Enrichment Of Proteins Research Articles

Performance and characterization of snail adhesive mucus as a bioflocculant against toxic Microcystis

Toxic Microcystis blooms are widespread in aquatic bodies, posing major threats to aquatic and human life. Recently, bioflocculants have attracted considerable attention as a promising biomaterial for Microcystis management. In search of a novel organism that can produce an efficient bioflocculant for controlling harmful algae sustainably, the native gastropod Cipangopaludina chinensis was co-cultured continuously with toxic Microcystis under different initial algal cell densities. The bioflocculation effect of snail mucus on toxic Microcystis, microcystin removal, and toxin accumulation in snails was investigated. In addition, the properties of the adhesive mucus were characterized using microscopic, X-ray diffraction, infrared spectroscopy, and polysaccharide and proteome analyses. Microcystis cells were captured and flocculated by the snail mucus; removal efficiencies of up to 89.9% and 84.8% were achieved for microalgae and microcystin-leucine arginine (MC-LR), respectively, when co-cultured with C. chinensis for only one day. After nine-day exposure, less than 5.49 µg/kg DW microcystins accumulated in the snails, indicating safety for human consumption. The snail mucus contained 104.3 µg/mg protein and 72.7 µg/mg carbohydrate, which provide several functional groups beneficial for Microcystis bioflocculation. The main monosaccharide subunits of polysaccharides are galactose, galactosamine, glucosamine, fucose, glucose, and mannose. Most of them are key components of polysaccharides in many bioflocculants. Gene Ontology analysis indicated the protein enrichment in binding processes and catalytic activity, which may account for Microcystis bioflocculation via protein binding or enzymatic reactions. The findings indicate that native C. chinensis secretes adhesive mucus that can act as bioflocculant for toxic Microcystis from ambient water and can be an effective and eco-friendly tool for Microcystis suppression.

MFGM-enriched whey displays antiviral activity against common pediatric viruses in vitro.

Among the most common mucosal viral infections in infants are rotavirus, one of the main causes of severe gastroenteritis in infants and children up to 5 years, and respiratory syncytial virus (RSV), one of the leading causes of lower respiratory tract infections. Both human milk and bovine milk derived factors may provide protection against mucosal viral infections. More recently, a similar activity of milk derived proteins was suggested for SARS-CoV-2. The goal of the current study was to test antiviral activity of the bovine milkfat globule membrane (MFGM) against rotavirus, RSV and SARS-CoV-2 and to further characterize MFGM-enriched whey to identify which components in MFGM-enriched whey may contribute to the inhibitory activity. The effects of MFGM-enriched whey, its whey protein isolate counterpart (WPI, obtained from the same production process) and a conventional whey protein concentrate (WPC) on rotavirus (strains Wa and SA114F), RSV (strain RSV-A2) and SARS-CoV-2 (Alpha variant) infectivity were determined using MA104 cells, human alveolar basal epithelial (A549) cells and monkey kidney (Vero E6) cells, respectively. The compounds were characterized in detail by LC-MS/MS and 31P-NMR to determine protein and phospholipid composition, respectively. Relative to its WPI counterpart, MFGM-enriched whey demonstrated a dose-dependent inhibition for both rotavirus and RSV whereas for SARS-CoV-2 inhibition was only observed at the highest concentration tested. Label-free quantification (LFQ) and intensity based absolute quantification (iBAQ) of identified proteins revealed a clear difference between MFGM-enriched whey and its controls including enrichment of known MFGM proteins and non-MFGM proteins that are enriched simultaneously, some of which have previously been demonstrated to display anti-viral activity. Although not completely absent from other whey protein preparations, MFGM-enriched whey had the highest specific and total phospholipid levels. MFGM-enriched whey displayed antiviral activity against multiple viruses of clinical importance. This study provides insights into the active components in MFGM-enriched whey and may contribute to previous clinical observations with MFGM-enriched formula demonstrating reduced respiratory and gastrointestinal infections in formula fed infants.

Engineered nanovesicles from activated neutrophils with enriched bactericidal proteins have molecular debridement ability and promote infectious wound healing.

