Extremely sensitive food-allergic patients may react to very small amounts of allergenic foods. Precautionary allergen labelling (PAL) warns from possible allergenic contaminations. We explored the ability of proteomic methods to identify minute amounts of milk/egg allergens in a brand of PAL-labelled milk- and egg-free biscuits. We evaluated the reactivity of children with severe milk and egg allergy, by oral food challenge. Traces of milk and/or egg allergens in biscuits were measured by two different liquid-chromatography-mass spectrometry methods. The binding of patient's serum with egg/milk proteins was assessed at immunoblotting. None of the patients reacted to biscuits. Egg and milk proteins were found under the limit of detection of 0.6 µg/g for milk and egg (method A), and of 0.1 and 0.3 µg /g for milk and egg, respectively (method B). The immunoblots did not show milk/egg proteins in the studied biscuits. Our biscuits did not contain allergens of clinical significance. Their milk/egg content is far lower than 4 µg of milk or egg protein per gram of product, the minimal doses considered theoretically capable of causing reactions. With high sensitivity, proteomic assessments predict the harmlessness of very small amount of allergenic foods and can be used to avoid unnecessary PAL.

The pressing threat of global warming poses significant risks to plant survival, adversely affecting their growth and agricultural productivity. It is crucial to understand how plants react to heat stress at the molecular level to develop crops that can withstand higher temperatures. In our study, we investigated the proteome dynamics of *Arabidopsis thaliana* seedlings under moderate heat stress conditions (30°C) using a combination of 15N-stable isotope labeling and the ProteinTurnover algorithm. This approach allowed us to closely examine the proteomic changes across different cellular compartments. Our findings revealed significant changes in the turnover rates of 571 proteins, with an average increase of 1.4-fold, indicating enhanced protein dynamics under heat stress. Notably, root soluble proteins showed more subtle changes, suggesting tissue-specific responses. We also detected significant turnover variations in proteins involved in redox signaling, stress response, and metabolism, highlighting the complex nature of these adaptive mechanisms. In contrast, proteins related to carbohydrate metabolism and mitochondrial ATP synthesis showed little change, underscoring their stability. This detailed analysis illuminates the proteomic adaptations of *Arabidopsis* seedlings to moderate heat stress, enhancing our understanding of plant thermal resilience and supporting efforts to develop thermotolerant crops.

The field of personalized medicine is undergoing a transformative shift through the integration of multi-omics data, which encompasses genomics, transcriptomics, proteomics, and metabolomics. This synergy allows for a comprehensive understanding of individual health by analyzing genetic, molecular, and biochemical profiles. The generation and integration of multi-omics data enable more precise and tailored therapeutic strategies, improving the efficacy of treatments and reducing adverse effects. However, several challenges hinder the full realization of personalized medicine. Key hurdles include the complexity of data integration across different omics layers, the need for advanced computational tools, and the high cost of comprehensive data generation. Additionally, issues related to data privacy, standardization, and the need for robust validation in diverse populations remain significant obstacles. Looking ahead, the future of personalized medicine promises advancements in technology and methodologies that will address these challenges. Emerging innovations in data analytics, machine learning, and high-throughput sequencing are expected to enhance the integration of multi-omics data, making personalized medicine more accessible and effective. Collaborative efforts among researchers, clinicians, and industry stakeholders are crucial to overcoming these hurdles and fully harnessing the potential of multi-omics for individualized healthcare.

Our understanding of the long-term consequences of chronic ionising radiation for living organisms remains scarce. Modern molecular biology techniques are helpful tools for researching pollutant effects on biota. To reveal the molecular phenotype of plants growing under chronic radiation exposure, we sampled Vicia cracca L. plants in the Chernobyl Exclusion Zone and in areas with normal radiation backgrounds. We performed a detailed analysis of soil and gene expression patterns, and made coordinated multi-omics analyses of plant samples, including transcriptomics, proteomics, and metabolomics. Chronic exposure to ionising radiation induced complex and multidirectional changes, including significant alterations in the metabolism and gene expression patterns of irradiated plants. We revealed profound changes in carbon metabolism, nitrogen reallocation, and photosynthesis. These plants were characterised by increased DNA damage, redox imbalance, and stress response reactions. The upregulation of histones, chaperones, peroxidases, and secondary metabolism were noted.

Cryptosporidiosis is a widespread disease caused by the parasitic protozoan Cryptosporidium spp., which infects various vertebrate species, including humans. Once unknown as a gastroenteritis-causing agent, Cryptosporidium spp. is now recognized as a pathogen causing life-threatening disease, especially in immunocompromised individuals such as AIDS patients. Advances in diagnostic methods and increased awareness have led to a significant shift in the perception of Cryptosporidium spp. as a pathogen. Nowadays, genomic and proteomic studies have played a main role in understanding the molecular biology of this complex-life-cycle parasite. Genomics has enabled the identification of numerous genes involved in the parasite's development and interaction with hosts. Proteomics has allowed for the identification of protein interactions, their function, structure, and cellular activity. The combination of these two approaches has significantly contributed to the development of new diagnostic tools, vaccines, and drugs for cryptosporidiosis. In this review, we summarize the major accomplishments in the field of Cryptosporidium research using genomics and proteomics.

