Melatonin protects TEGDMA-induced preodontoblast mitochondrial apoptosis via the JNK/MAPK signaling pathway

Resin monomer-induced dental pulp injury presents a pathology related to mitochondrial dysfunction. Melatonin has been regarded as a strong mitochondrial protective bioactive compound from the pineal gland. However, it remains unknown whether melatonin can prevent dental pulp from resin monomer-induced injury. The aim of this study is to investigate the effects of melatonin on apoptosis of mouse preodontoblast cells (mDPC6T) induced by triethylene glycol dimethacrylate (TEGDMA), a major component in dental resin, and to determine whether the JNK/MAPK signaling pathway mediates the protective effect of melatonin. A well-established TEGDMA-induced mDPC6T apoptosis model is adopted to investigate the preventive function of melatonin by detecting cell viability, apoptosis rate, expressions of apoptosis-related proteins, mitochondrial ROS (mtROS) production, mitochondrial membrane potential (MMP) and adenosine triphosphate (ATP) level. Inhibitors of MAPKs are used to explore which pathway is involved in TEGDMA-induced apoptosis. Finally, the role of the JNK/MAPK pathway is verified using JNK agonists and antagonists. Our results show that melatonin attenuates TEGDMA-induced mDPC6T apoptosis by reducing mtROS production and rescuing MMP and ATP levels. Furthermore, mitochondrial dysfunction and apoptosis are alleviated only by the JNK/MAPK inhibitor SP600125 but not by other MAPK inhibitors. Additionally, melatonin downregulates the expression of phosphorylated JNK and counteractes the activating effects of anisomycin on the JNK/MAPK pathway, mimicking the effects of SP600125. Our findings demonstrate that melatonin protects mDPC6T cells against TEGDMA-induced apoptosis partly through JNK/MAPK and the maintenance of mitochondrial function, offering a novel therapeutic strategy for the prevention of resin monomer-induced dental pulp injury.

Cysteine Counting via Isotopic Chemical Labeling for Intact Mass Proteoform Identifications in Tissue

Top-down proteomics, the tandem mass spectrometric analysis of intact proteoforms, is the dominant method for proteoform characterization in complex mixtures. While this strategy produces detailed molecular information, it also requires extensive instrument time per mass spectrum obtained and thus compromises the depth of proteoform coverage that is accessible on liquid chromatography time scales. Such a top-down analysis is necessary for making original proteoform identifications, but once a proteoform has been confidently identified, the extensive characterization it provides may no longer be required for a subsequent identification of the same proteoform. We present a strategy to identify proteoforms in tissue samples on the basis of the combination of an intact mass determination with a measured count of the number of cysteine residues present in each proteoform. We developed and characterized a cysteine tagging chemistry suitable for the efficient and specific labeling of cysteine residues within intact proteoforms and for providing a count of the cysteine amino acids present. On simple protein mixtures, the tagging chemistry yields greater than 98% labeling of all cysteine residues, with a labeling specificity of greater than 95%. Similar results are observed on more complex samples. In a proof-of-principle study, proteoforms present in a human prostate tumor biopsy were characterized. Observed proteoforms, each characterized by an intact mass and a cysteine count, were grouped into proteoform families (groups of proteoforms originating from the same gene). We observed 2190 unique experimental proteoforms, 703 of which were grouped into 275 proteoform families.

Phosphorylation of enteroviral 2Apro at Ser/Thr125 benefits its proteolytic activity and viral pathogenesis