Bacterial infections pose a considerable threat to skin wounds, particularly in the case of challenging-to-treat diabetic wounds. Systemic antibiotics often struggle to penetrate deep wound tissues and topically applied antibiotics may lead to sensitization, necessitating the development of novel approaches for effectively treating germs in deep wound tissues. Neutrophils, the predominant immune cells in the bloodstream, rapidly release an abundance of molecules via degranulation upon activation, which possess the ability to directly eliminate pathogens. This study was designed to develop novel neutrophil cell engineered nanovesicles (NVs) with high production and explore their bactericidal properties and application in promoting infectious wound healing. Neutrophils were isolated from peripheral blood and activated in vitro via phorbol myristate acetate (PMA) stimulation. Engineered NVs were prepared by sequentially extruding activated neutrophils followed by ultracentrifugation and were compared with neutrophil-derived exosomes in terms of morphology, size distribution and protein contents. The bactericidal effect of NVs in vitro was evaluated using the spread plate technique, LIVE/DEAD backlight bacteria assay and observation of bacterial morphology. The therapeutic effects of NVs in vivo were evaluated using wound contraction area measurements, histopathological examinations, assessments of inflammatory factors and immunochemical staining. Activated neutrophils stimulated with PMA in vitro promptly release a substantial amount of bactericidal proteins. NVs are similar to exosomes in terms of morphology and particle size, but they exhibit a significantly higher enrichment of bactericidal proteins. In vitro, NVs demonstrated a significant bactericidal effect, presumably mediated by the enrichment of bactericidal proteins such as lysozyme. These NVs significantly accelerated wound healing, leading to a marked reduction in bacterial load, downregulation of inflammatory factors and enhanced collagen deposition in a full-thickness infectious skin defect model. We developed engineered NVs derived from activated neutrophils to serve as a novel debridement method targeting bacteria in deep tissues, ultimately promoting infectious wound healing.

Immunoaffinity-free chromatographic purification of ovarian cancer biomarker CA125 (MUC16) from blood serum enables mass spectrometry characterization.

The enrichment of trace proteins from human fluid samples is of great importance in diverse clinical and industrial applications. In clinical diagnostics, such enrichment may enable detection of trace proteins that serve as biomarkers of disease. Affinity-based approaches, such as immunoaffinity pulldown, are widely used to enrich trace proteins, but this strategy relies on the availability and performance of antibodies that act on all proteoforms in an unbiased manner. Our prior work to characterize MUC16 (the mucin protein that carries the ovarian cancer biomarker CA125) by mass spectrometry successfully overcame the reliance on affinity-based enrichment and was used to enrich this biomarker from ascites of individual ovarian cancer patients, however, this strategy was not demonstrated on clinically relevant volumes of serum, a biofluid that is more accessible than ascites. The present work developed a non-affinity-based chromatographic method to enrich MUC16 from serum. The enriched MUC16 sample was further processed using a Midi Top 14 abundant protein depletion column. Peptides identified using bottom-up proteomics yielded 1-8% coverage of MUC16. Additionally, MUC16 was detected in samples containing less than the clinical cut-off level of CA125 (35 U mL-1), suggesting that this strategy of enrichment and bottom-up proteomics can enable analysis of CA125 from the serum of individuals with early-stage ovarian cancer and those whose tumors express CA125 (MUC16) at low levels.

Unique Behavior of Bacterially Expressed Rat Carnitine Palmitoyltransferase 2 and Its Catalytic Activity.

Mammalian type 2 carnitine parmitoyltransferase (EC 2.3.1.21), abbreviated as CPT2, is an enzyme involved in the translocation of fatty acid into the mitochondrial matrix space, and catalyzes the reaction acylcarnitine + CoA = acyl-CoA + carnitine. When rat CPT2 was expressed in Escherichia coli, its behavior was dependent on the presence or absence of i) its mitochondrial localization sequence and ii) a short amino acid sequence thought to anchor it to the mitochondrial inner membrane: CPT2 containing both sequences behaved as a hydrophobic protein, while recombinant CPT2 lacking both regions behaved as a water soluble protein; if only one region was present, the resultant proteins were observed in both fractions. Because relatively few protein species could be obtained from bacterial lysates as insoluble pellets under the experimental conditions used, selective enrichment of recombinant CPT2 protein containing both hydrophobic sequences was easily achieved. Furthermore, when CPT2 enriched in insoluble fraction was resuspended in an appropriate medium, it showed catalytic activity typical of CPT2: it was completely suppressed by the CPT2 inhibitor, ST1326, but not by the CPT1 inhibitor, malonyl-CoA. Therefore, we conclude that the bacterial expression system is an effective tool for characterization studies of mammalian CPT2.