The physiological process of iodine uptake in the thyroid is used for 131I treatment of thyroid diseases. Children are more sensitive to radiation compared to adults and may react differently to 131I exposure. The aims of this study were to evaluate the effects on thyroid protein expression in young and adult rats one year after 131I injection, and identify potential biomarkers related to 131I exposure, absorbed dose, and age. Twelve Sprague Dawley Rats (young and adults) were i.v. injected with 50 kBq or 500 kBq 131I and were killed twelve months later. Twelve untreated rats were used as age-matched controls. Quantitative proteomics, statistical analysis and evaluation of biological effects was performed. The effects of irradiation were most prominent in young rats. Protein biomarker candidates were proposed related to age, absorbed dose, thyroid function and cancer and a panel was proposed for 131I exposure. In conclusion, the proteome of rat thyroid was differentially regulated twelve months after low-intermediate dose exposure to 131I in both young and adult rats. Several biomarker candidates are proposed for 131I exposure, age, and many of them are known to be related to thyroid function or thyroid cancer. Further research on human samples are needed for validation.

Background and Objectives: Proteomics encompasses the exploration of protein composition, regulation, function, and pathways. Its influence spans diverse clinical fields and holds promise in addressing various women’s health conditions, including cancers, osteoporosis, and cardiovascular disorders. However, no comprehensive summary of proteomics and menopausal health exists. Our objective was to summarize proteomic profiles associated with diseases and disorders in peri and postmenopausal women. Materials and Methods: We conducted a comprehensive search of databases including PubMed, Google Scholar, Cochrane database, Elsevier, and ScienceDirect until 2022. A total of 253 studies were identified, 41 studies met the inclusion criteria to identify data of interest. These included study design, disease, and proteomics/proteins of significance as described by the authors. Results: The 41 studies, covered diverse areas including bone disorders (10 studies), cardiovascular diseases (5 studies), oncological malignancies (10 studies), and conditions such as obesity, nonalcoholic liver disease, the effects of hormone replacement therapy, and neurological diseases (16 studies). Results of our study indicate that proteomic profiles correlate with heart disease in peri- and postmenopausal women, with distinct sex differences. Furthermore, proteomic profiles significantly differed between women with and without osteoporosis. Additionally, patients with breast, ovarian, and endometrial cancer exhibited notable variations in proteomic profiles compared to those without these conditions. Conclusions: Proteomics has the potential to enhance risk assessment and disease monitoring in peri- and postmenopausal women. By analyzing unique protein profiles, clinicians can identify individuals with heightened susceptibility to specific diseases or those already affected by established conditions. This review suggests that there is sufficient preliminary data for proteomics in peri- and postmenopausal women for early identification of cardiovascular disease, osteoporosis, and cancers, in disease monitoring, and in tailoring individualized therapies. Rigorous validation studies involving large populations are essential before drawing definitive conclusions regarding the clinical applicability of proteomic findings.

Background: Proteins targeted by the Ubiquitin Proteasome System (UPS) are identified for degradation by the proteasome, which has been implicated in the development of neuro-degenerative diseases. Major histocompatibility complex (MHC) molecules present peptides broken down by the proteasome and are involved in neuronal plasticity, regulating synapse number and axon regeneration in the central or peripheral nervous system during develop-ment and in brain diseases. The mechanisms governing these effects are mostly unknown, but evidence from different compartments of the cerebral cortex indicates the presence of im-mune-like MHC receptors in the central nervous system. Methods: We have used human induced pluripotent stem cells (iPSC) differentiated to neural stem cells and then to motor neurons as a developmental model to better understand the structure of the proteasome in developing motor neurons. We perform a proteomic analysis of starting human skin fibroblasts, their matching iPSC, differentiated neural stem cells and motor neurons that highlighted significant differences in the constitutive proteasome and immunoproteasome subunits during development towards motor neurons from iPSC. Results: Proteomic analysis showed that the catalytic proteasome subunits expressed in fi-broblasts differ to those in neural stem cells and motor neurons. Western blot analysis con-firmed the proteomic data, particularly the decreased expression of Beta5i (PSMB8) subunit immunoproteasome. Conclusion: The constitutive proteasome subunits are upregulated in iPSC from HFF and the immunoproteasome subunit beta 5i expression is higher in MN than NSC suggesting a im-munoproteasome phenotype in MN. The immunoproteasome may have implications on motor neuron development and neurodevelopmental diseases that warrants further investi-gation.

