Biology subjects

Lin, W.

Publications and source records attributed to Lin, W..

At least 127 records · Page 7Linked to original sources

bioRxiv2022

Response of sugarcane rhizosphere soil fungal communities on a temporal gradient to changes in critical growth periods

Understanding the normal variation of the sugarcane rhizosphere fungal microbiota throughout its life cycle is essential for the development of agricultural practices for fungal diseases (e.g., sugarcane tip rot, sugarcane red rot, and sugarcane smut) and ecological health associated with the microbiota. Therefore, we performed high-throughput sequencing of 18S rDNA of soil samples using the Illumina sequencing platform for correlation analysis of sugarcane rhizosphere microbiota time series, covering information from 84 samples in four growth periods. The results revealed that the sugarcane rhizosphere fungi possessed the maximum fungal richness in July (Tillering). Rhizosphere fungi are closely associated with sugarcane growth, including Ascomycota, Basidiomycota, and Ochrophyta showed high abundance in a stage-specific manner. Through the Manhattan plots, 11 fungal genera were found to show a decreasing trend throughout the sugarcane growth period, and two fungal genera were significantly enriched at three stages of sugarcane growth (p < 0.05) including Pseudallescheria and Nectriaceae. In addition, soil pH, soil temperature (Tem), total nitrogen (TN) and total potassium (TP) were important drivers of fungal community structure at different stages of sugarcane growth. Using structural equation modeling (SEM) found that sugarcane disease status showed a significant and strong negative effect with selected soil properties, suggesting that poor soil may increase the likelihood of sugarcane disease. In addition changes in sugarcane rhizosphere community structure over time were mainly influenced by stochastic factors, but the contribution decreased to the lowest value after the sugarcane root adaptation system was stabilized (Maturity). IMPORTANCERhizosphere microbes are closely related to plant growth, and more studies have shown that the rhizosphere fungal microbial community has an important influence on plant health and growth status. However, little is known about the response of the rhizosphere fungal community to plant growth during the critical plant reproductive period. In this study, we analyzed the important response of the rhizosphere fungal community of sugarcane through the pattern of abundance changes in its critical growth nodes by various methods to investigate the subtle changes in the assembly of the rhizosphere fungal community with the growth of sugarcane. Our work provides innovative ideas for the prevention of soil-borne diseases in plants and also provides a solid basis for the development of microbial models of crops rhizosphere soil.

microbiology↗

bioRxiv2022

Jointly analyzing the association of human milk nutrients with cognition and temperament traits during the first 6 months of life

Early dietary exposure via human milk (HM) components offers a window of opportunity to support cognitive and temperamental development. While several studies have focused on associations of few pre-selected HM components with cognition and temperament, it is highly plausible that HM components synergistically and jointly support cognitive and behavioral development in early life. We aimed to discern the combined associations of a wide array of HM nutrients with cognition and temperament during the first six months of life and explore if there were persistent effects up to 18 months old, when HM is the primary source of an infants nutrition. The Mullen Scales of Early Learning and Infant Behavior Questionnaires-Revised were used to assess cognition and temperament, respectively, of fifty-four exclusively/predominantly breastfed infants in the first 6 months of life, whose follow-ups were conducted at 6-9, 9-12 and 12-18 months old. HM samples were obtained from the mothers of the participants at less than 6 months of life and analyzed for fatty acids (total monounsaturated fatty acids, polyunsaturated fatty acid, total saturated fatty acid (TSFA), arachidonic acid (ARA), docosahexaenoic acid (DHA), ARA/DHA, omega-6/omega-3 polyunsaturated fatty acids ratio (n-6/n-3)), phospholipids (phosphatidylcholine, phosphatidylethanolamine (PE), phosphatidylinositol (PI), sphingomyelin) and choline (free choline, phosphocholine (PCho), glycerophosphocholine). Feature selection was performed to select nutrients associated with cognition and temperament, respectively. The combined effects of selected nutrients were analyzed using multiple regression. A positive association between the arachidonic acid (ARA) and surgency was observed (p = 0.024). Significant effect of DHA, n-6/n-3, PE and TSFA concentrations on receptive language (R2 = 0.39, p = 0.025), and the elevated ARA, PCho, and PI with increased surgency (R2 = 0.43, p = 0.003) was identified, suggesting that DHA and ARA may have distinct roles for temperament and language functions. Furthermore, the exploratory association analyses suggest that the effects of HM nutrients on R.L. and surgency may persist beyond the first 6 months of life, particularly surgency at 12-18 months (p = 0.002). Our studies highlighted that various HM nutrients work together to support the development of cognition and temperament traits during early infancy.

