Temporal dynamics of stress response in Halomonas elongata to NaCl shock: physiological, metabolomic, and transcriptomic insights.

BACKGROUND: The halophilic bacterium Halomonas elongata is an industrially important strain for ectoine production, with high value and intense research focus. While existing studies primarily delve into the adaptive mechanisms of this bacterium under fixed salt concentrations, there is a notable dearth of attention regarding its response to fluctuating saline environments. Consequently, the stress response of H. elongata to salt shock remains inadequately understood. RESULTS: This study investigated the stress response mechanism of H. elongata when exposed to NaCl shock at short- and long-time scales. Results showed that NaCl shock induced two major stresses, namely osmotic stress and oxidative stress. In response to the former, within the cell's tolerable range (1-8% NaCl shock), H. elongata urgently balanced the surging osmotic pressure by uptaking sodium and potassium ions and augmenting intracellular amino acid pools, particularly glutamate and glutamine. However, ectoine content started to increase until 20 min post-shock, rapidly becoming the dominant osmoprotectant, and reaching the maximum productivity (1450 ± 99 mg/L/h). Transcriptomic data also confirmed the delayed response in ectoine biosynthesis, and we speculate that this might be attributed to an intracellular energy crisis caused by NaCl shock. In response to oxidative stress, transcription factor cysB was significantly upregulated, positively regulating the sulfur metabolism and cysteine biosynthesis. Furthermore, the upregulation of the crucial peroxidase gene (HELO_RS18165) and the simultaneous enhancement of peroxidase (POD) and catalase (CAT) activities collectively constitute the antioxidant defense in H. elongata following shock. When exceeding the tolerance threshold of H. elongata (1-13% NaCl shock), the sustained compromised energy status, resulting from the pronounced inhibition of the respiratory chain and ATP synthase, may be a crucial factor leading to the stagnation of both cell growth and ectoine biosynthesis. CONCLUSIONS: This study conducted a comprehensive analysis of H. elongata's stress response to NaCl shock at multiple scales. It extends the understanding of stress response of halophilic bacteria to NaCl shock and provides promising theoretical insights to guide future improvements in optimizing industrial ectoine production.

Biodegradation of penicillin G sodium by Sphingobacterium sp. SQW1: Performance, degradation mechanism, and key enzymes.

Biodegradation is an efficient and cost-effective approach to remove residual penicillin G sodium (PGNa) from the environment. In this study, the effective PGNa-degrading strain SQW1 (Sphingobacterium sp.) was screened from contaminated soil using enrichment technique. The effects of critical operational parameters on PGNa degradation by strain SQW1 were systematically investigated, and these parameters were optimized by response surface methodology to maximize PGNa degradation. Comparative experiments found the extracellular enzyme to completely degrade PGNa within 60 min. Combined with whole genome sequencing of strain SQW1 and LC-MS analysis of degradation products, penicillin acylase and ß-lactamase were identified as critical enzymes for PGNa biodegradation. Moreover, three degradation pathways were postulated, including ß-lactam hydrolysis, penicillin acylase hydrolysis, decarboxylation, desulfurization, demethylation, oxidative dehydrogenation, hydroxyl reduction, and demethylation reactions. The toxicity of PGNa biodegradation intermediates was assessed using paper diffusion method, ECOSAR, and TEST software, which showed that the biodegradation products had low toxicity. This study is the first to describe PGNa-degrading bacteria and detailed degradation mechanisms, which will provide new insights into the PGNa biodegradation.

The Impact of 90 Parkinson's Disease-Risk Single Nucleotide Polymorphisms on Urinary Bis(monoacylglycerol)phosphate Levels in the Prodromal and PD Cohorts.

Parkinson's disease (PD) is a common neurodegenerative disorder with a prolonged prodromal phase. Higher urinary bis(monoacylglycerol)phosphate (BMP) levels associate with LRRK2 (leucine-rich repeat kinase 2) and GBA1 (glucocerebrosidase) mutations, and are considered as potential noninvasive biomarkers for predicting those mutations and PD progression. However, their reliability has been questioned, with inadequately investigated genetics, cohorts, and population. In this study, multiple statistical hypothesis tests were employed on urinary BMP levels and sequences of 90 PD-risk single nucleotide polymorphisms (SNPs) from Parkinson's Progression Markers Institution (PPMI) participants. Those SNPs were categorized into four groups based on their impact on BMP levels in various cohorts. Variants rs34637584 G/A and rs34637584 A/A (LRRK2 G2019S) were identified as the most relevant on increasing urinary BMP levels in the PD cohort. Meanwhile, rs76763715 T/T (GBA1) was the primary factor elevating BMP levels in the prodromal cohort compared to its T/C and C/C variants (N370S) and the PD cohort. Proteomics analysis indicated the changed transport pathways may be the reasons for elevated BMP levels in prodromal patients. Our findings demonstrated that higher urinary BMP levels alone were not reliable biomarkers for PD progression or gene mutations but might serve as supplementary indicators for early diagnosis and treatment.