High blood cholesterol levels are one of the main risks for atherosclerotic disease. A purified aqueous extract of Fucus vesiculosus, characterized as rich in phlorotannins and peptides, was described as having the capacity to inhibit cholesterol biosynthesis and intestinal absorption. In this work, the effect of this extract on intestinal cells metabolites and proteins was analysed, aiming to expand the knowledge about its mode of action targeting cholesterol metabolism, in particular exogenous cholesterol absorption and transport. Caco-2 cells differentiated into enterocytes were exposed to the purified aqueous extract of F. vesiculosus and analysed by undirected metabolomics and proteomics. The results of the metabolomic analysis showed only statistically significant differences in glutathione content of the cells exposed to the extract relatively to the control cells, with a decreased glutathione expression in exposed cells. The proteomic analysis showed an increased expression for cells exposed to the extract of NPC1, an important protein known to be involved in cholesterol transport. To extent of our knowledge this is the first study using untargeted metabolomics and proteomic analysis to study the effect of F. vesiculosus on differentiated Caco-2 cells, which aims to provide some insight about the molecular mechanism of extract compounds on intestinal cells.

Staphylococcus aureus and coagulase-negative staphylococci account for about 80% of infections associated with medical devices and are associated with increased virulence due to their ability to form biofilm. In this study, we aimed to construct a comprehensive reference map followed by significant pathway analysis in the proteome of S. aureus biofilm grown for 3-days as compared with 24 h planktonic using a high-resolution TMT based MS. We identified proteins associated with secondary metabolites, ABC transporters, biosynthesis of amino acids, response to stress, and amino sugar and nucleotide sugar metabolism were significantly upregulated in the 3-day biofilm. In contrast, proteins associated with virulence factors, microbial metabolism in diverse environments, translation, and energy metabolism were significantly downregulated. GO functional annotation indicated that more proteins are involved in metabolic processes, catalytic activity, and binding in biofilm, respectively. Among the significantly dysregulated proteins, hyaluronidase (hysA) in conjunction with chitinase may play a significant role in the elimination and/or prevention of biofilm development. This study advances the current S. aureus subproteomes, identified potential pathways significant to biofilm biology and helped to understand their potential role in S. aureus which may shed light on developing new therapeutic regimes including antibiofilm agents in the treatment of biofilm-infections related with implantable medical devices.

Thymomas (TH) are a unique group of heterogeneous tumors of the thymic epithelium. In particular, the subtypes B2 and B3 tend to be aggressive and metastatic. Radical tumor resection remains the only curative option for localized tumors, while more advanced TH require multimodal treatment. Deep sequencing analyses have failed to identify known oncogenic driver mutations in TH, with the notable exception of the GTF2I mutation, which occurs predominantly in type A and AB TH. However, there are multiple alternative non-mutational mechanisms (e.g., perturbed thymic developmental programs, metabolism, non-coding RNA networks) that control cellular behavior and tumorigenesis through deregulation of critical molecular pathways. Here, we attempted to show how the results of studies investigating such alternative mechanisms could be integrated into a current model of TH biology. This model could be used to focus ongoing research and therapeutic strategies.

Information regarding physiological and molecular plant responses to the treatment with new biofertilizers is limited. In this study a fast-composting soil amendment (FCA), obtained from solid waste by means of a Fenton reaction, was tested to evaluate the effects on the growth of Lactuca sativa L. var. longifolia seedlings. Growth rate, leaves and roots biomass, chlorophyll concentration and total soluble proteins of seedlings treated with the 2% FCA soil amendment showed significant increase in comparison with control seedlings. Leaf proteomic analysis revealed that the FCA soil amendment induced the up-regulation of proteins belonging to photosynthesis machinery, carbohydrate metabolism and promoted the up-regulation of the water stress response. Root proteomics indicated that FCA strongly induced the organs morphogenesis and developments; root cap development, lateral root formation, post-embryonic root morphogenesis were the main biological processes enriched by the treatment. Overall, our data suggest that addition of FCA formulation to the base soils might ameliorate plant growth by inducing carbohydrates primary metabolism and the differentiation of a robust root system.

Tritordeum is an amphiploides species resulting from the hybridization between durum wheat (T. durum) and wild barley (H. chilense). This new cereal is considered a natural crop as it is obtained by traditional breeding techniques. Given its appreciable organoleptic characteristics, agronomic features, presence of interesting components, and good technological properties, tritordeum is of promising interest for the development of health-oriented foods. In this study, we evaluated two registered tritordeum cultivars, Bulel and Aucan. T. durum (Provenzal) was employed as the positive control. The extracted proteins were digested by gastric /pancreatic proteases and their biological effects on Caco-2 differentiated on transwell inserts were determined. Changes in cell viability, monolayer permeability, organization of F-actin microfilaments, and ER stress, triggered by protein-digested samples (DPs) were inspected. Our results showed that exposure to Provenzal-DPs promptly disrupted the tight junction barrier. Conversely, Aucan-DPs did not enhance monolayer permeability; whereas, Bulel-DPs exerted only slight effects. Provental-DPs-induced toxicity was also confirmed by changes in cell viability and by the deep reorganization of the enterocyte cytoskeleton. In contrast, Aucan-DPs and Bulel-DPs did not affect monolayer viability and cytoskeleton structure. Overall, our findings suggest that both tritordeum cultivars could be potential candidates for mitigating the toxicity of wheat flour.