developmental biology↗

bioRxiv2022

Uncovering the "ZIP code" for bZIP dimers reveals novel motifs, regulatory rules and one billion years of cis-element evolution

Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. For example, dimerization properties of the basic leucine zipper (bZIP) family play a critical role in regulating the unique biological functions in all eukaryotes. However, the molecular mechanism underlying the binding sequence and functional specificity of homo- versus heterodimers remains elusive. To fill this gap, we developed a double DNA Affinity Purification sequencing (dDAP-seq) technique that maps heterodimer DNA binding sites in an endogenous genome context. Our genome-wide binding profiles of twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis revealed that heterodimerization significantly expands the DNA binding preferences of bZIP TFs. Analysis of the heterodimer target genes in stress response and development suggest heterodimerization gives rise to regulatory responses that are distinct from the homodimers. In addition to the classic ACGT elements recognized by plant bZIPs, we found that the C/S1 heterodimers bound to motifs that might share an origin with the GCN4 cis-elements in yeast that diverged from plants more than one billion years ago. Importantly, heterodimer binding specificities can be distinguished by their relative preference for ACGT motifs versus GCN4-related motifs. More broadly, our study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.

molecular biology↗

bioRxiv2022

Thermophoresis of Molecules and Structures of different Sizes in Self-assembled Biomatrices

Upon subjecting biomolecules to non-equilibrium conditions, many biochemical and biophysical features such as biomolecular diffusion, protein folding, interaction kinetics, as well as enzyme-catalyzed reactions can be characterized in an aqueous solution. However, most assays under non-equilibrium conditions cannot be performed in complex self-assembled biomatrices (e.g. extracellular matrices) due to the limitations associated with sample handling, reaction design, and optical detection. Herein, we report the study of biomolecular thermodiffusion in non-covalently assembled synthetic or naturally derived hydrogels. This approach has been demonstrated with a large variety of analytes, including small molecules, polysaccharides, DNAs, DNA origami, and proteins in various polymer networks. The in-biomatrix method has also shown advantages over in-solution measurements: First, it allows us to analyze biomolecules in 3D matrices in a high-throughput fashion. Second, the aggregation of analytes can be remarkably prevented. Although the underlying physics of thermodiffusion is still not well-understood, we demonstrated that the thermodiffusion of surrounding networks will enhance the thermodiffusion of the analyte, an effect counteracting the hindered movement by the polymer network.

biophysics↗

bioRxiv2022

Multifaceted Atlases of the Human Brain in its Infancy

Brain atlases agglomerate structural and functional features of a population of individuals in a standard coordinate space. Here, we introduce for the first time a collection of atlases that charts postnatal development of the human brain in a spatio-temporally dense manner from two weeks to two years of age. Atlases capturing month-to-month changes of the human brain are essentially nonexistent for the first two years of life -- the critical developmental period during which the brain is evolving in virtually all facets at an exponential pace. This unmet need is compounded by the lack of atlases that provide a unified and holistic picture of the brain from both the perspectives of cortical surface convolutions and tissue volumetric characteristics. Existing surface and volumetric atlases are typically constructed independently in different coordinate spaces, causing discrepancies and complications in multifaceted analyses. Our month-specific conjoint surface and volumetric atlases chart normative patterns and capture key traits of early brain development and are therefore critical for identifying aberrations from normal developmental trajectories. Our atlases represent a major advance toward providing the neuroscience community an invaluable resource to facilitate the understanding of early structural and functional development by mapping multiple measurements of infant brains in a common reference frame for precise spatio-temporal quantification of cortical and subcortical changes.

