Li X et al. (2025) Nature "Systems-level design principles of metabolic rewiring in an animal."

Wang W, Hodder T, Walhout AJM, Yilmaz LS, Myers CL, Li X, Zhang H

[Nature, 2025]

The regulation of metabolism is vital to any organism and can be achieved by transcriptionally activating or repressing metabolic genes^1-3. Although many examples of transcriptional metabolic rewiring have been reported⁴, a systems-level study of how metabolism is rewired in response to metabolic perturbations is lacking in any animal. Here we apply Worm Perturb-Seq (WPS)-a high-throughput method combining whole-animal RNA-interference and RNA-sequencing⁵-to around 900 metabolic genes in the nematode Caenorhabditis elegans. We derive a metabolic gene regulatory network (mGRN) in which 385 perturbations are connected to 9,414 genes by more than 110,000 interactions. The mGRN has a highly modular structure in which 22 perturbation clusters connect to 44 gene expression programs. The mGRN reveals different modes of transcriptional rewiring from simple reaction and pathway compensation to rerouting and more complex network coordination. Using metabolic network modelling, we identify a design principle of transcriptional rewiring that we name the compensation-repression (CR) model. The CR model explains most transcriptional responses in metabolic genes and reveals a high level of compensation and repression in five core metabolic functions related to energy and biomass. We provide preliminary evidence that the CR model may also explain transcriptional metabolic rewiring in human cells.

Li X et al. (2011) Mol Biochem Parasitol "Transgenesis in the parasitic nematode Strongyloides ratti."

Pearce EJ, Lok JB, Shao H, Massey HC, Nolan TJ, Viney ME, Li X, Junio A

[Mol Biochem Parasitol, 2011]

Strongyloides and related genera are advantageous subjects for transgenesis in parasitic nematodes, primarily by gonadal microinjection as has been used with Caenorhabditis elegans. Transgenesis has been achieved in Strongyloides stercoralis and in Parastrongyloides trichosuri, but both of these lack well-adapted, conventional laboratory hosts in which to derive transgenic lines. By contrast, Strongyloides ratti develops in laboratory rats with high efficiency and offers the added advantages of robust genomic and transcriptomic databases and substantial volumes of genetic, developmental and immunological data. Therefore, we evaluated methodology for transgenesis in S. stercoralis as a means of transforming S. ratti. S. stercoralis-based GFP reporter constructs were expressed in a proportion of F1 transgenic S. ratti following gonadal microinjection into parental free-living females. Frequencies of transgene expression in S. ratti, ranged from 3.7% for pAJ09 to 6.8% for pAJ20; respective frequencies for these constructs in S. stercoralis were 5.6% and 33.5%. Anatomical patterns of transgene expression were virtually identical in S. ratti and S. stercoralis. This is the first report of transgenesis in S. ratti, an important model organism for biological investigations of parasitic nematodes. Availability of the rat as a well-adapted laboratory host will facilitate derivation of transgenic lines of this parasite.

Li X et al. (2024) Cell Biochem Funct "Impacts of P4-ATPase Deletion on Membrane Asymmetry and Disease Development."

Li S, Wang Q, Zhang W, Zou W, Li X

[Cell Biochem Funct, 2024]

Phospholipids exhibit an asymmetrical distribution on the cell membrane. P4-ATPases, type IV lipid flippases, are responsible for establishing and maintaining this phospholipid compositional asymmetry. The essential β subunit CDC50 (also known as TMEM30) assists in the transport and proper functioning of P4-ATPases. Deletion of P4-ATPases and its β subunit disrupts the membrane asymmetry, impacting the growth and development and leading to various diseases affecting the nervous, skeletal muscle, digestive, and hematopoietic systems. This review discusses the crucial roles of P4-ATPases and their β subunit in Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, and mammals, offering valuable insights for future research.

Li X et al. (2019) Sci Adv "Requirement for translocon-associated protein (TRAP) in insulin biogenesis."

Arvan P, Li X, Dumas KJ, Cha J, Liu M, Flibotte S, Xu J, Qi L, Itani OA, Delaney CE, Yang J, Shih HJ, Haataja L, Hu PJ

[Sci Adv, 2019]

The mechanistic basis for the biogenesis of peptide hormones and growth factors is poorly understood. Here, we show that the conserved endoplasmic reticulum membrane translocon-associated protein (TRAP), also known as signal sequence receptor 1, plays a critical role in the biosynthesis of insulin. Genetic analysis in the nematode <i>Caenorhabditis elegans</i> and biochemical studies in pancreatic cells reveal that TRAP deletion impairs preproinsulin translocation while unexpectedly disrupting distal steps in insulin biogenesis including proinsulin processing and secretion. The association of common intronic single-nucleotide variants in the human TRAP gene with susceptibility to type 2 diabetes and pancreatic cell dysfunction suggests that impairment of preproinsulin translocation and proinsulin trafficking may contribute to the pathogenesis of type 2 diabetes.