Infertility affects millions worldwide, posing a significant global health challenge. The proteomic analysis of follicular fluid provides a comprehensive view of the complex molecular landscape within ovarian follicles, offering valuable information on the factors influencing oocyte development and on the overall reproductive health. The follicular fluid is derived from the plasma and contains various proteins that can have different roles in oocyte health and infertility and this fluid is a critical microenvironment for the developing oocytes as well. Using HPLC/MS method we investigated the protein composition of the follicular fluid and after classification we did relative quantification of the identified proteins in the pregnant (P) and non-pregnant (NP) groups. Based on the protein-protein interaction analysis ALB and ApoA1 was found to be hub proteins and the quantitative comparison of the P and NP groups resulted significantly lower concentration of ApoA1 and HDL-cholesterol in the P group. As both molecules are involved in the cholesterol transport, we also investigated their role in the development of oocytes and in the prediction of fertility.

Proteomics in respiratory allergic diseases has such a battery of techniques and programs that one would almost think that there is nothing impossible to find, invent or mold. All these resources that we document here, are involved in solving problems in allergic diseases, both diagnostic, prognostic, treatment and immunotherapy development. The main perspectives, according to this version, are in three strands and / or lockout immunological system: 1) In blocking the diapedesis of cells involved, 2) modifications and blocking of paratopes and epitopes being understood by modifications to antibodies, antagonism or blocking them and 3) blocking FcεR1 receptors to prevent specific IgEs from sticking to mast cells and basophils. These tools and targets in the allergic landscape are, in our view, the prospects in the field.

Medicinal plants produce various bioactive molecules with potential anticancer properties with favorable safety profiles. We investigated the comprehensive composition of Vernonia amygdalina leaf extract and its cytotoxic effects via apoptosis in HeLa cells. The metabolomics approach was conducted to gather the metabolite profile of the extract. Proteomics was performed to understand the comprehensive mechanistic pathways of action. The apoptosis was visualized by cellular staining and the apoptotic proteins were evaluated. V. amygdalina leaf extract exhibited dose-dependent cytotoxic effects on both HeLa and Vero cells after 24 h of exposure, however, a higher concentration was required for Vero cells cytotoxicity. The metabolomic profile indicated that majority of metabolites were alkaloids, phenolic compounds, and steroids. The cytotoxic pathways involved the response to stress and cell death which was similar to doxorubicin. The upstream regulatory proteins, PTEN and XBP1, were significantly altered supporting the regulation of apoptosis and cell death. The levels of apoptotic proteins, JNK, p53, and caspase-9 were significantly increased. These provided strong evidence that V. amygdalina leaf extract related to the induction of apoptosis and highlighted its potential for the development of chemotherapy.

Abatacept (CTLA4-Ig) – a monoclonal antibody which restricts T cell activation – is an effective treatment for rheumatoid arthritis (RA). Herein, we aimed to investigate for biomarkers of response to abatacept. We performed a detailed immunological profiling of CTLA4-treated RA patients’ peripheral blood (PB) cells and sera using flow cytometry and proteomics analysis, respectively. At 6 months of treatment, 34.5% of patients attained clinical response. Notably, baseline levels of Th1 and myeloid cell populations were significantly elevated in PB of responders compared to non-responders (P-value<0.05). Additionally, proteomics analysis revealed 10 amongst 303 molecules which were associated with clinical responses. Should the present data be confirmed in a larger cohort could be of clinical value.

With a view to understand and resolve the complexity of the food matrix, ohmic technologies alone or in combination were extensively employed. In this sense, the newest developments and advances of proteomics, metabolomics, lipidomics whith their unique benefits could simplify and understand the link between physiological and pathological activities in biology, physiology, pathology, and food science and processing. This review aims to briefly introduce the basis of proteomics, metabolomics, lipidomics, then expansively review their impact on the assessment of meat quality and safety. Here, also, we discuss the application of proteomics, metabolomics, lipidomics for the authentication and adulteration of meat and meat derivatives from different sources, and provides some perspectives regarding the use of emerging techniques such as rapid mass spectrometry (MS) and non-invasive measurements for the analysis of meat quality and safety. This paper summarizes all significant investigation in these matters, and underlines the advances in analytical chemistry technologies and meat science areas. By emphasizing the requirement for additional examinations, this paper attempts a comprehensive knowledge of “foodomics” and their potential to improve their employment in meat science.