neuroscience↗

bioRxiv2022

Structural and functional alterations of neuromuscular synapses in a mouse model of ACTA1 congenital myopathy

Mutations in skeletal muscle -actin (Acta1) cause a variety of myopathies. In a mouse model of congenital myopathy, heterozygous Acta1 (H40Y) knock-in (Acta1+/Ki) mice exhibit features of human nemaline myopathy, including premature lethality, severe muscle weakness, reduced mobility, and the presence of nemaline rods in muscle fibers. In this study, we investigated the structure and function of the neuromuscular junction (NMJ) in the Acta1+/Ki mice. We found marked impairments in NMJ structure in the mutant mice, including fragmented endplates and nerve terminals, reduced density of acetylcholine receptors (AChRs) on endplate membranes, reduced nerve occupancy at endplates, and increased numbers of muscle fiber subsynaptic nuclei. We compared the NMJs in three different types of muscles - the extensor digitorum longus (EDL, composed of fast-twitch muscle fibers), soleus (Sol, enriched in slow-twitch fibers) and the triangularis sterni muscle (TS, a mixed fiber type muscle). Among these three types of muscles, EDL was affected to the greatest extent, suggesting that fast-twitch fibers may be most susceptible to NMJ fragmentation in Acta1+/Ki nemaline myopathy. Electrophysiological analysis of mutant NMJs showed a reduced quantal size (reduced mEPP amplitude), increased mEPP frequency, and increased quantal content, but normal EPP amplitude compared to wild type (WT) NMJs. The results suggest that affected synapses may have undergone homeostatic compensation to maintain normal levels of neurotransmitter release. In addition, paired-pulse facilitation was reduced and synaptic depression under repetitive nerve stimulation was enhanced, indicating shortterm synaptic plasticity was compromised in the mutant mice. Key pointsO_LIMice heterozygous for an Acta1 (H40Y) knock-in mutation exhibit clinical features of human nemaline myopathy. We report structural and functional alterations of neuromuscular synapses in these mutant mice. The NMJ impairments include endplate fragmentation, reduced endplate nerve occupancy, and increased numbers of subsynaptic nuclei in muscle fibers. C_LIO_LINeuromuscular synaptic transmission was compromised - demonstrating both increased quantal content and changes in short-term synaptic plasticity. C_LIO_LIIncreases in spontaneous neurotransmitter release and quantal content suggest homeostatic compensation of synapses to maintain normal transmitter release in the mutant NMJs. C_LI

neuroscience↗

bioRxiv2022

Genetic deletion of Kiaa1109 in mice leads to developmental defects at the neuromuscular junction

KIAA1109 (4932438A13Rik) is a novel gene linked to Alkuraya-Kucinska Syndrome, an autosomal recessive disorder with severe brain malformations and arthrogryposis in humans. The role of KIAA1109 in mammalian development and function remains poorly understood. Here, we characterize mutant mice deficient in Kiaa1109 (Kiaa1109-/-). We report that Kiaa1109-/- mice died during perinatal stages. These Kiaa1109-/- embryos exhibited impaired intramuscular nerve growth and reduced sizes of the neuromuscular junction (NMJ) compared with their littermate controls. Electrophysiological analysis further revealed defects in neuromuscular synaptic transmission in Kiaa1109-/- embryos. Notably, the frequency of spontaneous neurotransmitter release was markedly increased, whereas evoked neurotransmitter release and quantal content were reduced. Furthermore, neuromuscular synapses in Kiaa1109-/- embryos failed to respond to a repetitive, low frequency stimulation (10Hz). These results demonstrate that KIAA1109 is required for survival in mice and for proper development and function of the NMJ. Significance StatementThis is the first report characterizing the phenotype of mutant mice deficient in KIAA1109 (4932438A13Rik), a novel gene in mammals. We show that KIAA1109 is required for survival in mice and that KIAA1109 plays important roles in normal development and function of the NMJ in mice.

