Biology subjects

Gao, E.

Publications and source records attributed to Gao, E..

16 recordsLinked to original sources

bioRxiv2026

BioMINTREL expands biological problem solving through cross-disciplinary representations

Biological research agents often rely on familiar analytical methods, limiting the questions explored in existing data. We introduce BioMINTREL, an AI agent that finds methods from other disciplines and connects them to biological measurements. It can draw on relationships among datasets and complementary ideas from several methods to develop new questions and analyses. We evaluate it on BioMDC-Bench, which assesses 228 possible applications of computational methods to biological tasks. Compared with GPT-5.4 mini and Qwen3.6-35B, BioMINTREL improves F1 agreement with human experts by up to 45.3 percentage points and increases coverage of applications supported by studies published in subsequent years by up to 58.8 percentage points. Four case studies on real data go beyond previous analyses to reveal dose-specific variant effects, constraints on spatial cell communication and routes through perturbation-response states, and identify the sampling needed to test whether rare high-state cells predict later lineage size. These results highlight BioMINTREL's potential to expand questions in existing data and suggest directions for subsequent research.

bioinformatics↗

bioRxiv2024

Podoplanin Positive Cell-derived Extracellular Vesicles Contribute to Cardiac Amyloidosis After Myocardial Infarction

BackgroundAmyloidosis is a major long-term complication of chronic disease; however, whether it represents one of the complications of post-myocardial infarction (MI) is yet to be fully understood. MethodsUsing wild-type and knocked-out MI mouse models and characterizing in vitro the exosomal communication between bone marrow-derived macrophages and activated mesenchymal stromal cells (MSC) isolated after MI, we investigated the mechanism behind Serum Amyloid A 3 (SAA3) protein overproduction in injured hearts. ResultsHere, we show that amyloidosis occurs after MI and that amyloid fibers are composed of macrophage-derived SAA3 monomers. SAA3 overproduction in macrophages is triggered by exosomal communication from a subset of activated MSC, which, in response to MI, acquire the expression of a platelet aggregation-inducing type I transmembrane glycoprotein named Podoplanin (PDPN). Cardiac MSCPDPN+ communicate with and activate macrophages through their extracellular vesicles or exosomes. Specifically, MSCPDPN+ derived exosomes (MSCPDPN+ Exosomes) are enriched in SAA3 and exosomal SAA3 protein engages with Toll-like receptor 2 (TRL2) on macrophages, triggering an overproduction and impaired clearance of SAA3 proteins, resulting in aggregation of SAA3 monomers as rigid amyloid deposits in the extracellular space. The onset of amyloid fibers deposition alongside extra-cellular-matrix (ECM) proteins in the ischemic heart exacerbates the rigidity and stiffness of the scar, hindering the contractility of viable myocardium and overall impairing organ function. Using SAA3 and TLR2 deficient mouse models, we show that SAA3 delivered by MSCPDPN+ exosomes promotes post-MI amyloidosis. Inhibition of SAA3 aggregation via administration of a retro-inverso D-peptide, specifically designed to bind SAA3 monomers, prevents the deposition of SAA3 amyloid fibrils, positively modulates the scar formation, and improves heart function post-MI. ConclusionOverall, our findings provide mechanistic insights into post-MI amyloidosis and suggest that SAA3 may be an attractive target for effective scar reversal after ischemic injury and a potential target in multiple diseases characterized by a similar pattern of inflammation and amyloid deposition. NOVELTY AND SIGNIFICANCEWhat is known? O_LIAccumulation of rigid amyloid structures in the left ventricular wall impairs ventricle contractility. C_LIO_LIAfter myocardial infarction cardiac Mesenchymal Stromal Cells (MSC) acquire Podoplanin (PDPN) to better interact with immune cells. C_LIO_LIAmyloid structures can accumulate in the heart after chronic inflammatory conditions. C_LI What information does this article contribute? O_LIWhether accumulation of cumbersome amyloid structures in the ischemic scar impairs left ventricle contractility, and scar reversal after myocardial infarction (MI) has never been investigated. C_LIO_LIThe pathophysiological relevance of PDPN acquirement by MSC and the functional role of their secreted exosomes in the context of post-MI cardiac remodeling has not been investigated. C_LIO_LIAmyloid structures are present in the scar after ischemia and are composed of macrophage-derived Serum Amyloid A (SAA) 3 monomers, although mechanisms of SAA3 overproduction is not established. C_LI SUMMARY OF NOVELTY AND SIGNIFICANCEHere, we report that amyloidosis, a secondary phenomenon of an already preexisting and prolonged chronic inflammatory condition, occurs after MI and that amyloid structures are composed of macrophage-derived SAA3 monomers. Frequently studied cardiac amyloidosis are caused by aggregation of immunoglobulin light chains, transthyretin, fibrinogen, and apolipoprotein in a healthy heart as a consequence of systemic chronic inflammation leading to congestive heart failure with various types of arrhythmias and tissue stiffness. Although chronic MI is considered a systemic inflammatory condition, studies regarding the possible accumulation of amyloidogenic proteins after MI and the mechanisms involved in that process are yet to be reported. Here, we show that SAA3 overproduction in macrophages is triggered in a Toll-like Receptor 2 (TLR2)-p38MAP Kinase-dependent manner by exosomal communication from a subset of activated MSC, which, in response to MI, express a platelet aggregation-inducing type I transmembrane glycoprotein named Podoplanin. We provide the full mechanism of this phenomenon in murine models and confirm SAA3 amyloidosis in failing human heart samples. Moreover, we developed a retro-inverso D-peptide therapeutic approach, "DRI-R5S," specifically designed to bind SAA3 monomers and prevent post-MI aggregation and deposition of SAA3 amyloid fibrils without interfering with the innate immune response.