The normal ageing process significantly affects resistance arteries, leading to various biological and physiological consequences. Systolic hypertension is a common occurrence in ageing individuals, accompanied by increased large artery stiffening, heightened pulsatility, small artery remodeling, and damage to critical microvascular structures. Starting from young adulthood, there is a progressive elevation in mean arterial pressure, supported by clinical and epidemiological evidence as well as findings from animal models. The myogenic response, a protective mechanism for the microcirculation, may face disruptions during ageing. Dysregulation of calcium entry channels (T-type, L-type, TRP channels), dysfunction in intracellular calcium storage and extrusion mechanisms, altered expression of potassium channels, and a change in smooth muscle calcium sensitization may contribute to age-related dysregulation of myogenic tone. Flow-mediated vasodilatation, a hallmark of endothelial function, is compromised in ageing. This result of endothelial dysfunction is related to oxidative stress, lower nitric oxide bioavailability and a low-grade inflammatory response, further exacerbating vascular dysfunction. Resistance artery remodeling in ageing emerges as a hypertrophic response of the vessel wall, often seen in conjunction with outward remodeling (in normotension), but can also present as inward hypertrophic remodeling (in hypertension). The remodeling process involves oxidative stress, inflammation, reorganization of extracellular matrix fiber proteins and actin cytoskeletal components. Reactive oxygen species (ROS) signaling and chronic low-grade inflammation, often referred to as "inflammaging”, play substantial roles in age-related vascular dysfunction. Due to its role in regulation of vascular tone as well as structural proteins, the RhoA/Rho-kinase pathway becomes a new target in age-related vascular dysfunction and associated diseases. Understanding the intricate interplay of these factors is crucial for developing targeted interventions to mitigate the consequences of ageing on resistance arteries and enhance overall vascular health.

Synthesis and antitumour activity of a palladium compound, [Bis (quinoline) palladium (II) chloride] (coded as NH1) alone and in combination along with its proposed mechanism of action has been described in the present study. Antitumour activity has been performed in seven different cancer cell lines using colorimetric 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay. The investigated palladium compound demonstrated superiority over clinical standard cisplatin against drug resistant ovarian cancer cell lines. NH1 also demonstrates 4.4 times greater activity than cisplatin against breast cancer model. Binary sequenced combination study showed that NH1 in combination with curcumin is mostly additive to antagonistic. However, combination of NH1 with 6-shogaol demonstrated synergism depending on dose and sequence. Proteomic study revealed that changes in expression of 14 proteins were significantly associated with anticancer mechanism of NH1. In vivo anticancer activity of NH1 at a dose of 0.75 mg/kg was also evaluated using Erlich Ascites Carcinoma (EAC) cell lines in Swiss-albino mice model. Preliminary toxicity study in Swiss-albino mice proved that NH1 is comparatively less toxic at both of the administered doses, either 2.5 mg/kg or 5 mg/kg. However, cisplatin demonstrated significant toxicity at both of the administered doses. Biochemical investigations also supported that NH1 demonstrated lesser toxicity profile towards liver or kidney compared to clinical standard cisplatin.

During meat processing, lactic acid bacteria (LAB) have to competitively adapt to the hostile en-vironment produced by curing additives (CA). The objective of this study was to investigate the ability of Latilactobacillus curvatus CRL 705, a bioprotective strain of meat origin, to adapt to CA. A physiological and proteomic approach was performed. CRL 705 was grown in a chemically de-fined medium (CDM) containing specific concentrations of CA (NaCl, nitrite, sucrose and ascor-bic acid). The results showed minor differences in growth kinetics in the presence of CA. Glucose consumption, present in CDM, and production of lactic acid and bacteriocins were not signifi-cantly affected. Proteomic analyses indicated that most of the identified proteins (36 out of 39) mainly related to carbohydrate metabolism (18%), posttranslational modifications (15.6%), energy production and conversion (11.1%), translation (11.1%) and nucleotide metabolism (8.9%), were under expressed. In response to the studied CA, CRL 705 slowed down its general metabolism, achieving slight changes in physiological and proteomic parameters. The observed performance is another characteristic that extends the well-known competitive profile of CRL 705 as a meat starter- and -bioprotective culture. This is the first report dealing with the impact of CA on LAB proteomics.

Preeclampsia (PE) is a serious complication of pregnancy with a pathogenesis that is not fully understood, though it involves the impaired invasion of extravillous trophoblasts (EVTs) into the decidual layer during implantation. Recently, others have found that diverse cell types, including EVTs, produce exosomes filled with molecular cargo (mainly proteins and RNAs) that can be transported to other cells and organs both locally and long-range. The cargo delivered by exosomes can signal to and modify the receiving cells and their environment, and EVT-derived exosomes may influence the pathogenesis of PE. Because the risk of PE is actually decreased by cigarette smoking, we considered the possibility that nicotine, a critical component of tobacco smoke, might protect against PE by modifying the content of exosomes from EVTs. In this study, we applied nicotine stimulation to cultured EVTs and subjected their secreted exosomes to proteomic analysis. We identified many proteins whose abundance in exosomes was modified by nicotine treatment of the donor EVTs, and we used bioinformatic annotation and network analysis to select five key hub proteins with potential roles in the pathogenesis or prevention of PE.