neuroscience↗

bioRxiv2022

Prospective Motion Correction and Automatic Segmentation of Penetrating Arteries in Phase Contrast MRI at 7 T

PurposeTo develop a prospective motion correction (MC) method for phase contrast (PC) MRI of penetrating arteries (PA) in centrum semiovale at 7 T and evaluate its performance using automatic PA segmentation. MethodsHead motion was monitored and corrected during the scan based on fat navigator images. Two convolutional neural networks (CNN) were developed to automatically segment PAs and exclude surface vessels. Real-life scans with MC and without MC (NoMC) were performed to evaluate the MC performance. Motion score was calculated from the range of translational and rotational motion parameters. MC vs NoMC pairs were divided according to their score differences into groups with similar, less, or more motions during MC. Data reacquisition was also performed to evaluate whether it can further improve PA visualization. ResultsIn the group with similar motion, more PA counts (NPA) were obtained with MC in 9 (60%) cases, significantly more than the number of cases (1) with less PAs (p = 0.011; binomial test). In the group with less motion during MC, MC images had more or similar NPA in all cases, while in the group with more motion during MC, the numbers of cases with less and more NPA during MC were not significantly different (3 vs 0). Data reacquisition did not further increase NPA. CNNs had higher sensitivity (0.85) and accuracy (Dice coefficient 0.85) of detecting PAs than a threshold based method. ConclusionsProspective MC and CNN based segmentation improved the visualization and delineation of PAs in PC MRI at 7 T.

bioengineering↗

bioRxiv2022

Epac1 regulates cellular SUMOylation by promoting the formation of SUMO-activating nuclear condensates

Protein SUMOylation plays an essential role in maintaining cellular homeostasis when cells are under stress. However, precisely how SUMOylation is regulated, and a molecular mechanism linking cellular stress to SUMOylation remains elusive. Herein, we report that cAMP, a major stress-response second messenger, acts through Epac1 as a regulator of cellular SUMOylation. The Epac1-associated proteome is highly enriched with components of the SUMOylation pathway. Activation of Epac1 by intracellular cAMP triggers phase separation and the formation of nuclear condensates containing Epac1 and general components of the SUMOylation machinery to promote cellular SUMOylation. Furthermore, genetic knockout of Epac1 obliterates oxidized low-density lipoprotein induced cellular SUMOylation in macrophages, leading to suppression of foam cell formation. These results provide a direct nexus connecting two major cellular stress responses to define a molecular mechanism in which cAMP regulates the dynamics of cellular condensates to modulate protein SUMOylation.

cell biology↗

bioRxiv2021

Generation of Infant-dedicated Fine-grained Functional Parcellation Maps of Cerebral Cortex

Infancy is a dynamic and immensely important period in human brain development. Studies of infant functional development using resting-state fMRI rely on precisely defined cortical parcellation maps. However, available adult-based functional parcellation maps are not applicable for infants due to their substantial differences in functional organizations. Fine-grained infant-dedicated cortical parcellation maps are highly desired but remain scarce, due to difficulties ranging from acquiring to processing of infant brain MRIs. In this study, leveraging 1,064 high-resolution longitudinal rs-fMRIs from 197 infants from birth to 24 months and advanced infant-dedicated processing tools, we create the first set of infant-specific, fine-grained cortical functional parcellation maps. Besides the conventional folding-based cortical registration, we specifically establish the functional correspondences across individuals using functional gradient densities and generate both age-specific and age-common fine-grained parcellation maps. The first set of comprehensive brain functional developmental maps are accordingly derived, and reveals a complex, hitherto unseen multi-peak fluctuation development pattern in temporal variations of gradient density, network sizes, and local efficiency, with more dynamic changes during the first 9 months than other ages. Our proposed method is applicable in generating fine-grained parcellations for the whole lifespan, and our parcellation maps will be available online to advance the neuroimaging field.