Enteroviral 2A proteinase (2A^pro ), a well-established and important viral functional protein, plays a key role in shutting down cellular cap-dependent translation, mainly via its proteolytic activity, and creating optimal conditions for Enterovirus survival. Accumulated data show that viruses take advantage of various signaling cascades for their life cycle; studies performed by us and others have demonstrated that the extracellular signal-regulated kinase (ERK) pathway is essential for enterovirus A71 (EV-A71) and other viruses replication. We recently showed that ERK1/2 is required for the proteolytic activity of viral 2A^pro ; however, the mechanism underlying the regulation of 2A^pro remains unknown. Here, we demonstrated that the 125th residue Ser125 of EV-A71 2A^pro or Thr125 of coxsackievirus B3 2A^pro , which is highly conserved in the Enterovirus, was phosphorylated by ERK1/2. Importantly, 2A^pro with phosphor-Ser/Thr125 had much stronger proteolytic activity toward eukaryotic initiation factor 4GI and rendered the virus more efficient for multiplication and pathogenesis in hSCARB2 knock-in mice than that in nonphospho-Ser/Thr125A (S/T125A) mutants. Notably, phosphorylation-mimic mutations caused deleterious changes in 2A^pro catalytic function (S/T125D/E) and in viral propagation (S125D). Crystal structure simulation analysis showed that Ser125 phosphorylation in EV-A71 2A^pro enabled catalytic Cys to adopt an optimal conformation in the catalytic triad His-Asp-Cys, which enhances 2A^pro proteolysis. Therefore, we are the first to report Ser/Thr125 phosphorylation of 2A^pro increases enteroviral adaptation to the host to ensure enteroviral multiplication, causing pathogenicity. Additionally, weakened viruses containing a S/T125A mutation could be a general strategy to develop attenuated Enterovirus vaccines.

Robust Dual-Biomimetic Titanium Dioxide-Cellulose Monolith for Enrichment of Phosphopeptides

Metal oxide affinity chromatography (MOAC) is considered to be one of the most effective methods for phosphopeptide enrichment. However, most of the materials used in the method are powder; frequent centrifugation is necessitated during the enrichment process, and potential risks of loss of peptides and materials and clogging of the column employed for liquid chromatography-mass spectrometry (LC-MS) arise. Moreover, the reusability of these materials to achieve sustainability was hardly investigated. To overcome these limitations, herein, inorganic titanium dioxide (TiO₂) was coated onto the skeletal surface of the organic cellulose monolith (CM) material with a coral-like structure via a sol-gel method. This produced an organic-inorganic hybrid TiO₂-CM material, which contained a combination of organic and inorganic substances, making it mimic the mollusk shell in terms of composition. The prepared TiO₂-CM material as monolith exhibited excellent mechanical strength and did not break during the enrichment process; thus, the tedious implementation of multiple centrifugation cycles was prevented, thereby streamlining the experimental procedure and avoiding the loss of peptides and materials. Moreover, a large amount of TiO₂ was introduced onto the surface of the CM material, and thus, the resultant TiO₂-CM material exhibited a large surface area. As a result, the fabricated TiO₂-CM material was successfully applied to the enrichment of phosphopeptides obtained from the tryptic digests of a BSA/β-casein (mass ratio, 500/1) mixture. The results were superior to those achieved for commercial TiO₂ beads, confirming that TiO₂-CM has excellent selectivity for phosphopeptides and reusability. Furthermore, 9287 unique phosphopeptides derived from the 2661 phosphoproteins were successfully identified from two milligrams of tryptic digests of Hela cell exosomes obtained through five independent replications after enriching using the TiO₂-CM material. The results indicated that the material has good application prospects in the analysis of protein phosphorylation. Furthermore, TiO₂-CM consists of green and cheap cellulose as the skeleton, and its synthesis process is environment-friendly, simple, and inexpensive.

Electrophoresis of Phosphoproteins on a Tandem Polymerized Gel

A substrate with n phosphorylated sites may have 2ⁿ phosphor-forms for temporal-spatial regulation of biological events. Because phosphates do not significantly change molecular masses but net charges of proteins, those isoforms cannot be separated by regular mass-based sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE). A tandem polymerized gel was developed to resolve phosphor-isoforms with different masses, charges, and posttranslational modifications. Without the usage of SDS, the electrophoresis was primarily performed on three adjacent acidic polyacrylamide gels. After being concentrated on a stacking gel, protonated proteins were then separated on the Zr⁴⁺ immobilized gel through the coordination of metal ions with phosphates followed by further charge and mass (z/m)-based electrophoretic separation on a TiO₂ containing gel. The presence of TiO₂ nanoparticles in the third gel is aimed for the initiation of the polymerization of acrylamide in acidic conditions upon ultraviolet irradiation. Distinct isoforms of α-S1-casein, α-S2-casein, β-casein, and κ casein model proteins located on 11, 8, 8, and 7 different bands of the tandem gel were unambiguously identified, respectively. With the tandem polymerized gel electrophoresis, new phosphorylation events that may occur simultaneously or sequentially were discovered in not only model proteins but also complex biological samples including human saliva, chicken egg, and sprouting maize. This provides a new tool to dissect complex biological processes that are triggered by dynamic phosphorylation events.