Cancer is a complex and heterogeneous disease, influenced by various factors that affect its progression and response to treatment. Although histopathological diagnosis is crucial for identifying and classifying cancer, it may not accurately predict the disease's development and evolution in all cases. To address this limitation, liquid biopsy has emerged as a valuable tool, enabling a more precise and non-invasive analysis of cancer. Liquid biopsy offers the ability to detect tumor DNA fragments, circulating tumor cells, and exosomes released by cancer cells into the bloodstream. Exosomes, in particular, have attracted significant attention in cancer research due to their specific protein composition, which can provide valuable insights into the disease. The protein profile of exosomes often differs from that of normal cells, reflecting the unique molecular characteristics of cancer. Analyzing these proteins can help identify cancer-associated markers that play critical roles in tumor progression, invasion, and metastasis. Ongoing research and clinical validation are essential to advance and effectively utilize protein biomarkers in cancer. Nevertheless, their potential to improve diagnosis and treatment is highly promising. This review discuss several exosome proteins of interest in breast cancer, particularly focusing on studies conducted in mammary tissue and cell lines in humans and experimental animals. Unfortunately, the studies conducted in the canine species are scarce. This emphasis sheds light on the limited research available in this field. Additionally, we present a curated selection of studies that have explored exosomal proteins as potential biomarkers, aiming to achieve the aforementioned benefits in breast cancer diagnosis, prognosis, monitoring, and treatment.

Proteomics is the study of cellular proteome by investigating how different proteins interact with each other and the roles they play in the organism. For mRNA expression levels do not always correlate well with protein expression levels, and the study of mRNA does not consider protein posttranslational modifications (PTMs), complex formation and localization; all of which are key to protein function. Quantitative proteomics uses mass spectrometry to identify and quantify proteins so as to find differentially expressed proteins under different condition. This allows us to gain biological insights under stress or other pathological conditions. posttranslational modifications, such as lysine acetylation, succinylation and lactylation, occur after protein biosynthesis and play vital roles in protein activity and cell physiology regulation. Here we present the mass spectrometry analysis in detail to unveil protein acylase and deacylase’ roles in metabolic regulation based on PTMomics lysine acetylome and suincylome.

Methionine oxidation to the sulfoxide form (MSox) is a poorly understood post-translational modification of proteins associated with nonspecific chemical oxidation from reactive oxygen species (ROS) whose chemistries are linked to various disease pathologies including neurodegeneration. Emerging evidence shows MSox site occupancy is in some cases under enzymatic regulatory control mediating cellular signaling including phosphorylation and/or calcium signaling, raising questions as to the speciation and functional nature of MSox across the proteome. The 5XFAD lineage of the C57BL/6 mouse has well-defined Alzheimer’s and aging states. Using this model, we analyzed age, sex and disease dependent MSox speciation in mouse hippocampus. In addition, we explore chemical stability and statistical variance of oxidized peptide signals to understand needed power for MSox based proteome studies. Our results identify mitochondrial and glycolytic pathway targets with increases in MSox with age as well as neuroinflammatory targets accumulating MSox with AD in proteome studies of mouse hippocampus. Further, the paper establishes a foundation for reproducible and rigorous experimental MSox-omics appropriate for biological discovery novel target identification, and biomarker analysis in ROS and other oxidation linked diseases.

Mesenchymal stem cells (MSCs) are an attractive therapeutic tool for tissue engineering and regenerative medicine owing to their regenerative and trophic properties. The best-known and most widely used are bone marrow MSCs which are currently being harvested and developed from a wide range of adult and perinatal tissues. MSCs from different sources are believed to have different secretion potentials and production which may influence their therapeutic effects. To confirm it, we performed a quantitative proteomic analysis based on the TMT technique of MSCs from three different sources: Wharton’s jelly (WJ), dental pulp (DP) and bone marrow (BM). Our analysis focused on MSC biological properties of interest for tissue engineering. We identified a total of 611 differentially expressed human proteins. WJ-MSCs showed the greatest variation compared with the other sources. WJ produced more extracellular matrix (ECM) proteins and ECM-affiliated proteins and appeared more able to modulate the inflammatory and immune response. BM-MSCs displayed enhanced differentiation and paracrine communication capabilities. DP-MSC appeared to promote exosome production. The results obtained confirm the existence of differences between WJ, DP and BM-MSC and the need to select the MSC origin according to the therapeutic objective sought.

This study aimed to investigate the venom sac extracts (VSE) of the European hornet (EH) Vespa crabro (Linnaeus, 1758) (Hymenoptera: Vespidae), focusing on the differences between stinging females, gynes (G) and workers (W), at the protein level. Using a quantitative “Sequential Window Acquisition of all Theoretical Fragment Ion Mass Spectra” (SWATH-MS) analysis, we identified and quantified a total of 240 proteins. Notably, within the group, 45.8 % (n = 110) showed significant differential expression between VSE-G and VSE-W. In this set, 57.3 % (n = 63) were upregulated and 42.7 % (n = 47) downregulated in the G. Additionally, the 200 quantified proteins from the class Insecta belong to 16 different species, six of them to the Hymenoptera/Apidae lineage, comprising seven proteins with known potential allergenicity. Thus, phospholipase A1 (Vesp v 1), phospholipase A1 verutoxin 2b (VT-2b), hyaluronidase A (Vesp v 2A), hyaluronidase B (Vesp v 2B), and venom allergen 5 (Vesp v 5) were significantly downregulated in the G, and vitellogenin (Vesp v 6) was upregulated. Overall, 46 % of the VSE proteins showed differential expression, with a majority being upregulated in G. Data are available via ProteomeXchange with identifier PXD047955. These findings shed light on the proteomic differences in VSE between EH castes, potentially contributing to our understanding of their behavior and offering insights for allergy research.