Differential temporal release and lipoprotein loading in B. thetaiotaomicron bacterial extracellular vesicles.

Bacterial extracellular vesicles (BEVs) contribute to stress responses, quorum sensing, biofilm formation and interspecies and interkingdom communication. However, the factors that regulate their release and heterogeneity are not well understood. We set out to investigate these factors in the common gut commensal Bacteroides thetaiotaomicron by studying BEV release throughout their growth cycle. Utilising a range of methods, we demonstrate that vesicles released at different stages of growth have significantly different composition, with early vesicles enriched in specifically released outer membrane vesicles (OMVs) containing a larger proportion of lipoproteins, while late phase BEVs primarily contain lytic vesicles with enrichment of cytoplasmic proteins. Furthermore, we demonstrate that lipoproteins containing a negatively charged signal peptide are preferentially incorporated in OMVs. We use this observation to predict all Bacteroides thetaiotaomicron OMV enriched lipoproteins and analyse their function. Overall, our findings highlight the need to understand media composition and BEV release dynamics prior to functional characterisation and define the theoretical functional capacity of Bacteroides thetaiotaomicron OMVs.

Measuring Piezo1 and Actin Polarity in Chemokine-Stimulated Jurkat Cells During Live-Cell Imaging.

The process of T-lymphocyte migration involves a complex interplay of chemical and mechanical signals. Mechanotransduction mechanisms in T lymphocytes enable them to efficiently navigate through diverse architectural and topographical features of the dynamic tissue macro- and micro-niches encountered during immune responses. Piezo1 mechanosensors are crucial for driving optimal T-cell migration by driving actin-cytoskeletal remodeling. Chemokine-stimulated T lymphocytes demonstrate significant asymmetry or polarity of Piezo1 and actin along the cell axis. The establishment and maintenance of polarity in migrating cells are paramount for facilitating coordinated and directional movements along gradients of chemokine signals. Live-cell imaging techniques are widely employed to study the trajectories of migrating cells. Our approach expands upon current methodologies by not only tracking migrating cells but also imaging fluorescently labeled cellular components. Specifically, our method enables measurement of protein enrichment in the front and rear halves of the moving cell by analyzing the temporal direction of cell trajectories, subsequently bisecting the cell into front-back halves, and measuring the intensities of the fluorescent signals in each cell half at each time frame. Our protocol also facilitates the quantification of the angular distribution of fluorescent signals, enabling visualization of the spatial distribution of signals relative to the direction of cell migration. The protocol describes the examination of polarity in chemokine-treated Jurkat cells transfected with Piezo1-mCherry and actin-GFP constructs. This approach can be extended to live-cell imaging and polarity assessment of other fluorescently labeled proteins. Key features • This experimental protocol allows real-time imaging of Jurkat cells expressing two fluorescent proteins (Piezo1 mCherry and actin-GFP). • Measures cell polarity by examining spatial enrichment of Piezo1 and actin proteins within the front and rear halves of a moving Jurkat cell. • The protocol enables analysis of cell polarity in 2D tracks of moving cells. • Polarity analysis includes measuring fluorescent signal intensities in front-rear halves of a moving cell and calculation of signal polarization angles relative to the cell trajectory.

Utilizing Proteomic Analysis to Assess the Biocompatibility and Growth Behavior of Human Immunodeficiency Virus-Associated Colorectal Cancer Cells on Polylactic Acid/Polyglycolic Acid Composite Scaffold