Li X et al. (2024) J Cell Biol "Coordination of RAB-8 and RAB-11 during unconventional protein secretion."

Wang J, Shi A, Lin L, Guo YR, Liu B, Wen Y, Li X

[J Cell Biol, 2024]

Multiple physiology-pertinent transmembrane proteins reach the cell surface via the Golgi-bypassing unconventional protein secretion (UcPS) pathway. By employing C. elegans-polarized intestine epithelia, we recently have revealed that the small GTPase RAB-8/Rab8 serves as an important player in the process. Nonetheless, its function and the relevant UcPS itinerary remain poorly understood. Here, we show that deregulated RAB-8 activity resulted in impaired apical UcPS, which increased sensitivity to infection and environmental stress. We also identified the SNARE VTI-1/Vti1a/b as a new RAB-8-interacting factor involved in the apical UcPS. Besides, RAB-11/Rab11 was capable of recruiting RABI-8/Rabin8 to reduce the guanine nucleotide exchange activity of SMGL-1/GEF toward RAB-8, indicating the necessity of a finely tuned RAB-8/RAB-11 network. Populations of RAB-8- and RAB-11-positive endosomal structures containing the apical UcPS cargo moved toward the apical side. In the absence of RAB-11 or its effectors, the cargo was retained in RAB-8- and RAB-11-positive endosomes, respectively, suggesting that these endosomes are utilized as intermediate carriers for the UcPS.

Li X et al. (2014) Genetics "Synthetic cytotoxicity: digenic interactions with TEL1/ATM mutations reveal sensitivity to low doses of camptothecin."

Hieter P, O'Neil NJ, Moshgabadi N, Li X

[Genetics, 2014]

Many tumors contain mutations that confer defects in the DNA-damage response and genome stability. DNA-damaging agents are powerful therapeutic tools that can differentially kill cells with an impaired DNA-damage response. The response to DNA damage is complex and composed of a network of coordinated pathways, often with a degree of redundancy. Tumor-specific somatic mutations in DNA-damage response genes could be exploited by inhibiting the function of a second gene product to increase the sensitivity of tumor cells to a sublethal concentration of a DNA-damaging therapeutic agent, resulting in a class of conditional synthetic lethality we call synthetic cytotoxicity. We used the Saccharomyces cerevisiae nonessential gene-deletion collection to screen for synthetic cytotoxic interactions with camptothecin, a topoisomerase I inhibitor, and a null mutation in TEL1, the S. cerevisiae ortholog of the mammalian tumor-suppressor gene, ATM. We found and validated 14 synthetic cytotoxic interactions that define at least five epistasis groups. One class of synthetic cytotoxic interaction was due to telomere defects. We also found that at least one synthetic cytotoxic interaction was conserved in Caenorhabditis elegans. We have demonstrated that synthetic cytotoxicity could be a useful strategy for expanding the sensitivity of certain tumors to DNA-damaging therapeutics.

Li X et al. (2024) Nat Commun "β-synuclein regulates the phase transitions and amyloid conversion of α-synuclein."

Huang K, Yu YV, Chen H, Cheng X, Xu L, Zhang Y, Yu L, Wang C, Xue W, Shi T, Song L, Li X, Xiao Y, Liu X, Chen Y, Zheng L, Petersen RB, Li N

[Nat Commun, 2024]

Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB) are neurodegenerative disorders characterized by the accumulation of &#x3b1;-synuclein aggregates. &#x3b1;-synuclein forms droplets via liquid-liquid phase separation (LLPS), followed by liquid-solid phase separation (LSPS) to form amyloids, how this process is physiologically-regulated remains unclear. &#x3b2;-synuclein colocalizes with &#x3b1;-synuclein in presynaptic terminals. Here, we report that &#x3b2;-synuclein partitions into &#x3b1;-synuclein condensates promotes the LLPS, and slows down LSPS of &#x3b1;-synuclein, while disease-associated &#x3b2;-synuclein mutations lose these capacities. Exogenous &#x3b2;-synuclein improves the movement defects and prolongs the lifespan of an &#x3b1;-synuclein-expressing NL5901 Caenorhabditis elegans strain, while disease-associated &#x3b2;-synuclein mutants aggravate the symptoms. Decapeptides targeted at the &#x3b1;-/&#x3b2;-synuclein interaction sites are rationally designed, which suppress the LSPS of &#x3b1;-synuclein, rescue the movement defects, and prolong the lifespan of C. elegans NL5901. Together, we unveil a Yin-Yang balance between &#x3b1;- and &#x3b2;-synuclein underlying the normal and disease states of PD and DLB with therapeutical potentials.