Integrated multi-omics profiling to dissect the spatiotemporal evolution of metastatic hepatocellular carcinoma.

Comprehensive molecular analyses of metastatic hepatocellular carcinoma (HCC) are lacking. Here, we generate multi-omic profiling of 257 primary and 176 metastatic regions from 182 HCC patients. Primary tumors rich in hypoxia signatures facilitated polyclonal dissemination. Genomic divergence between primary and metastatic HCC is high, and early dissemination is prevalent. The remarkable neoantigen intratumor heterogeneity observed in metastases is associated with decreased T cell reactivity, resulting from disruptions to neoantigen presentation. We identify somatic copy number alterations as highly selected events driving metastasis. Subclones without Wnt mutations show a stronger selective advantage for metastasis than those with Wnt mutations and are characterized by a microenvironment rich in activated fibroblasts favoring a pro-metastatic phenotype. Finally, metastases without Wnt mutations exhibit higher enrichment of immunosuppressive B cells that mediate terminal exhaustion of CD8+ T cells via HLA-E:CD94-NKG2A checkpoint axis. Collectively, our results provide a multi-dimensional dissection of the complex evolutionary process of metastasis.

Efficient degradation of soybean protein B3 subunit in soy sauce by ultrasound-assisted prolyl endopeptidase and its primary mechanism.

Prolyl endopeptidase can partially degrade soybean protein B3 subunit and alleviate soy sauce secondary precipitate. In this study, the influences of ultrasound-assisted prolyl endopeptidase on the degradation of soybean protein B3 subunit of soy sauce and primary mechanism were investigated using SDS-PAGE, MALDI-TOF-MS, circular dichromatic spectrometer, fluorescence spectra, etc. Results showed that ultrasound-assisted prolyl endopeptidase enhanced 72% degradation rate of B3 subunit and reduced soy sauce secondary precipitate remarkably, meanwhile significantly increased content of organic taste compounds of soy sauce compared with control (p < 0.05). Sonication markedly reduced percentage of α-helix and increased percentage of random coil, made hydrophobic amino acids inside prolyl endopeptidase exposed to its surface and enhanced its flexibility, which facilitated the binding of prolyl endopeptidase active center with B3 subunit and finally enhanced the latter's degradation rate and appearance quality of soy sauce. This work laid a foundation for solving soy sauce secondary precipitate.

Machine learning methods for predicting the key metabolic parameters of Halomonas elongata DSM 2581 T.

Ectoine is generally produced by the fermentation process of Halomonas elongata DSM 2581 T, which is one of the primary industrial ectoine production techniques. To effectively monitor and control the fermentation process, the important parameters require accurate real-time measurement. However, for ectoine fermentation, three critical parameters (cell optical density, glucose, and product concentration) cannot be measured conveniently in real-time due to time variation, strong coupling, and other constraints. As a result, our work effectively created a series of hybrid models to predict the values of these three parameters incorporating both fermentation kinetics and machine learning approaches. Compared with the traditional machine learning models, our models solve the problem of insufficient data which is common in fermentation. In addition, a simple kinetic modeling is only applicable to specific physical conditions, so different physical conditions require refitting the function, which is tedious to operate. However, our models also overcome this limitation. In this work, we compared different hybrid models based on 5 feature engineering methods, 11 machine-learning approaches, and 2 kinetic models. The best models for predicting three key parameters, respectively, are as follows: CORR-Ensemble (R2: 0.983 ± 0.0, RMSE: 0.086 ± 0.0, MAE: 0.07 ± 0.0), SBE-Ensemble (R2: 0.972 ± 0.0, RMSE: 0.127 ± 0.0, MAE: 0.078 ± 0.0), and SBE-Ensemble (R2:0.98 ± 0.0, RMSE: 0.023 ± 0.001, MAE: 0.018 ± 0.001). To verify the universality and stability of constructed models, we have done an experimental verification, and its results showed that our proposed models have excellent performance. KEY POINTS: • Using the kinetic models for producing simulated data • Through different feature engineering methods for dimension reduction • Creating a series of hybrid models to predict the values of three parameters in the fermentation process of Halomonas elongata DSM 2581 T.