neuroscience↗

bioRxiv2021

HybridDTA: Hybrid Data Fusion through Pairwise Training for Drug-Target Affinity Prediction

Candidate compounds with high binding affinities toward a target protein are likely to be developed as drugs. Deep neural networks (DNNs) have attracted increasing attention for drug-target affinity (DTA) estimation owning to their efficiency. However, the negative impact of batch effects caused by measure metrics, system technologies, and other assay information is seldom discussed when training a DNN model for DTA. Suffering from the data deviation caused by batch effects, the DNN models can only be trained on a small amount of "clean" data. Thus, it is challenging for them to provide precise and consistent estimations. We design a batch-sensitive training framework, namely BatchDTA, to train the DNN models. BatchDTA implicitly aligns multiple batches toward the same protein, alleviating the impact of the batch effects on the DNN models. Extensive experiments demonstrate that BatchDTA facilitates four mainstream DNN models to enhance the ability and robustness on multiple DTA datasets. The average concordance index (CI) of the DNN models achieves a relative improvement of 4.0%. BatchDTA can also be applied to the fused data collected from multiple sources to achieve further improvement.

bioinformatics↗

bioRxiv2021

MiR-144 regulates adipogenesis by mediating formation of C/EBPα-FoxO1 protein complex

Excessive adipogenesis caused obesity, which was a serious risk of health and led to a series of diseases, including type II diabetes (T2D) for example. Adipocyte as the basic unit of adipose tissue has emerged as one of significant target of the treatment of obesity-related metabolic syndromes by revealed its adipogenic molecular mechanism. MicroRNAs (miRNAs) have been demonstrated involving adipogenesis, and played a crucial role in the competitive endogenous RNA (ceRNA) effect. Besides that, C/EBP as a crucial adipogenic regulator still lacked epigenetic explanation during pre-adipocyte adipogenesis. In this study, we first verified FoxO1 was one of the ceRNA of C/EBP. They co-regulated adipogenesis through formed a protein complex that directly bound to its promoter to activate AdipoQ, and AdipoQ (Adiponectin) was a negative adipocytokines that suppressed adipogenesis, which played an important role in retaining adipogensis balance. Moreover, an adipose tissue specific enriched miRNA, miR-144 was the key regulator of the ceRNA effect between C/EBP and FoxO1, which mediated the C/EBP-FoxO1 complex formation, thus altered AdipoQ, furthermore regulated pre-adipocyte adipogenesis. This research will provide a new supplementary idea of the C/EBP epigenetic role in pre-adipocyte adipogenesis.

cell biology↗

bioRxiv2021

Eicosanoids in the pancreatic tumor microenvironment: a multicellular, multifaceted progression

Eicosanoids, oxidized fatty acids that serve as cell-signaling molecules, have been broadly implicated in tumorigenesis. To identify eicosanoids relevant to pancreatic tumorigenesis, we profiled normal pancreas and pancreatic ductal adenocarcinoma (PDAC) in mouse models and patient samples using mass spectrometry. We interrogated RNA sequencing datasets for eicosanoid synthase or receptor expression. Findings were confirmed by immunostaining. In murine models, we identified elevated levels of PGD2, prostacyclin, and thromboxanes in neoplasia while PGE2, 12-HHTre, HETEs, and HDoHEs are elevated specifically in tumors. Analysis of scRNA-seq datasets suggests that PGE2 and prostacyclins are derived from fibroblasts, PGD2 and thromboxanes from myeloid cells, and PGD2 and 5-HETE from tuft cells. In patient samples, we identified a transition from PGD2 to PGE2-producing enzymes in the epithelium during the transition to PDAC, fibroblast/tumor expression of PTGIS, and myeloid/tumor cell expression of TBXAS1. Altogether, our analyses identify key changes in eicosanoid species during pancreatic tumorigenesis and the cell types responsible for their synthesis.

cancer biology↗

bioRxiv2021

Genomically hardwired regulation of gene activity orchestrates cellular iron homeostasis in Arabidopsis