immunology↗

bioRxiv2024

Machine Learning Models for Cardiovascular Disease Prediction: A Comparative Study

Cardiovascular diseases (CVDs) pose a significant threat to global public health, affecting individuals across various age groups. Factors such as cholesterol levels, smoking, alcohol consumption, and physical inactivity contribute to their onset and progression. Enhancing our understanding of CVD etiology and informing targeted interventions for disease prevention and management remains a critical challenge. In this study, we address the task of predicting the likelihood of individuals developing CVDs using machine learning techniques. Specifically, we explore three approaches: the k-nearest neighbors (KNN) algorithm, logistic regression, and the random forest algorithm. Leveraging a comprehensive dataset sourced from Kaggle, encompassing 11 relevant factors, we conduct a series of experiments to identify the most influential predictors of CVDs. Our analysis aims not only to forecast disease occurrence but also to elucidate the primary determinants contributing to its manifestation. Through comparative analysis of the three methodologies, we demonstrate that the random forest algorithm exhibits superior performance in terms of predictive accuracy. This research represents a significant step towards leveraging machine learning techniques to enhance our understanding of CVD dynamics and inform targeted interventions for disease prevention and management.

cancer biology↗

bioRxiv2023

Loss of Myeloid Cell-Specific β2-Adrenergic Receptor Expression Ameliorates Cardiac Function and Remodeling after Acute Ischemia

Myeloid cells, including neutrophils, monocytes and macrophages, accumulate quickly after ischemic injury in the heart where they play integral roles in the regulation of inflammation and repair. We previously reported that deletion of {beta}2-adrenergic receptor ({beta}2AR) in all cells of hematopoietic origin resulted in generalized disruption of immune cell responsiveness to injury, but with unknown impact on myeloid cells specifically. To investigate this, we crossed floxed {beta}2AR (F/F) mice with myeloid cell-expressing Cre (LysM-Cre) mice to generate myeloid cell-specific {beta}2AR knockout mice (LB2) and subjected them to myocardial infarction (MI). Via echocardiography and immunohistochemical analyses, LB2 mice displayed better cardiac function and less fibrotic remodeling after MI than the control lines. Despite similar accumulation of myeloid cell subsets in the heart at 1-day post-MI, LB2 mice displayed reduced numbers of Nu by 4 days post-MI, suggesting LB2 hearts have enhanced capacity for Nu efferocytosis. Indeed, bone marrow-derived macrophage (BMDM)-mediated efferocytosis of Nu was enhanced in LB2-versus F/F-derived cells in vitro. Mechanistically, several pro-efferocytosis-related genes were increased in LB2 myeloid cells, with annexin A1 (Anxa1) in particular elevated in several myeloid cell types following MI. Accordingly, shRNA-mediated knockdown of Anxa1 in LB2 bone marrow prior to transplantation into irradiated LB2 mice reduced Mac-induced Nu efferocytosis in vitro and prevented the ameliorative effects of myeloid cell-specific {beta}2AR deletion on cardiac function and fibrosis following MI in vivo. Altogether, our data reveal a previously unrecognized role for {beta}2AR in the regulation of myeloid cell-dependent efferocytosis in the heart following injury.