Physiological metabolic topology analysis of Halomonas elongata DSM 2581T in response to sodium chloride stress.

The halophilic bacterium Halomonas elongata DSM 2581T generally adapts well to high level of salinity by biosynthesizing ectoine, which functions as an important compatible solute protecting the cell against external salinity environment. Halophilic bacteria have specific metabolic activities under high-salt conditions and are gradually applied in various industries. The present study focuses on investigating the physiological and metabolic mechanism of H. elongata DSM 2581T driven by the external salinity environment. The physiological metabolic dynamics under salt stress were investigated to evaluate the effect of NaCl stress on the metabolism of H. elongata. The obtained results demonstrated that ectoine biosynthesis transited from a nongrowth-related process to a growth-related process when the NaCl concentration varied from 1% to 13% (w/v). The maximum biomass (Xm = 41.37 g/L), and highest ectoine production (Pm = 12.91 g/L) were achieved under 8% NaCl. Moreover, the maximum biomass (Xm ) and the maximum specific growth rates (µm ) showed a first rising and then declining trend with the increased NaCl stress. Furthermore, the transcriptome analysis of H. elongata under different NaCl concentrations demonstrated that both 8% and 13% NaCl conditions resulted in increased expressions of genes involved in the pentose phosphate pathway, Entner-Doudoroff pathway, flagellar assembly pathway, and ectoine metabolism, but negatively affected the tricarboxylic acid cycle and fatty acid metabolism. At last, the proposed possible adaptation mechanism under the optimum NaCl concentration in H. elongata was described.

An Efficient High-Throughput Screening of High Gentamicin-Producing Mutants Based on Titer Determination Using an Integrated Computer-Aided Vision Technology and Machine Learning.

The "design-build-test-learn" (DBTL) cycle has been adopted in rational high-throughput screening to obtain high-yield industrial strains. However, the mismatch between build and test slows the DBTL cycle due to the lack of high-throughput analytical technologies. In this study, a highly efficient, accurate, and noninvasive detection method of gentamicin (GM) was developed, which can provide timely feedback for the high-throughput screening of high-yield strains. First, a self-made tool was established to obtain data sets in 24-well plates based on the color of the cells. Subsequently, the random forest (RF) algorithm was found to have the highest prediction accuracy with an R2 value of 0.98430 for the same batch. Finally, a stable genetically high-yield strain (998 U/mL) was successfully screened out from 3005 mutants, which was verified to improve the titer by 72.7% in a 5 L bioreactor. Moreover, the verified new data sets were updated on the model database in order to improve the learning ability of the DBTL cycle.

Trappc9 Deficiency Impairs the Plasticity of Stem Cells.

Genetic mutations of trappc9 cause intellectual disability with the atrophy of brain structures and variable obesity by poorly understood mechanisms. Trappc9-deficient mice develop phenotypes resembling pathological changes in humans and appear overweight shortly after weaning, and thus are useful for studying the pathogenesis of obesity. Here, we investigated the effects of trappc9 deficiency on the proliferation and differentiation capacity of adipose-derived stem cells (ASCs). We isolated ASCs from mice before overweight was developed and found that trappc9-null ASCs exhibited signs of premature senescence and cell death. While the lineage commitment was retained, trappc9-null ASCs preferred adipogenic differentiation. We observed a profound accumulation of lipid droplets in adipogenic cells derived from trappc9-deficient ASCs and marked differences in the distribution patterns and levels of calcium deposited in osteoblasts obtained from trappc9-null ASCs. Biochemical studies revealed that trappc9 deficiency resulted in an upregulated expression of rab1, rab11, and rab18, and agitated autophagy in ASCs. Moreover, we found that the content of neural stem cells in both the subventricular zone of the lateral ventricle and the subgranular zone of the dentate gyrus vastly declined in trappc9-null mice. Collectively, our results suggest that obesity, as well as brain structure hypoplasia induced by the deficiency of trappc9, involves an impairment in the plasticity of stem cells.

Accurate and online quantification of viable Rhodobacter sphaeroides cells using a flow cytometry-dielectric spectroscopy (FCM-DS) method.