Mast1 mediates radiation-induced gastric injury via the P38 MAPK pathway

Radiation-induced gastric injury is a serious adverse effect and reduces the efficacy of radiotherapy treatment. However, the mechanisms underlying radiation-induced stomach injury remain unclear. Here, mouse stomach and gastric epithelial cells were irradiated with different doses of X-ray radiation. The results showed that radiation induced gastric injury in vivo and in vitro. Differentially expressed functional mRNAs in irradiation-induced gastric tissues were screened from the Gene Expression Omnibus (GEO) database. We found that the expression of microtubule-associated serine/threonine kinase 1 (Mast1) was downregulated in mouse gastric tissues and gastric epithelial cells after irradiation. Furthermore, functional assays showed that knockdown of Mast1 inhibited growth and promoted apoptosis in gastric epithelial cells, while overexpression of Mast1 protected gastric epithelial cells from radiation damage. Mechanistically, Mast1 negatively regulated radiation-induced injury in gastric epithelial cells by inhibiting the activation of P38. The apoptosis caused by knockdown of Mast1 in gastric epithelial cells could be partially reversed by the P38 inhibitor SB203580. Moreover, data from several gastric cancer cell lines and online databases revealed that Mast1 was not involved in the development of gastric cancer. Collectively, our findings demonstrated that Mast1 is essential for radiation-induced gastric injury, providing a promising prognostic and therapeutic target.

Two-dimensional guanidinium-based covalent organic nanosheets for controllable recognition and specific enrichment of global/multi-phosphopeptides

Highly specific capture of phosphopeptides, especially multi-phosphopeptides, from complex biological samples is critical for comprehensive phosphoproteomic analysis, but it still poses great challenges due to the lack of affinity material with ideal enrichment efficiency. Here, two-dimensional (2D) covalent organic framework (COFs) nanosheets was applied for selective separation of phosphopeptides for the first time. Particularly, by incorporating guanidinium units, the 2D guanidinium-based COF nanosheets (denoted as TpTG_Cl CONs) exhibited controllable and specific enrichment performance towards global/multi-phosphopeptides. TpTG_Cl CONs was easy to prepare and showed large surface area, low steric hindrance, abundant accessible interaction sites and high chemical stability. Taking these merits together, TpTG_Cl CONs exhibited excellent efficiency for phosphopeptide enrichment, such as low detection limits (0.05 fmol μL^-1 for global phosphopeptides and 0.1 fmol μL^-1 for multi-phosphopeptides), high selectivity (1:5000 of molar ratios of β-casein/BSA for both global and multi-phosphopeptides), high adsorption capacity (100 mg g^-1 for global phosphopeptides and 50 mg g^-1 for multi-phosphopeptides). Furthermore, TpTG_Cl CONs could be reused due to the high chemical stability. In addition, TpTG_Cl CONs were successfully applied to controllable and specific capture of endogenous global/multi-phosphopeptides from human serum and human saliva, indicating its good potential in rapid and sensitive detection of biomarkers from biological fluid. Finally, rat liver protein digest was used to confirm the high specificity of TpTG_Cl CONs towards multi-phosphopeptides and demonstrated its potential as an ideal enrichment probe for comprehensive phosphoproteomic analysis.