Iron (Fe) is an essential micronutrient that plays pivotal roles as electron donor and catalyst across organisms. In plants, variable, often insufficient Fe supply necessitates mechanisms that constantly attune Fe uptake rates and recalibrate cellular Fe homeostasis. Here, we show that short-term (0.5, 6, and 12 h) exposure of Arabidopsis thaliana plants to Fe deficiency triggered massive changes in gene activity governed by transcription and alternative splicing (AS), regulatory layers that were to a large extent mutually exclusive. Such preclusion was not observed for genes that are directly involved in the acquisition of Fe, which appears to be concordantly regulated by both expression and AS. Generally, genes with lower splice site strengths and higher intron numbers were more likely to be regulated by AS, no dependence was on gene architecture was observed for transcriptionally controlled genes. Conspicuously, specific processes were associated with particular genomic features and biased towards either regulatory mode, suggesting that genomic hardwiring is functionally biased. Early changes in splicing patterns were, in many cases, congruent with later changes in transcript or protein abundance, thus contributing to the pronounced transcriptome-proteome discordance observed in plants.

plant biology↗

bioRxiv2021

Peptide Scanning of SARS-CoV and SARS-CoV-2 Spike Protein Subunit 1 Reveals Potential Additional Receptor Binding Sites

The binding of SARS-CoV and SARS-CoV-2 to the ACE2 receptor on human cells is mediated by the spike protein subunit 1 (S1) on the virus surfaces, while the receptor binding domains (RBDs) of S1 are the major determinants for the interaction with ACE2 and dominant targets of neutralizing antibodies. However, at the virus-host interface, additional biomolecular interactions, although being relatively weak in affinity and low in specificity, could also contribute to viral attachment and play important roles in gain- or loss-of-function mutations. In this work, we performed a peptide scanning of the S1 domains of SARS-CoV and SARS-CoV-2 by synthesizing 972 16-mer native and mutated peptide fragments using a high throughput in situ array synthesis technology. By probing the array using fluorescently labelled ACE2, a number of previously unknown potential receptor binding sites of S1 have been revealed. 20 peptides were synthesized using solid phase peptide synthesis, in order to validate and quantify their binding to ACE2. Four ACE2-binding peptides were selected, to investigate whether they can be assembled through a biotinylated peptide/neutravidin system to achieve high affinity to ACE2. A number of constructs exhibited high affinity to ACE2 with Kd values of pM to low nM.

biochemistry↗

bioRxiv2021

Improving Timeliness in the Neglected Tropical Diseases Preventive Chemotherapy Donation Supply Chain through Information Sharing: A Retrospective Empirical Analysis