immunology↗

bioRxiv2023

Prolonged activity-deprivation causes pre- and postsynaptic compensatory plasticity at neocortical excitatory synapses

Homeostatic plasticity stabilizes firing rates of neurons, but the pressure to restore low activity rates can significantly alter synaptic and cellular properties. Most previous studies of homeostatic readjustment to complete activity silencing in rodent forebrain have examined changes after two days of deprivation, but it is known that longer periods of deprivation can produce adverse effects. To better understand the mechanisms underlying these effects and to address how presynaptic as well as postsynaptic compartments change during homeostatic plasticity, we subjected mouse cortical slice cultures to a more severe five-day deprivation paradigm. We developed and validated a computational framework to measure the number and morphology of presynaptic and postsynaptic compartments from super resolution light microscopy images of dense cortical tissue. Using these tools, combined with electrophysiological miniature excitatory postsynaptic current measurements, and synaptic imaging at the electron microscopy level, we assessed the functional and morphological results of prolonged deprivation. Excitatory synapses were strengthened both presynaptically and postsynaptically. Surprisingly, we also observed a decrement in the density of excitatory synapses, both as measured from colocalized staining of pre- and postsynaptic proteins in tissue, and from the number of dendritic spines. Overall, our results suggest that cortical networks deprived of activity progressively move towards a smaller population of stronger synapses. SIGNIFICANCE STATEMENTBlocking activity in neocortical slice cultures produced coordinated pre and postsynaptic changes at excitatory synapses. Functional and structural assays suggest that deprivation results in fewer excitatory synapses, but each is strengthened both pre- and postsynaptically. This may contribute to the emergence of epileptiform activity.

neuroscience↗

bioRxiv2023

Cardiac-targeted rAAV5-S100A1 gene therapy protects against adverse remodeling and contractile dysfunction in post-ischemic hearts

Toxicity by recombinant adeno-associated viruses (rAAV) in clinical gene therapy trials (e.g., by rAAV9-mediated fatal liver failure) significantly impairs translation of preclinical rAAV-based cardiac gene therapies employing these vectors. For rAAV5 - a capsid that has shown long-term safety in clinical trials - our translational study demonstrates effective transduction of the left ventricle (LV) of healthy pigs via catheter-based retrograde intravenous delivery (CRID) by means of luciferase reporter gene biodistribution analyses. Combination of rAAV5 with the cardioprotective human gene S100A1 (hS100A1) prevents LV myocardial infarct (MI) enlargement and improves LV systolic contractile performance in a porcine model of post-MI chronic cardiac dysfunction. Use of a cardiac-biased promoter ensured the cardiac-directed expression of the therapeutic human transgene without signs of clinical toxicity. The beneficial effects of rAAV5-hS100A1 were linked to an attenuated activity of post-MI inflammatory gene networks and this was further validated in a murine model. These novel data together with proven scalable producibility and low pre-existing immunity against rAAV5 in humans may collectively advance clinical translation of rAAV5-hS100A1 as a gene therapy medicinal product (GTMP) for a common cardiovascular disease, such as chronic heart failure (CHF). HighlightsO_LIRecent fatal adverse events in recombinant adeno-associated virus (AAV)-based clinical gene therapy trials advise the use of rAAV serotypes with proven long-term clinical safety, such as rAAV5, for the pre-clinical development and clinical translation of rAAV-based cardiac gene therapy medicinal products. C_LIO_LIIn a biodistribution and therapeutic proof-of-concept study in farm pigs, rAAV5 was identified as an effective viral vector for cardiac gene transfer and gene therapy for post-ischemic cardiac dysfunction when applied by a standardized cardiac-targeted catheter-based route of administration with the luciferase reporter and cardioprotective human gene S100A1 (hS100A1), respectively. C_LIO_LIA systems biology analysis linked the novel finding of mitigated inflammatory and activated cardioprotective gene network activities in rAAV5-hS100A1 treated postischemic myocardium with improved study left ventricular ejection fraction and prevention of myocardial infarct extension, respectively, which warrants further mechanistic molecular studies. C_LIO_LISince rAAV5 has been recently approved for clinical use in a non-cardiac indication and cardiac-targeted S100A1 gene therapy has been effective in numerous pre-clinical animal models of acute and chronic cardiac dysfunction, our translational data support an expedited developmental path for rAAV5-hS100A1 throughout investigational new drug-enabling studies towards a first-in-human clinical trial for post-myocardial infarction heart failure. C_LI