Accurate and online quantification of viable cells is one of the necessary requirements during the microbial fermentation process for high productivity. The flow cytometry (FCM)-based method accurately quantifies viable cells, but this offline method cannot reflect the counts constantly. The dielectric spectroscopy (DS) sensor is widely utilized to monitor viable cells online; however, accurately converting the capacitance value of the DS sensor to the viable bacterial cell counts has barely been tried. We have developed a method by coupling the principles and techniques of FCM and the DS sensor to quantify viable Rhodobacter sphaeroides cells. Using specific fluorescent antibodies and propidium iodide (PI), viable R. sphaeroides cells were accurately quantified within 30 min by FCM. The DS sensor was combined with the FCM to create a direct capacitance-viable cell count quantification system. The LOD (limit of detection) of the FCM-DS method was 8 × 108 CFU/mL, RSD (relative standard deviation) < 5%, along with good reproducibility of the results. Finally, the viable cell count, obtained from the FCM-DS method, was applied to regulate the specific oxygen uptake rate (QO2) that increased the production of coenzyme Q10 by 8.1%. Together, our results strongly suggest that viable cells can be accurately quantified online by the integrated FCM-DS method, which would help to devise precise fermentation control strategies.

Corrigendum: Propofol Alleviates DNA Damage Induced by Oxygen Glucose Deprivation and Reperfusion via FoxO1 Nuclear Translocation in H9c2 Cells.

[This corrects the article DOI: 10.3389/fphys.2019.00223.].

Antibiotic residue and toxicity assessment of wastewater during the pharmaceutical production processes.

Various pollutants are released during pharmaceutical production processes, which is of great concern. Most studies have focused on the terminal treatment results of mixed pharmaceutical wastewater, and further research on wastewater from the production processes is required. This study investigated the wastewater quality indicators, residual antibiotics, and biological toxicity of the wastewater during the production process in a large pharmaceutical producing factory in Northern China. The wastewater contained numerous organic pollutants, with the chemical oxygen demand (COD) values ranging from 2.0 × 103 to 2.6 × 105 mg L-1 and the total nitrogen (TN) values ranging from 1.3 × 103 to 2.0 × 104 mg L-1. High concentrations of cephalexin and cefradine remained in the wastewater of the production workshop, with the highest concentration of cefradine reaching 1328 mg L-1. The wastewater from the oxidation and solvent recovery workshops was more toxic to Vibrio fischeri and Daphnia magna than that of other workshops. Moreover, the biological acute toxicity of wastewater was significantly correlated with the concentration of COD and TN (p < 0.01). This study provides new insights into the treatment of antibiotic production wastewater, illuminating the incomplete extraction of products and the significant risk posed by pharmaceutical wastewater to the environment.

CUMS and dexamethasone induce depression-like phenotypes in mice by differentially altering gut microbiota and triggering macroglia activation.

BACKGROUND: Although the link between gut microbiota and depression has been suggested, changes of gut microbiota vary largely among individuals with depression. AIMS: Explore the heterogeneity of microbiota-gut-brain axis and new pathogenic characteristics in murine models of depression. METHODS: Adolescent female mice were randomly divided into control (CON) group (n=10), chronic unexpected mild stress (CUMS) group (n=15) and dexamethasone (DEX) group (n=15). Mice in the DEX group were gavaged twice a day with 0.2 mg/kg of DEX for 5 weeks, whereas CON mice were given the same amount of solvent. Mice in the CUMS group were exposed to stressors. After behavioural evaluations, all mice were sacrificed for harvesting tissues and blood samples. Enzyme-linked immunosorbent assay (ELISA) was conducted for measuring levels of corticosterone (CORT) and interleukin-1ß (IL-1ß) in sera, whereas levels of protein expression in colon and hippocampal tissues were examined by western blot. Faecal microbial communities were analysed by sequencing 16S rDNAs. RESULTS: Mice in CUMS and DEX groups exhibited severe depression-like behaviours. Compared with CON mice, CUMS-exposed mice showed a significant increase in both α and ß diversity. Prevotellaceae and Desulfovibrio were enriched, whereas Bacilli were decreased in the faeces of mice in the CUMS group. DEX-treated mice had a decrease in the abundance of Clostridium XVIII. Levels of occludin in colon tissue of DEX-treated mice were reduced. Relative to mice in the CON and CUMS groups, DEX-treated mice contained higher serum levels of CORT and IL-1ß. Compared with CON mice, mice in the DEX and CUMS groups had higher levels of IL-1ß in sera and lower levels of glial fibrillary acidic protein (GFAP), Nestin, Synapsin-1 and P2Y12 receptor in the hippocampus. CONCLUSIONS: Changes of gut microbiota diversity, intestinal integrity and neuroinflammation in the brain contribute to CUMS-induced depression, whereas pathobionts and excessive immunosuppression with damaged neuronal synapses is a basis of the DEX-induced depression.

