Project description:Proteins in the EVs of MCF-10A and MDA-MB-231 cells were determined by mass spectrometry using a timsTOF Pro mass spectrometer (Bruker) coupled to an Aurora Ultimate reverse-phase column (IonOpticks)
Project description:The field of graft preservation has made considerable strides in recent years improving outcomes related to solid organ restoration and regeneration. In lungs, the use of ex vivo lung perfusion (EVLP) in line with devices and treatments has shown promising results within preclinical and clinical studies with the potential to improve graft quality. The benefit of the therapy would be to render marginal and declined donor lungs suitable for transplantation, ultimately increasing the donor pool available for transplantation. Additionally, such therapies used in machine perfusion could also increase preservation time, facilitating logistical planning. Cytokine adsorption has been demonstrated as a potentially safe and effective therapy when applied to the EVLP circuit and post transplantation. The mechanism by which this treatment improves the donor lung on a molecular basis is not yet fully elucidated. We hypothesized that there were characteristic inflammatory and immunomodulatory differences between lungs treated with and without cytokine adsorption, reflecting in proteomic changes in gene ontology pathways and across inflammation-related proteins. In the current study we investigate the molecular mechanisms and signaling pathways of how cytokine adsorption impacts the lung function when used during EVLP and when used post transplantation as hemoperfusion in a porcine model. Lung tissue from EVLP and post lung transplantation were analyzed for their proteomic profile using mass spectrometry. The inflammatory and immune processes were compared between the treated and the non-treated groups to show the differences occurring between the forms of graft preservation.
Project description:Understanding how genetic variation translates into complex phenotypes remains a fundamental challenge. Here, we address this by mapping genome-to-proteome relationships in 800 progeny of a cross between two yeast strains adapted to distinct environments. Despite the modest genetic distance between the parents, we observed remarkable proteomic diversity and mapped over 6,400 genotype-protein associations, with more than 1,600 linked to individual genetic variants. Proteomic adaptation emerged from a conserved network of cis- and trans-regulatory variants, often originating from proteins not traditionally linked to gene regulation. This atlas allowed us to forecast organismal fitness effects across diverse conditions. By connecting genomic and proteomic landscapes at unprecedented resolution, our study provides a framework for predicting the phenotypic outcomes of natural genetic variation.
Project description:Treatment of Mycobacterium tuberculosis infections is a challenging task due to a growing number of resistant clinical isolates as well as an almost empty drug development pipeline. To identify new antibiotic hits, we screened a focused library of 400 synthetic compounds derived from a recently discovered molecule with promising anti-mycobacterial activity. A suite of more potent hit molecules was deciphered with sub-micromolar activity. Utilising tailored affinity-based probes for chemical proteomic investigations, we successfully pinpointed the mycolic acid transporter MmpL3 and two epoxide hydrolases, EphD and EphF, also linked to mycolic acid biosynthesis, as specific targets of the compounds. These targets were thoroughly and independently validated by activity assays, under- and overexpression, resistance generation, and proteomic studies. Structural refinement of the most potent hit molecules led to the development of a new lead compound that demonstrates enhanced biological activity in M. tuberculosis, low human cytotoxicity, and improved solubility and oral bioavailability − traits that are often challenging to achieve with anti-mycobacterial drugs. Overall, drug-likeness, as well as the dual mode of action, addressing the mycolic acid cell wall assembly at two distinct steps, holds significant potential for further in vivo applications.
Project description:All samples were processed by DIA individually to assess the proteome differences. MS1 and MS2 data were all acquired, and samples acquisition by random order. The iRT kit (Ki3002, Biognosys AG, Switzerland) was added to all of the samples to calibrate the retention time of extracted peptide peaks. The statistical analysis of the DIA dataset was performed by Spectronaut 16 (Biognosys AG, Switzerland) including data normalization and relative protein quantification.
Project description:The process of chondrogenesis in deer antlers is very similar to that of mammalian cartilage formation. Antlers can regenerate at an alarming rate (up to 2 cm per day). To meet the rapid growth of antlers, paracrine factors play an important role. These paracrine factors promote the proliferation and growth of chondrocytes, regulate cartilage development and modulate cartilage phenotype. The application of stem cell paracrine factors for the treatment of cartilage defects avoids the problems of immunocompatibility, tumorigenicity, embolization, and infection. This study demonstrates that ASC-CM can effectively repair cartilage defects using in vitro and in vivo methods, providing a suitable cell source and pathway for cartilage repair and providing ideas for mechanisms to promote cartilage regeneration.
Project description:Coronaviruses constitute a constant threat as documented by the recent emergence of SARS-CoV-2 that has caused more than 2,5 million deaths worldwide. Despite this our understanding of coronaviruses and how they interact with their host is very limited. Here we describe a novel phage display library for the discovery of viral short linear interaction motifs (SLiMs) from RNA viruses that mediate binding to human host factors. We utilize this library to uncover the unique patterns of viral SLiMs mediating SARS-CoV-2 - host factor interactions. This established a specific interaction between the human G3BP1/2 proteins and an xFG peptide motif in the viral nucleocapside (N) protein that when disrupted reduce viral replication and infection. We show that the N protein through this xFG motif modulates the G3BP1/2 host interactome by competing with numerous cellular xFG containing proteins and inhibits G3BP1/2 mediated stress granule formation. Collectively our work outlines a strategy for system-wide understanding of viral-host factor interactions that provides both mechanistic insight and pinpoints therapeutically relevant interactions for development of novel antiviral strategies.
Project description:In this study, a unique tea cultivar ‘Anxi kucha’ was discovered for the first time, which is rich in both secondary metabolites. In the targeted data, theacrine (17.44 mg/g) was detected only in the ‘Anxi kucha’ tea plant in the test materials. The content of EGCG3"Me in ‘Anxi kucha’ (11.25mg/g), ‘Tieguanyin’ (5.32mg/g) and ‘Fudingdabaicha’ (0.93mg/g) showed high, medium and low changes. Through proteomics and transcriptomics, it was identified that the key pathways for the synthesis of theacrine and EGCG3"Me were the purine metabolism pathway and the flavonoid biosynthesis pathway, respectively. Combined proteome-transcriptome-metabolome analysis showed that SAMS3, APRT1, IMPDH, and TCS1 were the main enzymes promoting theacrine synthesis; CHI1, CHI2, FLS2 and LAR1 were the main enzymes that promote the synthesis of EGCG3"Me. The results of transcription factor analysis showed that MYB4 and bHLH74 had positive regulatory effects on the synthesis of theacrine and EGCG3"Me. Theacrine and EGCG3"Me are both bitter compounds. This study provides a valuable material rich in theacrine and EGCG3"Me, which provides a material basis for further development and utilization in the field of tea health food and a theoretical basis for studying the functional components of tea.