Li X et al. (2011) PLoS Genet "Specific SKN-1/Nrf stress responses to perturbations in translation elongation and proteasome activity."

Glover-Cutter KM, Li X, Matilainen O, Blackwell TK, Holmberg CI, Jin C

[PLoS Genet, 2011]

SKN-1, the Caenorhabditis elegans Nrf1/2/3 ortholog, promotes both oxidative stress resistance and longevity. SKN-1 responds to oxidative stress by upregulating genes that detoxify and defend against free radicals and other reactive molecules, a SKN-1/Nrf function that is both well-known and conserved. Here we show that SKN-1 has a broader and more complex role in maintaining cellular stress defenses. SKN-1 sustains expression and activity of the ubiquitin-proteasome system (UPS) and coordinates specific protective responses to perturbations in protein synthesis or degradation through the UPS. If translation initiation or elongation is impaired, SKN-1 upregulates overlapping sets of cytoprotective genes and increases stress resistance. When proteasome gene expression and activity are blocked, SKN-1 activates multiple classes of proteasome subunit genes in a compensatory response. SKN-1 thereby maintains UPS activity in the intestine in vivo under normal conditions and promotes survival when the proteasome is inhibited. In contrast, when translation elongation is impaired, SKN-1 does not upregulate proteasome genes, and UPS activity is then reduced. This indicates that UPS activity depends upon presence of an intact translation elongation apparatus; and it supports a model, suggested by genetic and biochemical studies in yeast, that protein synthesis and degradation may be coupled processes. SKN-1 therefore has a critical tissue-specific function in increasing proteasome gene expression and UPS activity under normal conditions, as well as when the UPS system is stressed, but mounts distinct responses when protein synthesis is perturbed. The specificity of these SKN-1-mediated stress responses, along with the apparent coordination between UPS and translation elongation activity, may promote protein homeostasis under stress or disease conditions. The data suggest that SKN-1 may increase longevity, not only through its well-documented role in boosting stress resistance, but also through contributing to protein homeostasis.

Li X et al. (2019) Cell Rep "Systems Properties and Spatiotemporal Regulation of Cell Position Variability during Embryogenesis."

Xu W, Fan R, Zhao Z, Xiao L, Ma X, Du Z, Li X

[Cell Rep, 2019]

An intriguing question in developmental biology is how do developmental processes achieve high reproducibility among individuals? An in-depth analysis of information contained in phenotypic variability provides an important perspective to address this question. In this work, we present a quantitative and functional analysis of cell position variability during Caenorhabditis elegans embryogenesis. We find that cell position variability is highly deterministic and regulated by intrinsic and extrinsic mechanisms. Positional variability is determined by cell lineage identity and is coupled to diverse developmental properties of cells, including embryonic localization, cell contact, and left-right symmetry. Temporal dynamics of cell position variability are highly concordant, and fate specification contributes to a systems-wide reduction of variability that could provide a buffering strategy. Positional variability is stringently regulated throughout embryogenesis and cell-cell junctions function to restrict variability. Our results provide insight into systems properties and spatiotemporal control of cellular variability during development.

Li X et al. (2010) PLoS Comput Biol "Learning "graph-mer" motifs that predict gene expression trajectories in development."

Leslie C, Li X, Panea C, Wiggins CH, Reinke V

[PLoS Comput Biol, 2010]

A key problem in understanding transcriptional regulatory networks is deciphering what cis regulatory logic is encoded in gene promoter sequences and how this sequence information maps to expression. A typical computational approach to this problem involves clustering genes by their expression profiles and then searching for overrepresented motifs in the promoter sequences of genes in a cluster. However, genes with similar expression profiles may be controlled by distinct regulatory programs. Moreover, if many gene expression profiles in a data set are highly correlated, as in the case of whole organism developmental time series, it may be difficult to resolve fine-grained clusters in the first place. We present a predictive framework for modeling the natural flow of information, from promoter sequence to expression, to learn cis regulatory motifs and characterize gene expression patterns in developmental time courses. We introduce a cluster-free algorithm based on a graph-regularized version of partial least squares (PLS) regression to learn sequence patterns--represented by graphs of k-mers, or "graph-mers"--that predict gene expression trajectories. Applying the approach to wildtype germline development in Caenorhabditis elegans, we found that the first and second latent PLS factors mapped to expression profiles for oocyte and sperm genes, respectively. We extracted both known and novel motifs from the graph-mers associated to these germline-specific patterns, including novel CG-rich motifs specific to oocyte genes. We found evidence supporting the functional relevance of these putative regulatory elements through analysis of positional bias, motif conservation and in situ gene expression. This study demonstrates that our regression model can learn biologically meaningful latent structure and identify potentially functional motifs from subtle developmental time course expression data.