pathology↗

bioRxiv2023

S100A1ct: a synthetic peptide derived from human S100A1 protein improves cardiac contractile performance and survival in pre-clinical heart failure models

BackgroundThe EF-hand Ca2+ sensor protein S100A1 has been identified as a molecular regulator and enhancer of cardiac performance. S100A1s ability to recognize and modulate the activity of targets such as SERCA2a and RyR2 in cardiomyocytes has mostly been ascribed to its hydrophobic C-terminal -helix (residues 75-94). Objective: We therefore hypothesized that a synthetic peptide consisting of residues 75-94 of S100A1 and an N-terminal solubilization tag (S100A1ct) could mimic the performance enhancing effects of S100A1 and may be suitable as a peptide therapeutic to improve the function of diseased hearts. Methods and Results: Applying an integrative translational research pipeline, ranging from computational molecular modeling to large animal cardiac disease models, we characterize S100A1ct as a cell-penetrating peptide with positive inotropic and antiarrhythmic properties in normal and failing myocardium in vitro and in vivo. This activity translates into improved contractile performance and survival in pre-clinical heart failure models with reduced ejection fraction after S100A1ct systemic administration. Mechanistically, S100A1ct exerts a fast and sustained dose-dependent enhancement of cardiomyocyte Ca2+ cycling and prevents {beta}-adrenergic receptor triggered Ca2+ imbalances by targeting SERCA2a and RyR2 activity. Modeling suggests that S100A1ct may stimulate SERCA2a by interacting with the sarcoplasmic transmembrane segments of the multi-span integral membrane Ca2+ pump. Incorporation of a cardiomyocyte targeting peptide tag into S100A1ct (cor-S100A1ct) further enhanced its biological and therapeutic potency in vitro and in vivo. Conclusion: S100A1ct peptide is a promising lead for the development of a novel peptide-based therapeutic against heart failure with reduced ejection fraction.

pharmacology and toxicology↗

bioRxiv2022

Effect and mechanism of black soybean peptides alleviating oxidative damage in the celiac disease cell model

Alpha gliadin peptide induces damage and apoptosis of intestinal cells and aggravates pathology of celiac disease (CD) by inducing oxidative stress. Therefore, inhibition or alleviation of oxidative stress in CD may be an effective approach to the adjunctive treatment of CD. Black soybean peptides (BSPs) have been shown to inhibit oxidative stress and inflammation. The effect of BSPs on CD remains unknown. In this paper, the effect and mechanism of BSPs on the -gliadin peptide (p31-43)-induced Caco-2 cytotoxicity were studied. We identified BSPs that alleviated the cytotoxicity of p31-43 in the CD cell model: Caco-2 cells were pre-treated with bioactive peptides for 3 hours before the addition of p31-43 for treatment for 24 hours, and then cells were collected for subsequent experiments. Our results show that p31-43 can significantly increase the ROS and MDA levels of Caco-2 cells, disrupt the glutathione redox cycle, reduce the activity of the antioxidant enzyme, and inhibit the activation of antioxidant signaling pathways. BSPs pretreatment can inhibit the increase of Keap1 protein induced by p31-43, activate antioxidant genes through Nrf2 protein, improve the activity of the antioxidant enzyme, alleviates glutathione redox cycle imbalance, promote the expression of GCLC or GCLM, and reduce oxidative damage. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/508472v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@b0b8c3org.highwire.dtl.DTLVardef@322434org.highwire.dtl.DTLVardef@1e70b77org.highwire.dtl.DTLVardef@1a1e8f9_HPS_FORMAT_FIGEXP M_FIG Pattern of BSPs against oxidative damage in CD cell mode. C_FIG

