Biology subjects

Wu, W.-J.

Publications and source records attributed to Wu, W.-J..

13 recordsLinked to original sources

bioRxiv2026

An adenylyl cyclase switch reroutes carbon from growth to virulence lipids in Mycobacterium tuberculosis

Anti-TB drugs act non-uniformly on Mycobacterium tuberculosis (Mtb) because of its distinct physiological states across diverse infection niches shaped by host-derived nutrients and stresses. Agonists of the adenylyl cyclase Rv1625c are a novel drug class that selectively inhibits Mtb growth in macrophages and cholesterol-rich conditions by an unknown mechanism. Combining condition-resolved transcriptomics, genome-scale metabolic modeling, and genetic perturbation, we show these agonists cause a blockade in the electron transport chain, which likely activates Rv1625c. The elevated cAMP in turn drives global transcriptional and post-translational remodeling of central carbon and lipid metabolism. The resulting methylcitrate cycle reversal chokes cholesterol breakdown products from entering central metabolism, diverting carbon toward cell wall and virulence-lipid (phthiocerol dimycocerosate) synthesis and inhibiting growth. These drugs thus hijack an endogenous switch that reroutes carbon from biomass to virulence-lipid production. Hence, nutrients that restore carbon flux and relieve ETC blockade reduce activity, whereas Rv1625c overexpression and ETC inhibitors potentiate drug action even in refractory conditions.

systems biology↗

bioRxiv2026

Monocyte-amplified transcriptional signatures of human diseases

Blood-based biomarkers discovered by machine learning often lack disease specificity and cross-population robustness for clinical applications. We describe a biomarker discovery strategy that exploits monocytes as circulating sentinels to amplify disease-perturbed signals in blood. This strategy leverages monocyteMINER, a mechanistic transcriptional regulatory network inferred from monocyte transcriptomes of 1,202 healthy individuals. As proof-of-concept, we uncovered a 31-gene atherosclerosis-perturbed network that underpins disease etiology, identifying diagnostic signatures for coronary artery disease (ARAP2, P2RY14, FKBP15) and acute myocardial infarction (SERPINA1, ASGR2). For tuberculosis (TB), monocyteMINER uncovered a 5-gene signature (MAS_TB_META5: ANKRD22, AIM2, VAMP5, GBP5, TGM2) from just 438 samples. MAS_TB_META5 outperformed 77 existing signatures across 18 cohorts (>4,400 patients, 12 countries), achieving WHO target product profile for high-sensitivity screening (including in advanced HIV patients), and predicting TB progression up to 5 years before diagnosis. Thus, our findings show that monocyteMINER offers a generalizable platform for discovering clinically actionable biomarkers for diverse diseases.

systems biology↗

bioRxiv2025

Host oxidative stress primes mycobacteria for rapid antibiotic resistance evolution

The rapid emergence of multidrug-resistant Mycobacterium tuberculosis (Mtb) threatens global TB control, yet the mechanisms enabling rapid evolution of drug resistance in Mtb remain poorly understood. Here we reveal that pre-existing mutations in oxidative stress response genes create permissive genomic backgrounds that accelerate high-level isoniazid resistance (INHR) without fitness costs, challenging the paradigm that resistance mutations always precede their fitness compensatory adaptations. Using M. smegmatis mc2155 (Msm) as a model, we show that brief exposure to sublethal INH (2x IC50) enriches for "low-level resistance and tolerance" (LLRT) mutants in a single step. These LLRT mutants, particularly those with ohrR loss-of-function mutations, acquire high-level resistance (> 500x IC50) at 6-fold higher rates than wildtype, primarily through otherwise-deleterious mycothiol biosynthesis mutations that become tolerable in the oxidative stress-buffered background. Crucially, we demonstrate that sublethal oxidative stress alone, mimicking host immune pressure, nearly tripled the rate of INH resistance evolution in Msm. Bayesian analysis of 1,578 clinical Mtb isolates from Vietnam confirmed that mutations in oxidative stress response genes were significantly associated with the emergence of INHR strains (p-value = 1.09x10-7). Independently, reanalysis of genome-wide CRISPRi screens revealed that the OSR network and high Bayes probability genes are functionally associated with treatment escape and survival with multiple antibiotics, including isoniazid, rifampicin, ethambutol, bedaquiline, vancomycin, clarithromycin, linezolid, and streptomycin. Our findings that host-imposed oxidative stress and inadequate drug penetration may synergistically prime Mtb populations for rapid resistance evolution suggest that targeting pre-resistance mechanisms, such as oxidative stress defenses, could help slow the emergence of antibiotic resistance in tuberculosis.

