research toward development of vaccines and novel anthelmintics.

Wang Z et al. (2018) Bioinformatics "Deep Reinforcement Learning of Cell Movement in the Early Stage of C. elegans Embryogenesis."

Li H, Xu Y, Bao Z, Li C, Wang Z, Wang D

[Bioinformatics, 2018]

Motivation: Cell movement in the early phase of C. elegans development is regulated by a highly complex process in which a set of rules and connections are formulated at distinct scales. Previous efforts have demonstrated that agent-based, multi-scale modeling systems can integrate physical and biological rules and provide new avenues to study developmental systems. However, the application of these systems to model cell movement is still challenging and requires a comprehensive understanding of regulatory networks at the right scales. Recent developments in deep learning and reinforcement learning provide an unprecedented opportunity to explore cell movement using 3D time-lapse microscopy images. Results: We present a deep reinforcement learning approach within an agent-based modeling system to characterize cell movement in the embryonic development of C. elegans. Our modeling system captures the complexity of cell movement patterns in the embryo and overcomes the local optimization problem encountered by traditional rule-based, agent-based modeling that uses greedy algorithms. We tested our model with two real developmental processes: the anterior movement of the Cpaaa cell via intercalation and the rearrangement of the superficial left-right asymmetry. In the first case, the model results suggested that Cpaaa's intercalation is an active directional cell movement caused by the continuous effects from a longer distance (farther than the length of two adjacent cells), as opposed to a passive movement caused by neighbor cell movements. In the second case, a leader-follower mechanism well explained the collective cell movement pattern in the asymmetry rearrangement. These results showed that our approach to introduce deep reinforcement learning into agent-based modeling can test regulatory mechanisms by exploring cell migration paths in a reverse engineering perspective. This model opens new doors to explore the large datasets generated by live imaging. Availability: Source code is available at https://github.com/zwang84/drl4cellmovement. Contact: dwang7@utk.edu, baoz@mskcc.org. Supplementary information: Supplementary data are available at Bioinformatics online.

Wang Z et al. (2023) Nat Commun "ACS-20/FATP4 mediates the anti-ageing effect of dietary restriction in C. elegans."

Zang X, Zhang S, Wu Z, Zou L, Wu D, Zhu M, Wang Z, Zhu H, Zhang Y, Wang Q, Lan J, Zhang H, Chen D

[Nat Commun, 2023]

Dietary restriction is an effective anti-ageing intervention across species. However, the molecular mechanisms from the metabolic aspects of view are still underexplored. Here we show ACS-20 as a key mediator of dietary restriction on healthy ageing from a genetic screen of the C. elegans acyl-CoA synthetase family. ACS-20 functions in the epidermis during development to regulate dietary restriction-induced longevity. Functional transcriptomics studies reveal that elevated expression of PTR-8/Patched is responsible for the proteostasis and lifespan defects of acs-20. Furthermore, the conserved NHR-23 nuclear receptor serves as a transcriptional repressor of ptr-8 and a key regulator of dietary restriction-induced longevity. Mechanistically, a specific region in the ptr-8 promoter plays a key role in mediating the transcription regulation and lifespan extension under dietary restriction. Altogether, these findings identify a highly conserved lipid metabolism enzyme as a key mediator of dietary restriction-induced lifespan and healthspan extension and reveal the downstream transcriptional regulation mechanisms.

Wang Z et al. (2022) Nat Mach Intell "Hierarchical deep reinforcement learning reveals novel mechanism of cell movement."

Bao Z, Yang J, Wang D, Wang Z, Xu Y

[Nat Mach Intell, 2022]

Time-lapse images of cells and tissues contain rich information of dynamic cell behaviors, which reflect the underlying processes of proliferation, differentiation and morphogenesis. However, we lack computational tools for effective inference. Here, we exploit Deep Reinforcement Learning (DRL) to infer cell-cell interactions and collective cell behaviors in tissue morphogenesis from 3D, time-lapse images. We used Hierarchical DRL (HDRL), known for multiscale learning and data efficiency, to examine cell migrations based on images with ubiquitous nuclear label and simple rules formulated from empirical statistics of the images. When applied to C. elegans embryogenesis, HDRL reveals a multi-phase, modular organization of cell movement. Imaging with additional cellular markers confirms the modular organization as a novel migration mechanism, which we term sequential rosettes. Furthermore, HDRL forms a transferable model that successfully differentiates sequential rosettes-based migration from others. Our study demonstrates a powerful approach to infer the underlying biology from time-lapse imaging without prior knowledge.

Wang Z et al. (2019) J Cell Sci "The RBG-1/RBG-2 complex modulates autophagy activity by regulating lysosomal biogenesis and function."

Zhao H, Zhao D, Zhang H, Sun Y, Wang Z, Yuan C, Wang X

[J Cell Sci, 2019]

Vici syndrome is a severe and progressive multisystem disease caused by mutations in the <i>EPG5</i> gene. In patient tissues and animal models, loss of <i>EPG5</i> function is associated with defective autophagy caused by accumulation of non-degradative autolysosomes, but very little is known about the mechanism underlying this cellular phenotype. Here we demonstrated that loss of function of the RBG-1/RBG-2 complex ameliorates the autophagy defect in <i>epg-5</i> mutants. The suppression effect is independent of the complex's activity as a RAB-3 GAP and a RAB-18 GEF. Loss of <i>rbg-1</i> activity promotes lysosomal biogenesis and function, and also suppresses the accumulation of non-functional autolysosomes in <i>epg-5</i> mutants. The mobility of late endosome/lysosome-associated RAB-7 is reduced in <i>epg-5</i> mutants, and this defect is rescued by simultaneous loss of function of <i>rbg-1</i> Expression of the GDP-bound form of RAB-7 also promotes lysosomal biogenesis and suppresses the autophagy defect in <i>epg-5</i> mutants. Our study reveals that the RBG-1/RBG-2 complex acts by modulating the dynamics of membrane-associated RAB-7 to regulate lysosomal biogenesis, and provides insights into the pathogenesis of Vici syndrome.