This research aimed to analyze the biocompatibility and growth behavior of human immunodeficiency virus (HIV)-associated colorectal cancer (CRC) cells on a polylactic acid/polyglycolic acid (PLA-PCL) composite nanofiber scaffold (CNS) using proteomic analysis. The PLA-PCL CNS was prepared using a gel extraction phase separation (GEPS) method in a dioxane/ethanol solvent system, and the effects of gel temperature, PLA-PCL mass ratio (MR), solvent-to-polymer MR on the structure and properties of the PLA-PCL CNS were analyzed. Subsequently, Lappaol F (LAF) was incorporated into the PLA-PCL CNS using electrospinning (ES) technology, and tissue specimens were obtained from HIV-associated CRC patients to investigate the impacts of LAF-PLA-PCL CNS on the growth behavior of HIV-associated CRC cells through mass spectrometry and bioinformatics analysis. Field emission scanning electron microscopy (FE-SEM) revealed that the CNS could be obtained at gel temperatures between −20 °C and −10 °C, PLA-to-PCL MRs of 1:1, 3:2, 7:3, and ethanol content of 5%–15%. X-ray diffraction (XRD) and differential scanning calorimetry (DSC) showed that the PLA-to-PCL MR of 70:30 exhibited compatibility and crystallinity of the PLA-PCL CNS, while the porosity increased with an increase in PCL content. Fourier-transform infrared spectroscopy (FTIR) analysis indicated a good biological activity of the PLA-PCL CNS. The relative cell proliferation (RCP) and cytotoxicity grades exhibited no marked differences (P >0.05) between the cancer cells cultured with DMEM and those with PLA-PCL scaffold extract over time. Proteomic analysis identified 127 differentially expressed proteins (DEPs) in HIV-associated CRC cells co-cultured with LAF-PLA-PCL CNS, and Gene Ontology (GO) protein and KEGG pathway enrichment analysis (KEGG analysis) revealed that the LAF-PLA-PCL NCS could affect the cell cycle (CC) of HIV-associated CRC cells. In conclusion, the PLA-PCL NCS exhibited good compatibility, crystallinity, and biological activity, while the LAF-PLA-PCL NCS showed the potential to inhibit cell proliferation by affecting the CC.

Neuregulin-1, a member of the epidermal growth factor family, mitigates STING-mediated pyroptosis and necroptosis in ischaemic flaps

Abstract Background Ensuring the survival of the distal end of a random flap during hypoperfusion (ischaemia) is difficult in clinical practice. Effective prevention of programmed cell death is a potential strategy for inhibiting ischaemic flap necrosis. The activation of stimulator of interferon genes (STING) pathway promotes inflammation and leads to cell death. The epidermal growth factor family member neuregulin-1 (NRG1) reduces cell death by activating the protein kinase B (AKT) signalling pathway. Moreover, AKT signalling negatively regulates STING activity. We aimed to verify the efficacy of NRG1 injection in protecting against flap necrosis. Additionally, we investigated whether NRG1 effectively enhances ischemic flap survival by inhibiting pyroptosis and necroptosis through STING suppression. Methods A random-pattern skin flap model was generated on the backs of C57BL/6 mice. The skin flap survival area was determined. The blood supply and vascular network of the flap was assessed by laser Doppler blood flow analysis. Cluster of differentiation 34 immunohistochemistry (IHC) and haematoxylin and eosin (H&E) staining of the flap sections revealed microvessels. Transcriptome sequencing analysis revealed the mechanism by which NRG1 promotes the survival of ischaemic flaps. The levels of angiogenesis, oxidative stress, necroptosis, pyroptosis and indicators associated with signalling pathways in flaps were examined by IHC, immunofluorescence and Western blotting. Packaging adeno-associated virus (AAV) was used to activate STING in flaps. Results NRG1 promoted the survival of ischaemic flaps. An increased subcutaneous vascular network and neovascularization were found in ischaemic flaps after the application of NRG1. Transcriptomic gene ontology enrichment analysis and protein level detection indicated that necroptosis, pyroptosis and STING activity were reduced in the NRG1 group. The phosphorylation of AKT and forkhead box O3a (FOXO3a) were increased after NRG1 treatment. The increased expression of STING in flaps induced by AAV reversed the therapeutic effect of NRG1. The ability of NRG1 to phosphorylate AKT-FOXO3a, inhibit STING and promote flap survival was abolished after the application of the AKT inhibitor MK2206. Conclusions NRG1 inhibits pyroptosis and necroptosis by activating the AKT-FOXO3a signalling pathway to suppress STING activation and promote ischaemic flap survival.

Exploring Potential Biomarkers of Early Thymoma based on Serum Proteomics.