microbiology↗

bioRxiv2025

Heat-responsive dynamic shifts in alternative splicing of the coral Acropora cervicornis

Climate change has caused drastic declines in corals. As sessile organisms, response to shifting environmental conditions may include changes in gene expression, epigenetic modifications, or the microbiome, but as of yet, a common mechanism of stress response, alternative splicing (AS), has been underexplored in corals. Using short-term acute thermal stress assays, we investigated patterns of AS in the scleractinian coral Acropora cervicornis during response to and a subsequent overnight recovery phase from low (33), medium (35), and high (37) levels of heat stress. We find that 40% of the genomic gene set is subject to AS. Our findings demonstrate conserved and dynamic shifts in splicing profiles during the heat treatment and subsequent recovery phase. AS increased in response to heat stress and was primarily dominated by intron retention in specific classes of transcripts, including those related to splicing regulation itself. While AS returned to baseline levels post-exposure to low heat, AS persisted even after reprieve from higher levels of heat stress. Partial overlap of AS transcripts with differentially expressed genes suggests that AS may represent a distinct and previously underappreciated regulatory mechanism for thermal stress response in corals.

genomics↗

bioRxiv2024

Genomes of Wiebesia fig wasps reveal the adaptation and codiversification in fig-fig wasp mutualism

Figs and fig wasps represent one of the most intimate examples of plant-pollinator coevolution. As figs diversified into geographically isolated populations, both figs and fig wasps underwent selective pressures driven by local adaptation and coevolution. Ficus pumila comprises two ecologically distinct varieties: the creeping fig (F. pumila var. pumila), which is widely distributed across the lowlands of East Asia, and the jelly fig (F. pumila var. awkeotsang), endemic to Taiwan and found at mid-elevations. To elucidate how codiversification with fig hosts influences the evolutionary trajectories of fig wasps, we analyzed the genomes of Wiebesia sp. 2 and sp. 3, the respective pollinators of creeping fig and jelly fig. Our demographic analysis indicates that vicariance during the Last Glacial Period facilitated ecological differentiation between these two fig-fig wasp pairs. Through comparative and population genomic analyses, we identified selection signals linked to habitat adaptation, with evolutionary rates corresponding to the life history traits of their host figs. Variations in host preference behavior, chemosensory gene expression, and adaptive duplications in olfactory receptors highlight potential mechanisms for adaptation to host floral scents. These findings collectively underscore how the obligate mutualism between figs and their pollinating wasps allows the ecological traits and habitat preferences of fig hosts to shape the evolutionary pathways of their pollinators, leaving distinct molecular imprints in the fig wasp genomes. This study demonstrates the capacity of tightly intertwined life cycles between plants and pollinators to drive adaptation and diversification.

evolutionary biology↗

bioRxiv2024

Gene Regulatory Network topology governs resistance and treatment escape in glioma stem-like cells

Poor prognosis and drug resistance in glioblastoma (GBM) manifests from heterogeneity and treatment-induced shifts in phenotypic states of tumor cells, including dedifferentiation to glioma stem-like cells (GSCs). This rare tumorigenic cell subpopulation is inherently resistant to temozolomide, undergoes proneural-to-mesenchymal transition (PMT) to evade therapy, and thereby drives recurrence. Through inference of transcriptional regulatory networks (TRNs) of patient-derived GSCs (PD-GSCs) at single-cell resolution, we demonstrate how topology of transcription factor interactions drives distinct trajectories of cell state transitions of susceptible and resistant PD-GSCs in response to cytotoxic drug treatment. By experimentally testing TRN simulation-based predictions, we show that drug treatment drives surviving cells of a PD-GSC along a trajectory of intermediate states, akin to a bottleneck in gene expression space, exposing vulnerability to potentiated killing by sequential addition of siRNA or a second drug targeting transcriptional programs governing non-genetic plasticity of a PD-GSC. Thus, our findings demonstrate an approach to uncover and use TRN topology of a PD-GSC to rationally predict combinatorial and sequential treatments that block treatment escape and acquired resistance in GBM.

systems biology↗

bioRxiv2022

Single-cell Sequencing Highlights Heterogeneity and Malignant Progression in Actinic Keratosis and Cutaneous Squamous Cell Carcinoma