cell biology↗

bioRxiv2022

Enhanced Single RNA Imaging Reveals Dynamic Gene Expression in Live Animals

Imaging endogenous mRNAs in live animals is technically challenging. Here we describe an MS2 based signal Amplification with Suntag System that enables live-cell RNA imaging of high temporal resolution and with 8xMS2 stem-loops, which overcomes the obstacle of inserting a 1,300 nt 24xMS2 into the genome for the imaging of endogenous mRNAs. Using this tool we were able to image the activation of gene expression and the dynamics of endogenous mRNAs in the epidermis of live C. elegans.

cell biology↗

bioRxiv2022

Deep Phosphoproteomic Elucidation of Metformin-Signaling in Heterogenous Colorectal Cancer Cells

The biguanide drug metformin is a safe and widely prescribed drug for type 2 diabetes. Interestingly, hundreds of clinical trials were set to evaluate the potential role of metformin in the prevention and treatment of cancer including colorectal cancer (CRC). To interrogate cell signaling events and networks in CRC and explore the druggability of the metformin-rewired phosphorylation network, we performed a proteomic and phosphoproteomic analysis on a panel of 12 molecularly heterogeneous CRC cell lines. Using in-depth data-independent analysis mass spectrometry (DIA-MS), we profiled a total of 10,142 proteins and 56,080 phosphosites (P-sites) in CRC cells treated with metformin for 30 minutes and 24 hours. Our results indicate that metformin does not directly trigger or inhibit any immediate phosphorylation events. Instead, it primarily remodels cell signaling in the long-term. Strikingly, the phosphorylation response to metformin was highly heterogeneous in the CRC panel, uncovering four groups of metformin responsivity. We further performed a network analysis to systematically estimate kinase/phosphatase activities and reconstruct signaling cascades in each cell line. We created a "MetScore" which catalogs the most consistently perturbed P-sites among CRC cells for future studies. Finally, we leveraged the metformin P-site signature to identify pharmacodynamic interactions revealing a number of candidate metformin-interacting drugs. Together, we provide a data resource using state-of-the-art phosphoproteomics to understand the metformin-induced cell signaling for potential cancer therapeutics.

cancer biology↗

bioRxiv2021

Investigation on the changes of Bifidobacterium and lactic acid bacteria in soybean meal fermented feed

The main objective of this research was to explore the dynamic changes of Bifidobacterium and lactic acid bacteria (LAB) in the process of feed fermentation under anaerobic condition, so as to increase the number of fermented bacteria of Bifidobacterium from the aspect of strain combination. The results showed that when Bifidobacterium lactis (B. lactis, i.e. Bifidobacterium animalis subsp. lactis) fermented with Bacillus coagulans or Lactobacillus paracasei, the maximum number of B. lactis in those samples was 9.42 times and 4.64 times of that of fermented sample with B. lactis only. The soybean meal was fermented by B. lactis, L. paracasei and B. coagulans, and the number of B. lactis reached the maximum after fermented 10 days, which was 6.13 times of that in unfermented sample. The reducing sugar content and highest activity of -galactosidase were higher than the control. These results suggest that B. coagulans and L. paracasei can promote the growth of B. lactis. It is inferred that B. coagulans can metabolize normally in aerobic, micro-aerobic and anaerobic environments, consume oxygen, produce digestive enzymes, and cooperate with L. paracasei to produce metabolic products benefit for the growth of B. lactis.

microbiology↗

bioRxiv2021

Lung Epithelial Cells Can Produce Antibodies Participating In Adaptive Humoral Immune Responses