Virus systems biology: Proteomics profiling of dynamic protein networks during infection

The host cell proteome undergoes a variety of dynamic changes during viral infection, elicited by the virus itself or host cell defense mechanisms. Studying these changes on a global scale by integrating functional and physical interactions within protein networks during infection is an important tool to understand pathology. Indeed, proteomics studies dissecting protein signaling cascades and interaction networks upon infection showed how global information can significantly improve understanding of disease mechanisms of diverse viral infections. Here, we summarize and give examples of different experimental designs, proteomics approaches and bioinformatics analyses that allow profiling proteome changes and host-pathogen interactions to gain a molecular systems view of viral infection.

MicroRNA-574-5p in gastric cancer cells promotes angiogenesis by targeting protein tyrosine phosphatase non-receptor type 3 (PTPN3)

We elucidate in this study that up-regulation of miR-574-5p in gastric cancer cells under hypoxic conditions contributed to angiogenesis. We found that miR-574-5p and HIF-1α were up-regulated in gastric cancer cells cultured under 2% O₂ or in medium containing CoCl_2, and in muscle tissues of mice injected with NaNO₂, indicating up-regulation of miR-574-5p in vitro or in vivo in response to hypoxic conditions. We hypothesized that up-regulation of miR-574-5p could promote angiogenesis. Transfection of gastric cancer cells with miR-574-5p mimics or inhibitor resulted in increase or decrease in the expression of VEGFA. Viability, migration, invasion and tube formation of HUVECs cultured with conditioned medium from SGC/574 cells transfected with miR-574-5p inhibitor were reduced. Tube formation of HUVECs cultured with conditioned medium from SGC-7901 cells transfected with miR-574-5p mimics was increased. An in vivo study demonstrated that inhibition of miR-574-5p in the tumor xenografts of mice reduced the expression of CD31 one of the endothelial cell markers. We identified PTPN3 a tyrosine phosphatase as a target of miR-574-5p that bound to the 3'UTR of PTPN3 mRNA to inhibit the expression of PTPN3. Furthermore, the data in this study demonstrated that inhibition of PTPN3 in gastric cancer cells enhanced phosphorylation of p44/42 MAPKs and promoted angiogenesis. We conclude that miR-574-5p in gastric cancer cells promoted angiogenesis via enhancing phosphorylation of p44/42 MAPKs by miR-574-5p inhibition of PTPN3 expression.

The role of stochastic sequestration dynamics for intrinsic noise filtering in signaling network motifs

The relation between design principles of signaling network motifs and their robustness against intrinsic noise still remains illusive. In this work we investigate the role of cascading for coping with intrinsic noise due to stochasticity in molecular reactions. We use stochastic approaches to quantify fluctuations in the terminal kinase of phosphorylation-dephosphorylation cascade motifs and demonstrate that cascading highly affects these fluctuations. We show that this purely stochastic effect can be explained by time-varying sequestration of upstream kinase molecules. In particular, we discuss conditions on time scales and parameter regimes which lead to a reduction of output fluctuations. Our results are put into biological context by adapting rate parameters of our modeling approach to biologically feasible ranges for general binding-unbinding and phosphorylation-dephosphorylation mechanisms. Overall, this study reveals a novel role of stochastic sequestration for dynamic noise filtering in signaling cascade motifs.

ProForma: A Standard Proteoform Notation

The Consortium for Top-Down Proteomics (CTDP) proposes a standardized notation, ProForma, for writing the sequence of fully characterized proteoforms. ProForma provides a means to communicate any proteoform by writing the amino acid sequence using standard one-letter notation and specifying modifications or unidentified mass shifts within brackets following certain amino acids. The notation is unambiguous, human-readable, and can easily be parsed and written by bioinformatic tools. This system uses seven rules and supports a wide range of possible use cases, ensuring compatibility and reproducibility of proteoform annotations. Standardizing proteoform sequences will simplify storage, comparison, and reanalysis of proteomic studies, and the Consortium welcomes input and contributions from the research community on the continued design and maintenance of this standard.

Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families

We present an open-source, interactive program named Proteoform Suite that uses proteoform mass and intensity measurements from complex biological samples to identify and quantify proteoforms. It constructs families of proteoforms derived from the same gene, assesses proteoform function using gene ontology (GO) analysis, and enables visualization of quantified proteoform families and their changes. It is applied here to reveal systemic proteoform variations in the yeast response to salt stress.