Comparative study of three types of mesenchymal stem cell to differentiate into pancreatic ß-like cells in vitro.

Type 1 diabetes (TID) is a chronic metabolic disease where the body produces insufficient or no insulin. Stem cells with multi-directional differentiation potential are transplanted and differentiate into ß-like cells in vivo to replace pancreatic ß cells, which has become a novel treatment strategy. The aim of the present study was to investigate the ability of three types of adult mesenchymal stem cell (MSC) to differentiate into pancreatic ß-like cells in vitro in order to identify suitable sources for the treatment of diabetes. The three MSC types were menstrual blood-derived MSCs (MENSCs), umbilical cord-derived MSCs (UCMSCs) and dental pulp MSCs (DPSCs). The differentiation method used in the present study was divided into three steps and the MSCs were differentiated into pancreatic ß-like cells in vitro. Among these MSCs, MENSCs had a greater ability to differentiate into islet ß-like cells in vitro, while UCMSCs and DPSCs exhibited a similar differentiation potency, which was relatively lower compared with that of MENSCs. The present results indicated that MENSCs may be a suitable cell source for the curative treatment of TID.

Development of a novel noninvasive quantitative method to monitor Siraitia grosvenorii cell growth and browning degree using an integrated computer-aided vision technology and machine learning.

The rapid, accurate and noninvasive detection of biomass and plant cell browning can provide timely feedback on cell growth in plant cell culture. In this study, Siraitia grosvenorii suspension cells were taken as an example, a phenotype analysis platform was successfully developed to predict the biomass and the degree of cell browning based on the color changes of cells in computer-aided vision technology. First, a self-made laboratory system was established to obtain images. Then, matrices were prepared from digital images by a self-developed high-throughput image processing tool. Finally, classification models were used to judge different cell types, and then a semi-supervised classification to predict different degrees of cell browning. Meanwhile, regression models were developed to predict the plant cell mass. All models were verified with a good agreement by biological experiments. Therefore, this method can be applied for low-cost biomass estimation and browning degree quantification in plant cell culture.

Characterization of the aroma-active compounds in black soybean sauce, a distinctive soy sauce.

Black soybean sauce's (BSS) aroma was scarcely investigated, which seriously affected BSS's quality and consumers' preference. Thus the aroma compounds in BSS were characterized using gas chromatography-mass spectrometry/gas chromatography-olfactometry coupling with recombination and omission experiments. Sensory evaluation showed the fruity odor was increased by 63% and the malty, alcoholic, floral, smoky, caramel-like and sour odors were decreased by 24-35% when compared to the control soy sauce (SS, p < 0.05). Totally, 126 volatile compounds, 44 aroma-active compounds and 22 vital aroma-active compounds were identified in BSS. Compared to SS, BSS exhibited a distinctive aroma characteristics which was caused by significantly higher odor activity values (OAVs) of 3-methylbutyl acetate (357%), ethyl propanoate (144%), ethyl 3-methylbutanoate (70%), ethyl 2-methylbutanoate (102%) and lower OAVs of 4-hydroxy-2,5-dimethyl-3(2H)-furanone (52%), 4-hydroxy-2-ethyl-5-methyl-3(2H)-furan-3-one (50%), ethanol (48%), 4-vinylguaiacol (41%), 3-methylthiopropanal (37%), 3-methylbutanol (33%), 4-ethylguaiacol (28%). The results would contribute to BSS's quality control and aroma improvement.

Rationally optimized generation of integrated Escherichia coli with stable and high yield lycopene biosynthesis from heterologous mevalonate (MVA) and lycopene expression pathways.