Early diagnosis remains difficult because the early symptoms of thymoma are atypical. This study aimed to analyze the changes of serum proteins in the early stage of thymoma (stage I/II) by proteomics method and to screen and validate candidate biomarkers. Proteins were extracted from 8 sera patients with stage I/II thymoma and 9 healthy controls. The levels of serum proteins were detected by data-independent acquisition (DIA) quantitative proteomics techniques, and the differential proteins were identified. The proteomic results were verified by enzyme-linked immunosorbent assay. Additionally, differentially expressed proteins were analyzed using receiver operating characteristic curves (ROC). There were 80 differentially expressed proteins between the patients with thymoma and the healthy control group, among which 39 were up-regulated and 41 were down-regulated. Differential protein enrichment is involved in environmental information processing, signaling molecules and interactions, and in the body system and the immune system. The analysis of receptor working characteristic curves showed that the areas under the curve of CORO1A, SAA1 and LTA4H were all larger than 0.8, indicating that these proteins had good diagnostic value. CORO1A, SAA1 and LTA4H may be new biomarkers for early screening of thymoma.

Utilizing the influence of protein enrichment of meal components as a strategy to possibly prevent undernutrition in the elderly: an in vitro approach.

Nutritional strategies are required to limit the prevalence of denutrition in the elderly. With this in mind, fortified meals can provide more protein, but their digestibility must be ensured. Using a dynamic in vitro digester, DIDGI®, programmed with the digestion conditions of the elderly, we evaluated the supplementation of each component of a meal and assessed protein digestibility, amino acid profile, micro-nutrients and vitamins bioaccessibility for a full course meal. Higher protein digestibility was evidenced for the fortified meal, with higher release of essential amino acids. Moreover the large increase of leucine released was comparable to the range advocated for the elderly to favour protein anabolism. This in vitro study underlines the interest of using dish formulations to meet the nutritional needs of seniors, which is why this work will be completed by a clinical study in nursing home.

Development of a Protein Enrichment and Detection Microfluidic Platform based on Ion Concentration Polarization (ICP) and Electrochemical Impedance Spectroscopy (EIS) Techniques

Development of a Protein Enrichment and Detection Microfluidic Platform based on Ion Concentration Polarization (ICP) and Electrochemical Impedance Spectroscopy (EIS) Techniques

Control of polymer-protein interactions by tuning the composition and length of polymer chains.

Nanomoduling the 3D shape and chemical functionalities in a synthetic polymer may create recognition cavities for biomacromolecule binding, which serves as an attractive alternative to natural antibodies with much less cost. To obtain fundamental understanding and predict molecular design rules of the polymer antibody, we analyze the complex structure between the biomarker protein epithelial cell adhesion molecule (EpCAM) and a series of polymer ligands via molecular dynamics (MD) simulations. For monomeric ligands, strong enrichment of aromatic residues in protein binding sites is revealed, in line with the reported observations for natural antibodies. Yet, for linear polymers with a growing degree of polymerization, for the first time, a drastic change is revealed on the type of enriched protein residues and the location of protein binding sites, driven by the increasing steric hindrance effect that makes the adsorption of the polymer in the protein exterior feasible. Varying the polymer length and monomeric composition also significantly affects the ligand binding affinity. Here, we have captured three distinct dependences of the ligand binding free energy on the degree of polymerization: for NIPAm based hydrophilic polymers, TBAm dominated hydrophobic polymers and AAc dominated charged polymers. These results can be rationalized by the complex structure and the composition of protein residues at the binding interface. The entire analysis demonstrates unique binding features for polymer ligands and the possibility to modulate their binding sites and affinity by engineering the polymer structure.

Culture of Fresh Water Fish Channa striatus Using Low-cost Feed and its Cost-benefit Analysis (Small Scale)

In India, the culture of murrels is still not common due to the lack of seed supply and knowledge of their feeding and breeding techniques. Given this, the present study is undertaken to culture this species and work out is economics as this is a prized fresh water fish Channa striatus. The seeds of C. striatus were collected from local breeders of the Kumbagonam area, Tamil Nadu, India. Seedlings were introduced into the two culture ponds separately. The stocking density was 400 numbers/tank. While in pond-1, the size of the fingerlings varied between 5-7 cm (ave. 6 cm) in pond-II, the size of the fingerlings varied between 10 and 12 cm (ave. 11 cm). The feed that was given to fish in both tanks consisted of chicken waste and fish waste which was obtained free of cost from the neighboring market and artificial feed (Make: Super enriched protein feed). The feed were given at the rate of 4% of the body weight. The results of monoculture of murrels for a period of six months was maintained. As evident from the table from an average individual weight of 400 to 510 g after a period of six months grew to an average weight of 350.3 g thus recording an average increase in weight of 60 g. The harvest details show that a total of 294.2 kg could be harvested after six months. The fishes were sold in two lots - the bigger sized fishes weighting 190.6 kg and the smaller sized fish weighting at total of 103.6 kg while the bigger fishes were sold at a rate of Rs.250 per kg, the smaller fishes were sold at a rate of Rs.200 per kg. The net income from bigger fishes was Rs.47650 and the net income from smaller fishes was Rs.20720. Thus, the total yield worked out Rs.68370. The profit during this term worked out to Rs. 52270. The results of the present study clearly show that Channa striatus culture is highly profitable for the farmers.