Cutaneous squamous cell carcinoma (cSCC) is the second most frequent of the keratinocyte-derived malignancies with actinic keratosis (AK) as a precancerous lesion. To comprehensively delineate the underlying mechanisms for the whole progression from normal skin to AK to invasive cSCC, we performed single-cell RNA-seq (scRNA-seq) to acquire the transcriptomes of 138,982 cells from 13 samples of six patients including AK, squamous cell carcinoma in situ (SCCIS), cSCC and their matched normal tissues, covering comprehensive clinical courses of cSCC. We identified diverse cell types, including important subtypes with different gene expression profiles and functions in major keratinocytes. In SCCIS, we discovered the malignant subtypes of basal cells with differential proliferative and migration potential. Differentially expressed genes (DEGs) analysis screened out multiple key driver genes including transcription factors (TFs) along AK to cSCC progression. Immunohistochemistry (IHC) / immunofluorescence (IF) experiments and single-cell ATAC sequencing (scATAC-seq) data verified the expression changes of these genes. The functional experiments confirmed the important roles of these genes in regulating cell proliferation, apoptosis, migration and invasion in cSCC tumor. Furthermore, we comprehensively described the tumor microenvironment (TME) landscape and potential keratinocyte-TME crosstalk in cSCC providing theoretical basis for immunotherapy. Together, our findings provide a valuable resource for deciphering the progression from AK to cSCC and identifying potential targets for anticancer treatment of cSCC.

cancer biology↗

bioRxiv2022

A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon

The scale of post-transcriptional regulation and the implications of its interplay with other forms of regulation on environmental acclimation is underexplored for organisms of the domain Archaea. Here, we have investigated the scale of post-transcriptional regulation in the extremely halophilic archaeon Halobacterium salinarum NRC-1 by integrating transcriptome-wide locations of transcript processing sites (TPS) and SmAP1 binding, genome-wide locations of antisense RNAs (asRNAs), and consequences of RNase_2099C knockout on differential expression of all genes. This integrated analysis has discovered that 54% of all protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for putative post-transcriptional processing and regulation, with about 20% of genes likely regulated by combinatorial schemes involving SmAP1, asRNAs, and RNase_2099C. Comparative analysis of mRNA levels (RNA-Seq) and protein levels (SWATH-MS) for 2,579 genes over four phases of batch culture growth in complex medium has generated additional evidence for conditional post-transcriptional regulation of 7% of all protein-coding genes. We demonstrate that post-transcriptional regulation may act to fine-tune specialized and rapid acclimation to stressful environments, e.g., as a switch to turn on gas vesicle biogenesis to promote vertical relocation in anoxic conditions and to modulate frequency of transposition by IS elements of the IS200/IS605, IS4, and ISH3 families. Findings from this study are provided as an atlas in a public web resource (https://halodata.systemsbiology.net). IMPORTANCEWhile the transcriptional regulation landscape of archaea has been extensively investigated, we currently have limited knowledge about post-transcriptional regulation and its driving mechanisms in this domain of life. In this study, we collected and integrated omics data from multiple sources and technologies to infer post-transcriptionally regulated genes and the putative mechanisms modulating their expression at the protein level in Halobacterium salinarum NRC-1. The results suggest that post-transcriptional regulation may drive environmental acclimation by regulating hallmark biological processes. To foster discoveries by other research groups interested in the topic, we extended our integrated data to the public in the form of an interactive atlas (https://halodata.systemsbiology.net).

systems biology↗

bioRxiv2021

MtrA regulation of essential peptidoglycan cleavage in Mycobacterium tuberculosis during infection

The success of Mycobacterium tuberculosis (Mtb) is largely due to its ability to withstand multiple stresses encountered in the host. Here, we present a data-driven model that captures the dynamic interplay of environmental cues and genome-encoded regulatory programs in Mtb. The model captures the genome-wide distribution of cis-acting gene regulatory elements and the conditional influences of transcription factors at those elements to elicit environment-specific responses. Analysis of transcriptional responses that may be essential for Mtb to survive acidic stress within the maturing macrophage, identified regulatory control by the MtrAB two-component signal system. Using genome-wide transcriptomics as well as imaging studies, we have characterized the MtrAB circuit by tunable CRISPRi knockdown in both Mtb and the non-pathogenic organism, M. smegmatis (Msm). These experiments validated the essentiality of MtrA in Mtb, but not Msm. We identified that MtrA regulates multiple enzymes that cleave cell wall peptidoglycan and is required for efficient cell division. Moreover, our results suggest that peptidoglycan cleavage, regulated by MtrA, is necessary for Mtb to survive intracellular stress. Further, we present MtrA as an attractive drug target, as even weak repression of mtrA results in loss of Mtb viability and completely clears the bacteria with low-dose isoniazid or rifampicin treatment.

systems biology↗

bioRxiv2021

A single-cell based precision medicine approach using glioblastoma patient-specific models