Wang Z et al. (2019) J Am Soc Mass Spectrom "Proteomic Analysis of FNR-Regulated Anaerobiosis in Salmonella Typhimurium."

Sun J, Tian M, Wang Z, Fu J, Yan A, Liu X, Xu Z, Liu Y

[J Am Soc Mass Spectrom, 2019]

Bacterial pathogens such as Salmonella enterica serovar Typhimurium (S. Typhimurium) have to cope with fluctuating oxygen levels during infection within host gastrointestinal tracts. The global transcription factor FNR (fumarate nitrate reduction) plays a vital role in the adaptation of enteric bacteria to the low oxygen environment. Nevertheless, a comprehensive profile of the FNR regulon on the proteome level is still lacking in S. Typhimurium. Herein, we quantitatively profiled S. Typhimurium proteome of an fnr-deletion mutant during anaerobiosis in comparison to its parental strain. Notably, we found that FNR represses the expression of virulence genes of Salmonella pathogenicity island 1 (SPI-1) and negatively regulates propanediol utilization by directly binding to the promoter region of the pdu operon. Importantly, we provided evidence that S. Typhimurium lacking fnr exhibited increased antibiotics susceptibility and membrane permeability as well. Furthermore, genetic deletion of fnr leads to decreased bacterial survival in a Caenorhabditis elegans infection model, highlighting an important role of this regulator in mediating host-pathogen interactions.

Wang Z et al. (2015) PLoS Genet "The nuclear receptor DAF-12 regulates nutrient metabolism and reproductive growth in nematodes."

Stoltzfus J, Lok JB, You YJ, Kliewer SA, Tang H, Mangelsdorf DJ, Wang Z, Ranjit N, Xie Y

[PLoS Genet, 2015]

Appropriate nutrient response is essential for growth and reproduction. Under favorable nutrient conditions, the C. elegans nuclear receptor DAF-12 is activated by dafachronic acids, hormones that commit larvae to reproductive growth. Here, we report that in addition to its well-studied role in controlling developmental gene expression, the DAF-12 endocrine system governs expression of a gene network that stimulates the aerobic catabolism of fatty acids. Thus, activation of the DAF-12 transcriptome coordinately mobilizes energy stores to permit reproductive growth. DAF-12 regulation of this metabolic gene network is conserved in the human parasite, Strongyloides stercoralis, and inhibition of specific steps in this network blocks reproductive growth in both of the nematodes. Our study provides a molecular understanding for metabolic adaptation of nematodes to their environment, and suggests a new therapeutic strategy for treating parasitic diseases.

Wang Z et al. (2016) PLoS One "An Observation-Driven Agent-Based Modeling and Analysis Framework for C. elegans Embryogenesis."

Ramsey BJ, Bao Z, Wang E, Wang Z, Wong K, Wang D, Li H

[PLoS One, 2016]

With cutting-edge live microscopy and image analysis, biologists can now systematically track individual cells in complex tissues and quantify cellular behavior over extended time windows. Computational approaches that utilize the systematic and quantitative data are needed to understand how cells interact in vivo to give rise to the different cell types and 3D morphology of tissues. An agent-based, minimum descriptive modeling and analysis framework is presented in this paper to study C. elegans embryogenesis. The framework is designed to incorporate the large amounts of experimental observations on cellular behavior and reserve data structures/interfaces that allow regulatory mechanisms to be added as more insights are gained. Observed cellular behaviors are organized into lineage identity, timing and direction of cell division, and path of cell movement. The framework also includes global parameters such as the eggshell and a clock. Division and movement behaviors are driven by statistical models of the observations. Data structures/interfaces are reserved for gene list, cell-cell interaction, cell fate and landscape, and other global parameters until the descriptive model is replaced by a regulatory mechanism. This approach provides a framework to handle the ongoing experiments of single-cell analysis of complex tissues where mechanistic insights lag data collection and need to be validated on complex observations.

Wang Z et al. (2014) J Cell Biol "UNC-6 (netrin) stabilizes oscillatory clustering of the UNC-40 (DCC) receptor to orient polarity."

Wang Z, Ziel JW, Linden LM, Sherwood DR, Chi Q, Hagedorn EJ, Naegeli KM, Savage NS

[J Cell Biol, 2014]

The receptor deleted in colorectal cancer (DCC) directs dynamic polarizing activities in animals toward its extracellular ligand netrin. How DCC polarizes toward netrin is poorly understood. By performing live-cell imaging of the DCC orthologue UNC-40 during anchor cell invasion in Caenorhabditis elegans, we have found that UNC-40 clusters, recruits F-actin effectors, and generates F-actin in the absence of UNC-6 (netrin). Time-lapse analyses revealed that UNC-40 clusters assemble, disassemble, and reform at periodic intervals in different regions of the cell membrane. This oscillatory behavior indicates that UNC-40 clusters through a mechanism involving interlinked positive (formation) and negative (disassembly) feedback. We show that endogenous UNC-6 and ectopically provided UNC-6 orient and stabilize UNC-40 clustering. Furthermore, the UNC-40-binding protein MADD-2 (a TRIM family protein) promotes ligand-independent clustering and robust UNC-40 polarization toward UNC-6. Together, our data suggest that UNC-6 (netrin) directs polarized responses by stabilizing UNC-40 clustering. We propose that ligand-independent UNC-40 clustering provides a robust and adaptable mechanism to polarize toward netrin.