Fine tuning contractility: atrial sarcomere function in health and disease.

The molecular mechanisms of sarcomere proteins underlie the contractile function of the heart. Although our understanding of the sarcomere has grown tremendously, the focus has been on ventricular sarcomere isoforms due to the critical role of the ventricle in health and disease. However, atrial-specific or -enriched myofilament protein isoforms, as well as isoforms that become expressed in disease, provide insight into ways this complex molecular machine is fine-tuned. Here, we explore how atrial-enriched sarcomere protein composition modulates contractile function to fulfill the physiological requirements of atrial function. We review how atrial dysfunction negatively affects the ventricle and the many cardiovascular diseases that have atrial dysfunction as a comorbidity. We also cover the pathophysiology of mutations in atrial-enriched contractile proteins and how they can cause primary atrial myopathies. Finally, we explore what is known about contractile function in various forms of atrial fibrillation. The differences in atrial function in health and disease underscore the importance of better studying atrial contractility, especially as therapeutics currently in development to modulate cardiac contractility may have different effects on atrial sarcomere function.

Proteomic Analysis of Gingival Crevicular Fluid During Tooth Eruption

Objective: Gingival crevicular fluid (GCF) is a biological fluid that has the unique capacity to reflect changes in periodontium to its protein composition, making it ideal for potential biomarkers. There is limited information about the mechanism of tooth eruption, for which GCF might provide valuable knowledge. This study aimed to provide a proteomic approach to investigate the composition of GCF obtained from two different supraosseous tooth eruption stages of permanent molars changes.
 Methods: GCF samples were taken from a total of 26 healthy children, whose permanent molar just emerged from the gingiva (5-8 years old) and the occlusal equilibrium stage (9-13 years old). Proteins were extracted with Bio-Rad Rehydration Buffer followed by ZebaTM Spin Desalting Column. GCF samples were separated with two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) followed by mass spectrometry- based protein identification.
 Results: A new optimized protocol with enriched protein extraction from GCF samples was developed. Several proteins related to tooth eruption were detected. It was determined that keratin type II cytoskeletal 4 and keratin type I cytoskeletal 9 decreased and albumin increased in GCF protein content in erupting teeth compared to those in the occlusal equilibrium phase.
 Conclusion: This methodology, which we have applied for 2D-PAGE of GCF, can also be a source for other studies. There is huge diagnostic potential in mass spectrometry technologies, this study can be carried forward by using other approaches.

Balance between Pro- and Antifibrotic Proteins in Mesenchymal Stromal Cell Secretome Fractions Revealed by Proteome and Cell Subpopulation Analysis.

Multipotent mesenchymal stromal cells (MSCs) regulate tissue repair through paracrine activity, with secreted proteins being significant contributors. Human tissue repair commonly results in fibrosis, where fibroblast differentiation into myofibroblasts is a major cellular mechanism. MSCs' paracrine activity can inhibit fibrosis development. We previously demonstrated that the separation of MSC secretome, represented by conditioned medium (CM), into subfractions enriched with extracellular vesicles (EV) or soluble factors (SF) boosts EV and SF antifibrotic effect. This effect is realized through the inhibition of fibroblast-to-myofibroblast differentiation in vitro. To unravel the mechanisms of MSC paracrine effects on fibroblast differentiation, we performed a comparative proteomic analysis of MSC secretome fractions. We found that CM was enriched in NF-κB activators and confirmed via qPCR that CM, but not EV or SF, upregulated NF-κB target genes (COX2, IL6, etc.) in human dermal fibroblasts. Furthermore, we revealed that EV and SF were enriched in TGF-β, Notch, IGF, and Wnt pathway regulators. According to scRNAseq, 11 out of 13 corresponding genes were upregulated in a minor MSC subpopulation disappearing in profibrotic conditions. Thus, protein enrichment of MSC secretome fractions and cellular subpopulation patterns shift the balance in fibroblast-to-myofibroblast differentiation, which should be considered in studies of MSC paracrine effects and the therapeutic use of MSC secretome.