BackgroundBillions of doses of medicines are donated for mass drug administrations in support of the World Health Organizations "Roadmap to Implementation," which aims to control, eliminate, and eradicate Neglected Tropical Diseases (NTDs). The supply chain to deliver these medicines is complex, with fragmented data systems and limited visibility on performance. This study empirically evaluates the impact of an online supply chain performance measurement system, "NTDeliver," providing understanding of the value of information sharing towards the success of global health programs. MethodsRetrospective secondary data was extracted from NTDeliver, which included 1,484 shipments for four critical medicines ordered by over 100 countries between February 28, 2006 and December 31, 2018. We applied statistical regression models to analyze the impact on key performance metrics, comparing data before and after the system was implemented. FindingsThe results suggest information sharing has a positive impact on three performance indicators: purchase order timeliness ({beta}=1.01, p<0.000), arrival timeliness ({beta}=0.53, p=0.09), and--most importantly--delivery timeliness ({beta}=0.73, p=0.03). Three variables indicated an increased positive impact when the data is publicly shared: shipment timeliness ({beta}=2.57, p=0.001), arrival timeliness ({beta}=2.88, p=0{middle dot}003), and delivery timeliness ({beta}=2.82, p=0.01). ConclusionsOur findings suggest that information sharing between the NTD program partners can help drive improved performance in the supply chain, and even more so when data is shared publicly. Given the large volume of medicine and the significant number of people requiring these medicines, information sharing has the potential to provide improvements to global health programs affecting the health of tens to hundreds of millions of people Author SummaryThe supply chain to deliver donated preventive chemotherapy medicines is complex due to the many stakeholders and partnerships participating, as well as challenging because the logistics are further complicated by delivery to remote destinations in developing countries. As MDA campaigns involve treating hundreds of thousands to millions of patients in endemic regions within entire countries over the course of days or weeks, close coordination and timing of medicine delivery is critical. Inefficiencies caused by fragmented data systems and limited transparency on supply chain performance further challenges the ability to identify shipment issues and explore the root cause of the issues. Prior to 2016, delivery was performing below standards, lagging as much as 40% below the WHO target of 80% on-time delivery. These delays result in wasted medicine donations, increased program costs, delayed MDAs, or sometimes even completely missed MDAs. In September 2016, an online supply chain performance measurement system, "NTDeliver," was launched by the NTD Supply Chain Forum (a public-private partnership focused on managing and improving the PC donation supply chain) to enhance supply chain performance and information transparency. Our findings suggest that information sharing through NTDeliver is positively associated with performance at several key stages in NTD supply chain and that information sharing has more substantial positive impact on performance when the information is made publicly accessible, focused towards country program managers. The study findings support investment in supply chain systems and commitment to data transparency, in the context of a growing focus on supply chain investment in NTD programs.

microbiology↗

bioRxiv2021

A multi-tiered map of EMT defines major transition points and identifies vulnerabilities

Epithelial to mesenchymal transition (EMT) is a complex cellular program proceeding through a hybrid E/M state linked to cancer-associated stemness, migration and chemoresistance. Deeper molecular understanding of this dynamic physiological landscape is needed to define events which regulate the transition and entry into and exit from the E/M state. Here, we quantified >60,000 molecules across ten time points and twelve omic layers in human mammary epithelial cells undergoing TGF{beta}-induced EMT. Deep proteomic profiles of whole cells, nuclei, extracellular vesicles, secretome, membrane and phosphoproteome defined state-specific signatures and major transition points. Parallel metabolomics showed metabolic reprogramming preceded changes in other layers, while single-cell RNA sequencing identified transcription factors controlling entry into E/M. Covariance analysis exposed unexpected discordance between the molecular layers. Integrative causal modeling revealed co-dependencies governing entry into E/M that were verified experimentally using combinatorial inhibition. Overall, this dataset provides an unprecedented resource on TGF{beta} signaling, EMT and cancer.

systems biology↗

bioRxiv2021

Mechano-transduction via the pectin-FERONIA complex regulates ROP6 GTPase signaling in Arabidopsis

During growth and morphogenesis, plant cells respond to mechanical stresses resulting from spatiotemporal changes in the cell wall that bear high internal turgor pressure. Microtubule (MT) arrays are re-organized to align in the direction of maximal tensile stress to guide the synthesis of cellulose, reinforcing the local cell wall. However, how mechanical forces regulate MT re-organization remains largely unknown. Here, we demonstrate that mechanical signaling that is based on the CrRLK1L subfamily receptor kinase FERONIA (FER) regulates the reorganization of cortical MT in cotyledon epidermal pavement cells (PC) in Arabidopsis. Recessive mutations in FER compromised MT response to mechanical perturbations such as single cell ablation, compression and Isoxaben treatment in these pavement cells. These perturbations promoted the activation of ROP6 GTPase that acts directly downstream of FER. Furthermore, defects in the ROP6 signaling pathway negated the reorganization of cortical MTs induced by these stresses. Finally, reduction in highly demethylesterified pectin, which binds the extracellular malectin domain of FER and is required for FER-mediated ROP6 activation, also impacted mechanical induction of cortical MT reorganization. Taken together our results suggest that the FER-pectin complex senses and/or transduce mechanical forces to regulate MT organization through activating the ROP6 signaling pathway in Arabidopsis.

cell biology↗