The stability and high productivity of heterogeneous terpenoid production in Escherichia coli expression system is one of the most key issues for its large scale industrialization. In the current study on taking lycopene biosynthesis as an example, an integrated Escherichia coli system has been generated successfully, which resulted into stable and high lycopene production. In this process, two modules of mevalonate (MVA) pathway and one module of lycopene expression pathway were completely integrated in the chromosome. Firstly, the copy number and integrated position of three modules of heterologous pathways were rationally optimized. Later, a strain DH416 equipped with heterogeneous expression pathways through chromosomal integration was efficiently derived from parental strain DH411. The evolving DH416 strain efficiently produced the lycopene level of 1.22 g/L (49.9 mg/g DCW) in a 5 L fermenter with mean productivity of 61.0 mg/L/h. Additionally, the integrated strain showed more genetic stability than the plasmid systems after successive 21st passage.

Parkinson's Disease Causative Mutation in Vps35 Disturbs Tetherin Trafficking to Cell Surfaces and Facilitates Virus Spread.

Parkinson's disease (PD) is the most common neurodegenerative movement disorder, characterized by progressive loss of dopaminergic neurons in the substantia nigra, intraneuronal deposition of misfolded proteins known as Lewy bodies, and chronic neuroinflammation. PD can arise from monogenic mutations, but in most cases, the etiology is unclear. Viral infection is gaining increasing attentions as a trigger of PD. In this study, we investigated whether the PD-causative 620 aspartate (D) to asparagine (N) mutation in the vacuolar protein sorting 35 ortholog (Vps35) precipitated herpes simplex virus (HSV) infection. We observed that ectopic expression of Vps35 significantly reduced the proliferation and release of HSV-1 virions; the D620N mutation rendered Vps35 a partial loss of such inhibitory effects. Tetherin is a host cell protein capable of restricting the spread of encapsulated viruses including HSV-1 and SARS-Cov-2, both of which are implicated in the development of parkinsonism. Compared with cells overexpressing wildtype Vps35, cells expressing mutant Vps35 with D620N had less Tetherin on cell surfaces. Real-time and static cell imaging revealed that Tetherin recycled through Vps35-positive endosomes. Expression of Vps35 with D620N reduced endosomal dynamics and frequency of motile Tetherin-containing vesicles, a sign of defective production of recycling carriers. Our study suggests that the D620N mutation in Vps35 hinders Tetherin trafficking to cell surfaces and facilitates virus spread.

Trappc9 deficiency in mice impairs learning and memory by causing imbalance of dopamine D1 and D2 neurons.

Genetic mutations in the gene encoding transport protein particle complex 9 (trappc9), a subunit of TRAPP that acts as a guanine nucleotide exchange factor for rab proteins, cause intellectual disability with brain structural malformations by elusive mechanisms. Here, we report that trappc9-deficient mice exhibit a broad range of behavioral deficits and postnatal delay in growth of the brain. Contrary to volume decline of various brain structures, the striatum of trappc9 null mice was enlarged. An imbalance existed between dopamine D1 and D2 receptor containing neurons in the brain of trappc9-deficient mice; pharmacological manipulation of dopamine receptors improved performances of trappc9 null mice to levels of wild-type mice on cognitive tasks. Loss of trappc9 compromised the activation of rab11 in the brain and resulted in retardation of endocytic receptor recycling in neurons. Our study elicits a pathogenic mechanism and a potential treatment for trappc9-linked disorders including intellectual disability.

Enhancer Reprogramming within Pre-existing Topologically Associated Domains Promotes TGF-ß-Induced EMT and Cancer Metastasis.

Transcription growth factor ß (TGF-ß) signaling-triggered epithelial-to-mesenchymal transition (EMT) process is associated with tumor stemness, metastasis, and chemotherapy resistance. However, the epigenomic basis for TGF-ß-induced EMT remains largely unknown. Here we reveal that HDAC1-mediated global histone deacetylation and the gain of specific histone H3 lysine 27 acetylation (H3K27ac)-marked enhancers are essential for the TGF-ß-induced EMT process. Enhancers gained upon TGF-ß treatment are linked to gene activation of EMT markers and cancer metastasis. Notably, dynamic enhancer gain or loss mainly occurs within pre-existing topologically associated domains (TADs) in epithelial cells, with minimal three-dimensional (3D) genome architecture reorganization. Through motif enrichment analysis of enhancers that are lost or gained upon TGF-ß stimulation, we identify FOXA2 as a key factor to activate epithelial-specific enhancer activity, and we also find that TEAD4 forms a complex with SMAD2/3 to mediate TGF-ß signaling-triggered mesenchymal enhancer reprogramming. Together, our results implicate that key transcription-factor (TF)-mediated enhancer reprogramming modulates the developmental transition in TGF-ß signaling-associated cancer metastasis.