The Enrichment of Whey Protein Isolate Hydrogels with Poly-γ-Glutamic Acid Promotes the Proliferation and Osteogenic Differentiation of Preosteoblasts.

Osseous disease accounts for over half of chronic pathologies, but there is a limited supply of autografts, the gold standard; hence, there is a demand for new synthetic biomaterials. Herein, we present the use of a promising, new dairy-derived biomaterial: whey protein isolate (WPI) in the form of hydrogels, modified with the addition of different concentrations of the biotechnologically produced protein-like polymeric substance poly-γ-glutamic acid (γ-PGA) as a potential scaffold for tissue regeneration. Raman spectroscopic analysis demonstrated the successful creation of WPI-γ-PGA hydrogels. A cytotoxicity assessment using preosteoblastic cells demonstrated that the hydrogels were noncytotoxic and supported cell proliferation from day 3 to 14. All γ-PGA-containing scaffold compositions strongly promoted cell attachment and the formation of dense interconnected cell layers. Cell viability was significantly increased on γ-PGA-containing scaffolds on day 14 compared to WPI control scaffolds. Significantly, the cells showed markers of osteogenic differentiation; they synthesised increasing amounts of collagen over time, and cells showed significantly enhanced alkaline phosphatase activity at day 7 and higher levels of calcium for matrix mineralization at days 14 and 21 on the γ-PGA-containing scaffolds. These results demonstrated the potential of WPI-γ-PGA hydrogels as scaffolds for bone regeneration.

Minor intron-containing genes as an ancient backbone for viral infection?

Minor intron-containing genes (MIGs) account for <2% of all human protein-coding genes and are uniquely dependent on the minor spliceosome for proper excision. Despite their low numbers, we surprisingly found a significant enrichment of MIG-encoded proteins (MIG-Ps) in protein-protein interactomes and host factors of positive-sense RNA viruses, including SARS-CoV-1, SARS-CoV-2, MERS coronavirus, and Zika virus. Similarly, we observed a significant enrichment of MIG-Ps in the interactomes and sets of host factors of negative-sense RNA viruses such as Ebola virus, influenza A virus, and the retrovirus HIV-1. We also found an enrichment of MIG-Ps in double-stranded DNA viruses such as Epstein-Barr virus, human papillomavirus, and herpes simplex viruses. In general, MIG-Ps were highly connected and placed in central positions in a network of human-host protein interactions. Moreover, MIG-Ps that interact with viral proteins were enriched with essential genes. We also provide evidence that viral proteins interact with ancestral MIGs that date back to unicellular organisms and are mainly involved in basic cellular functions such as cell cycle, cell division, and signal transduction. Our results suggest that MIG-Ps form a stable, evolutionarily conserved backbone that viruses putatively tap to invade and propagate in human host cells.

RBFOX2 deregulation promotes pancreatic cancer progression and metastasis through alternative splicing

RNA splicing is an important biological process associated with cancer initiation and progression. However, the contribution of alternative splicing to pancreatic cancer (PDAC) development is not well understood. Here, we identify an enrichment of RNA binding proteins (RBPs) involved in splicing regulation linked to PDAC progression from a forward genetic screen using Sleeping Beauty insertional mutagenesis in a mouse model of pancreatic cancer. We demonstrate downregulation of RBFOX2, an RBP of the FOX family, promotes pancreatic cancer progression and liver metastasis. Specifically, we show RBFOX2 regulates exon splicing events in transcripts encoding proteins involved in cytoskeletal remodeling programs. These exons are differentially spliced in PDAC patients, with enhanced exon skipping in the classical subtype for several RBFOX2 targets. RBFOX2 mediated splicing of ABI1, encoding the Abelson-interactor 1 adapter protein, controls the abundance and localization of ABI1 protein isoforms in pancreatic cancer cells and promotes the relocalization of ABI1 from the cytoplasm to the periphery of migrating cells. Using splice-switching antisense oligonucleotides (AONs) we demonstrate the ABI1 ∆Ex9 isoform enhances cell migration. Together, our data identify a role for RBFOX2 in promoting PDAC progression through alternative splicing regulation.