Many challenges in proteomics result from the high-throughput nature of the experiments. The paper first presents pre-analytical problems, which still occur, although the call for standardisation in omics has been ongoing for many years. This article also discusses aspects, which affect bioinformatic analysis, based on three sets of reference data measured with different orbitrap instruments. Despite continuous advances in mass spectrometer technology as well as analysis software, data set-wise quality control is still necessary and decoy-based estimation, although challenged by modern instruments, should be utilized. We draw attention to the fact that numerous young researchers perceive proteomics as a mature, readily applicable technology. However, it is important to emphasize that the maximum potential of the technology can only be realized by an educated handling of its limitations.

Excessive nitrogen application has become a hidden danger threatening the sustainable development of agriculture. Exploring the potential genes will help to improve the nitrogen availability of wheat through molecular breeding. We therefore conducted wheat transcriptomics and proteomics researches under complete culture medium without nitrogen (N0) and complete culture medium with nitrogen (N1). The results showed that, the nitrogen deficit decreased the fresh weight, N content and net photosynthetic rate of winter wheat. 3949 and 2675 differentially expressed genes (DEGs) were identified in the shoot and root, respectively, while 164 and 129 differentially expressed proteins (DEPs) were identified in the shoot and root respectively. 9 genes in shoot and 26 genes in root showed the same trends in RNA and protein levels. 5 genes in shoot and 4 genes in root showed the opposite trends in RNA and protein levels. Pathway enrichment of wheat transcriptome and proteome under nitrogen deficit proposed 3 candidate genes related to photosynthesis in shoot, 4 candidate genes related to carbon metabolism in shoot, and 12 candidate genes related to carbon metabolism in root. Meanwhile, the chromosomal and subcellular localization of these genes were listed, which will provide reference for improving nitrogen availability through molecular breeding.

Preeclampsia (PE) is a complex and multifaceted obstetric syndrome characterized by several distinct molecular subtypes. It complicates up to 5% of pregnancies and significantly contributes to maternal and newborn morbidity, thereby diminishing the long-term quality of life for affected women. Due to the widespread dissatisfaction with the effectiveness of existing approaches for assessing PE risk, there is a pressing need for ongoing research to identify newer, more accurate predictors. This study aimed to investigate early changes in the maternal serum proteome and associated signaling pathways. The levels of 125 maternal serum proteins at 11-13 weeks of gestation were quantified using liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM MS) with the BAK-125 kit. Ten serum proteins emerged as potential early markers for PE: Apolipoprotein M (APOM), Complement C1q subcomponent subunit B (C1QB), Lysozyme (LYZ), Prothrombin (F2), Albumin (ALB), Zinc-alpha-2-glycoprotein (AZGP1), Tenascin-X (TNXB), Alpha-1-antitrypsin (SERPINA1), Attractin (ATRN), and Apolipoprotein A-IV (APOA4). Notably, nine of these proteins have previously been associated with PE in prior research, underscoring the consistency and reliability of our findings. These proteins play key roles in critical molecular processes, including complement and coagulation cascades, platelet activation, and insulin-like growth factor pathways. To improve the early prediction of PE, a highly effective Support Vector Machine (SVM) model was developed, analyzing 19 maternal serum proteins from the first trimester. This model achieved an Area Under the Curve (AUC) of 0.91, with 87% sensitivity and 95% specificity, and a hazard ratio (HR) of 13.5 (4.6 - 40.8) with p&lt;0.001. These findings demonstrate that serum protein-based SVM models possess significantly higher predictive power compared to the routine first-trimester screening test, highlighting their superior utility in the early detection and risk stratification of PE.

Mouse wild-derived strains (WDS) combine the advantages of classical laboratory stocks and wild animals, and thus appear as promising tools for diverse biomedical and evolutionary studies. We employed 18 WDS representing three non-synanthropic species (Mus spretus, M. spicilegus, and M. macedonicus) and three house mouse subspecies (M. musculus musculus, M. m. domesticus, M. m. castaneus) which are all important human commensals to explore whether the number of major urinary protein (MUP) genes and their final protein levels in the urine are correlated with the level of commensalism. Contrary to expectations, MUP copy number (CN) and protein excretion in the strains derived from M. m. castaneus, which is supposed to be the strongest commensal, were not significantly different from the non-commensal species. Regardless of an overall tendency for higher MUP amounts in taxa with higher CN, there is no significant correlation at the strain level. Our study thus suggests that the expansion of the Mup cluster, which appeared before the house mouse diversification, is unlikely to facilitate commensalism with humans in the three house mouse subspecies. Finally, we found considerable variation among con(sub)specific WDS, warning against generalisations of results based on a few strains.