It is generally believed that the main source of antibodies is B lymphocytes. In this study, our results first revealed that B cell-deficient mice could not produce antibodies specific for TI-Ags; however, mice with B cell deficiency could produce TD-Ag-specific antibodies, although antibody production was delayed compared with that in BALB/c mice after primary TD-Ag challenge. Subsequently, we identified that mouse lung epithelial cells could produce and secrete Ig, including IgM, IgA or IgG, which could display TD-Ag-specific antibody activity. Notably, the production of TD-Ag-specific antibodies by lung epithelial cells was found to be dependent on CD4+ T cells but not CD8+ T cells. Our findings indicate for the first time that B cells are not the only source of TD-Ag-specific antibodies but are essential for rapid TD-Ag-specific antibody production by non-B cells. This discovery may reveal a new mechanism for the production of specific antibodies.

immunology↗

bioRxiv2020

Data-independent Acquisition-based Proteome and Phosphoproteome Profiling across Six Melanoma Cell Lines Reveals Determinants of Proteotypes

Human cancer cell lines are widely used in pharmacological and systems biological studies. The rapid documentation of the steady-state gene expression landscape of the cells used in a particular experiment may help to improve the reproducibility of scientific research. Here we applied a data-independent acquisition mass spectrometry (DIA-MS) method, coupled with a peptide spectral-library free data analysis workflow, to measure both proteome and phosphoproteome of a melanoma cell line panel with different metastatic properties. For each cell line, the single-shot DIA-MS detected 8,100 proteins and almost 40,000 phosphopeptides in the respective measurement of two hours. Benchmarking the DIA-MS data towards the RNA-seq data and tandem mass tag (TMT)-MS results from the same set of cell lines demonstrated comparable qualitative coverage and quantitative reproducibility. Our data confirmed the high but complex mRNA~protein and protein~phospsite correlations. The results successfully established DIA-MS as a strong and competitive proteotyping approach for cell lines. The data further showed that all subunits of Glycosylphosphatidylinositol (GPI)-anchor transamidase complex were overexpressed in metastatic melanoma cells and identified altered phosphoprotein modules such as BAF complex and mRNA splicing between metastatic and primary cells. This study provides a high-quality resource for calibrating DIA-MS performance, benchmarking DIA bioinformatic algorithms, and exploring the metastatic proteotypes in melanoma cells.

systems biology↗

bioRxiv2020

A Peptide of the Amino-Terminus of GRK2 Induces Hypertrophy and Yet Elicits Cardioprotection after Pressure Overload

G protein-coupled receptor (GPCR) kinase 2 (GRK2) expression and activity are elevated early on in response to several forms of cardiovascular stress and are a hallmark of heart failure. Interestingly, though, in addition to its well-characterized role in regulating GPCRs, mounting evidence suggests a GRK2 “interactome” that underlies a great diversity in its functional roles. Several such GRK2 interacting partners are important for adaptive and maladaptive myocyte growth; therefore, an understanding of domain-specific interactions with signaling and regulatory molecules could lead to novel targets for heart failure therapy. While elevated cardiac levels and activity of GRK2 contribute to adverse heart remodeling and contractile dysfunction, inhibition of GRK2 via overexpression of a carboxyl-terminal peptide, βARKct, or its amino-terminal domain Regulator of G protein Signaling (RGS) homology domain (βARKrgs) can enhance cardiac function and can prevent heart failure development via Gβγ or Gαq sequestration, respectively. Previously, our lab investigated cardiac-specific transgenic expression of a fragment of this RGS domain (βARKnt) (residues 50-145). In contrast to βARKrgs this fragment did not alter acute hypertrophy after pressure overload or demonstrate RGS activity in vivo against Gq-mediated signaling. Herein, we subjected these transgenic mice to pressure overload and found that unlike their littermate controls or previous GRK2 fragments, they exhibited an increased left ventricular wall thickness and mass prior to cardiac stress that underwent proportional hypertrophic growth to controls after acute pressure overload. Importantly, despite this enlarged heart, βARKnt mice did not undergo the expected transition to heart failure observed in controls. Further, βARKnt expression limited adverse left ventricular remodeling and increased cell survival signaling. These data support the idea that the βARKnt peptide embodies a distinct functional interaction and novel means of cardioprotection during pressure-overload induced heart failure.Competing Interest StatementThe authors have declared no competing interest.AbbreviationsGPCRG protein-coupled receptor;GRK2G protein-coupled receptor kinase 2;RGSregulator of G protein Signaling domain;βARbeta-adrenergic receptor;LVleft ventricular;TACtransverse aortic constriction;αMHCα-myosin heavy chain;NLCnon-transgenic littermate control;WGAwheat germ agglutinin;IPimmunoprecipitation;IP3Inositol 1,4,5-trisphosphate;125I-CYP[125I]cyanopindolol;HFpEFheart failure with preserved ejection fraction;HFrEFheart failure with reduced ejection fraction;InsRinsulin receptor;IRSinsulin receptor substrate;PI3Kphosphoinositide 3-kinase;PDK1 and 2phosphatidylinositol-dependent kinases;PKB/Aktprotein kinase B;AS160Akt substrate of 160 kilodaltons;GAPGTPase-activating protein;GSK3βglycogen synthase kinase 3β.View Full Text