Glioblastoma (GBM) is a heterogeneous tumor made up of cell states that evolve over time. Here, we modeled tumor evolutionary trajectories during standard-of-care treatment using multimodal single-cell analysis of a primary tumor sample, corresponding mouse xenografts subjected to standard of care therapy, and recurrent tumor at autopsy. We mined the multimodal data with single cell SYstems Genetics Network AnaLysis (scSYGNAL) to identify a network of 52 regulators that mediate treatment-induced shifts in xenograft tumor-cell states that were also reflected in recurrence. By integrating scSYGNAL-derived regulatory network information with transcription factor accessibility deviations derived from single-cell ATAC-seq data, we developed consensus networks that regulate subpopulations of primary and recurrent tumor cells. Finally, by matching targeted therapies to active regulatory networks underlying tumor evolutionary trajectories, we provide a framework for applying single-cell-based precision medicine approaches in a concurrent, neo-adjuvant, or recurrent setting. SummaryInference of mechanistic drivers of therapy-induced evolution of glioblastoma at single cell resolution using RNA-seq and ATAC-seq from patient samples and model systems undergoing standard-of-care treatment informs strategy for identification of tumor evolutionary trajectories and possible cell state-directed therapeutics.

systems biology↗

bioRxiv2020

Predictive regulatory and metabolic network models for systems analysis of Clostridioides difficile

Though Clostridioides difficile is among the most studied anaerobes, the interplay of metabolism and regulation that underlies its ability to colonize the human gut is unknown. We have compiled public resources into three models and a portal to support comprehensive systems analysis of C. difficile. First, by leveraging 151 transcriptomes from 11 studies we generated a regulatory model (EGRIN) that organizes 90% of C. difficile genes into 297 high quality conditional co-regulation modules. EGRIN predictions, validated with independent datasets, recapitulated and extended regulons of key transcription factors, implicating new genes for sporulation, carbohydrate transport and metabolism. Second, by advancing a metabolic model, we discovered that 15 amino acids, diverse carbohydrates, and 10 metabolic genes are essential for C. difficile growth within an intestinal environment. Finally, by integrating EGRIN with the metabolic model, we developed a PRIME model that revealed unprecedented insights into combinatorial control of essential processes for in vivo colonization of C. difficile and its interactions with commensals. We have developed an interactive web portal (http://networks.systemsbiology.net/cdiff-portal/) to disseminate all data, algorithms, and models to support collaborative systems analyses of C. difficile.

systems biology↗

bioRxiv2020

Genetic program activity delineates risk, relapse, and therapy responsiveness in Multiple Myeloma

Despite recent advancements in the treatment of multiple myeloma (MM), nearly all patients ultimately relapse and many become refractory to their previous therapies. Although many therapies exist with diverse mechanisms of action, it is not yet clear how the differences in MM biology across patients impacts the likelihood of success for existing therapies and those in the pipeline. Therefore, we not only need the ability to predict which patients are at high risk for disease progression, but also a means to understand the mechanisms underlying their risk. We hypothesized that knowledge of the biological networks that give rise to MM, specifically the transcriptional regulatory network (TRN) and the mechanisms by which mutations impact gene regulation, would enable improved predictions of disease progression and actionable insights for treatment. Here we present a method to infer TRNs from multi-omics data and apply it to the generation of a MM TRN that links chromosomal abnormalities and somatic mutations to downstream effects on gene expression via perturbation of transcriptional regulators. We find that 141 genetic programs underlie the disease and that the activity profile of these programs fall into one of 25 distinct transcriptional states. These transcriptional signatures prove to be more predictive of outcomes than do mutations and reveal plausible mechanisms for relapse, including the establishment of an immuno-suppressive microenvironment. Moreover, we observe subtype-specific vulnerabilities to interventions with existing drugs and motivate the development of new targeted therapies that appear especially promising for relapsed refractory MM.

systems biology↗

bioRxiv2019

Defective intestinal repair after short-term high fat diet due to loss of efferocytosis

Defective tissue repair is a hallmark of many inflammatory disorders including, inflammatory bowel disease (IBD). While it is clear that high fat diets (HFD) can exacerbate inflammatory disease by increasing inflammation, the direct effect of lipids on tissue homeostasis and repair remains undefined. We show here that short term exposure to HFD directly impairs barrier repair after intestinal epithelial damage by interfering with recognition and uptake of apoptotic neutrophils by intestinal macrophages. Apoptotic neutrophil uptake induces macrophage IL-10 production, which is lacking after intestinal damage in the context of HFD. Overexpression of IL-10 rescues repair defects after HFD treatment, but not if epithelial cells lack the IL-10 receptor, highlighting the key role of IL-10 in barrier repair. These findings demonstrate a previously unidentified mechanism by which dietary lipids directly interfere with homeostatic processes required to maintain tissue integrity.

cell biology↗