physiology↗

bioRxiv2020

Global impact of phosphorylation on protein endurance

Post-translational modifications such as phosphorylation can have profound effects on the physicochemical and biological properties of proteins. However, high-throughput and systematic approaches have not yet been developed to assess the effects of specific modification types and sites on protein lifetime, which represents a key parameter for understanding signaling rewiring and drug development. Here we describe a proteomic method, DeltaSILAC, to quantify the impact of site-specific phosphorylation on the endurance of thousands of proteins in live cells. Being configured on the reproducible data-independent acquisition mass spectrometry (DIA-MS), the pulse labeling approach using stable isotope-labeled amino acids in cells (SILAC), together with a novel peptide-level matching strategy, this multiplexed assay revealed the global delaying effect of phosphorylation on protein turnover in growing cancer cells. Further, we identified local sequence and structural features in proximity to the phosphorylated sites that could be associated with protein endurance alterations. We found that phosphorylated sites accelerating protein turnover are functionally selected for cell fitness and evolutionarily conserved. DeltaSILAC provides a generalizable approach for prioritizing the effects of phosphorylation sites on protein lifetime in the context of cell signaling and disease biology, which is highly complementary to existing methods. Finally, DeltaSILAC is widely applicable to diverse post-translational modification types and different cell systems.

systems biology↗

bioRxiv2019

Activation or inhibition of PPARα-mediated fatty acid β-oxidation does not active cardiomyocyte proliferation in normal or infarcted adult mice

ObjectivesPPAR genes are known as the important regulators of fatty acid oxidation and energy homeostasis. PPAR is highly expressed in the embryonic and adult heart. Previous studies from infant mouse hearts have suggested that activation of PPAR using GW7647 treatment or cardiac-restricted activation of PPAR using MHC-PPAR transgenic mice enhanced fatty acid {beta}-oxidation and promoted cardiomyocyte proliferation rate in the postnatal day 4 mouse heart. Here, we further investigate the impact of PPAR-mediated fatty acid {beta}-oxidation on cardiomyocyte proliferation in the adult mouse heart.\n\nMethods and ResultsAdult wild-type (C57BL/6J) mice were subjected to five injections of GW7647, a highly specific PPAR agonist, or vehicle (saline). Cardiomyocyte proliferation was analyzed by quantification of DNA synthesis via ethynyldeoxyuridine (EdU) incorporation and quantification of cells undergoing mitosis using phosphorylated histone H3 (PH3). GW7647 treatment resulted in activation of PPAR target genes associated with fatty acid metabolism and {beta}-oxidation, validating its biological activity. However, GW7647 treatment did not active cardiomyocyte proliferation in the normal heart. In parallel, mice were subjected to myocardial infarction (MI) using permanent coronary artery occlusion. Both GW7647-treatd wild-type mice and MHC-PPAR transgenic mice showed no significant differences in cardiomyocyte DNA synthesis and mitosis compared with vehicle-treated wild-type mice after MI. Furthermore, inhibition of PPAR-mediated fatty acid {beta}-oxidation using etomoxir (ETO) treatment had no impact on cardiomyocyte proliferation in both normal and infarcted hearts of wild-type mice compared with vehicle treatment.\n\nSummaryThese findings suggest that activation or inhibition of PPAR-mediated fatty acid {beta}-oxidation did not active cardiomyocyte proliferation in normal or infarcted hearts of adult mice. Any effects on cardiac function observed following PPAR activation treatment is independent of enhanced cardiomyocyte renewal in the adult heart.

cell biology↗