Rationale: Post-hepatectomy liver failure (PHLF) remains a significant risk for patients undergoing partial hepatectomy (PHx). Reliable prognostic markers and treatments to enhance liver regeneration are lacking. Plasma nanoparticles, including lipoproteins, exosomes, and extracellular vesicles (EVs), can reflect systemic and tissue-wide proteostasis and stress, potentially aiding liver regeneration. However, their role in PHLF is still unknow. Methods: Our study included 9 patients with hepatocellular carcinoma (HCC) undergoing PHx: 3 patients with PHLF, 3 patients undergoing the Associating Liver Partition and Portal vein Ligation for Staged hepatectomy (ALPPS) procedure and three matched controls without complications after PHx. Patient plasma was collected before (PRE), 1 and 5 days (POD1, POD5) after PHx. EVs were isolated by ultracentrifugation and extracted proteins subjected to quantitative mass spectrometry using a super-SILAC mix prepared from primary and cancer cell-lines. Results: We identified 2625 and quantified 2570 proteins in EVs in PHx patients. Among these, 53 proteins were significantly upregulated and 32 were downregulated in patients with PHLF compared to those without PHLF. Furthermore, 110 proteins were upregulated and 78 were downregulated in PHLF compared to patients undergoing ALPPS. The EV-proteomic signature in PHLF indicates significant disruptions in protein translation, proteostasis, intracellular vesicle biogenesis, as well as alterations in proteins involved in extracellular matrix (ECM) remodeling, metabolic and cell cycle pathways, present already before PHx. Conclusion: Longitudinal proteomic analysis of EV´s circulating in human patient plasma undergoing PHx uncovers proteomic signatures associated with PHLF which reflect dying hepatocytes and endothelial cells and are present before PHx already. Our results support EVs as potential biomarkers and therapeutic targets for liver regeneration and failure.

Helicobacter pylori infection affects over 50% of the world population and leads to chronic inflammation and gastric disorders, being the main pathogen correlated to gastric cancer development. The increasing on antibiotic resistance levels is a major global concern and alternative treatments are needed. Soybean peptides and other compounds might be an alternative in the treatment to avoid, eradicate and/or control symptoms of H. pylori infection. This study aimed to characterize a lunasin-enriched soybean extract (LSE) by proteomics tools and to evaluate its antioxidant, anti-inflammatory and antibacterial properties against H. pylori infection. By LC-MS/MS analysis, 124 proteins were identified, with the 2S albumin (lunasin and large chain subunits) being the fourth most abundant protein (8.9%). Lunasin consisted of 44 amino acid residues and an intramolecular disulfide bond. LSE at a low dose (0.0625 mg/mL) reduced ROS production in both H. pylori-infected and non-infected AGS gastric cells. This led to a significant reduction of 6.71% in the levels of pro-inflammatory interleukin (IL)-8. LSE also showed antibacterial activity against H. pylori which can be attributed to other soybean proteins and phenolic compounds. Our findings suggest that LSE might be a promising alternative in the management of H. pylori infection and associated symptoms.

Global warming poses a threat to plant survival, impacting growth and agricultural yield. Protein turnover, a critical regulatory mechanism balancing protein synthesis and degradation, is crucial for cellular response to environmental changes. We investigated the effects of elevated temperature on proteome dynamics in Arabidopsis thaliana seedlings using 15N-stable isotope labeling and ul-tra-performance liquid chromatography-high resolution mass spectrometry, coupled with the ProteinTurnover algorithm. Analyzing different cellular fractions from plants grown under 22°C and 30°C growth conditions, we found significant changes in the turnover rates of 571 proteins, with a median 1.4-fold increase, indicating accelerated protein dynamics under thermal stress. Notably, soluble root fraction proteins exhibited smaller turnover changes, suggesting tissue-specific adap-tations. Significant turnover alterations occurred with redox signaling, stress response, protein folding, secondary metabolism, and photorespiration, indicating complex responses enhancing plant thermal resilience. Conversely, proteins involved in carbohydrate metabolism and mito-chondrial ATP synthesis showed minimal changes, highlighting their stability. This analysis high-lights the intricate balance between proteome stability and adaptability, advancing our under-standing of plant responses to heat stress and supporting the development of improved thermo-tolerant crops.

Primulina serrulata is a valuable ornamental herb with rosette leaves and vibrant flowers. Some leaves exhibit a bright and distinct white color along the upper veins, enhancing their ornamental value, while others are less white or entirely green. This variation is observed among adult leaves in natural habitats and among young leaves from seedlings grown in the laboratory. TMT-labeled proteomic technology was employed to study the protein-level biogenesis of white-veined (WV) leaves of P. serrulata. The chlorophyll (Chl) content was significantly lower in the WV group than in the control group. A total of 6,261 proteins were identified, revealing 69 differentially expressed proteins (DEPs), with 44 down-regulated and 25 up-regulated in WV plants. Some DEPs associated with chloroplasts and Chl biosynthesis were down-regulated, leading to the absence of green coloration. Concurrently, gene ontology enrichment analysis further underscored an insufficiency of magnesium , the key element in Chl biosynthesis. Many DEPs associated with abiotic or biotic stresses were down-regulated, suggesting an overall weakening of stress resistance with certain compensatory mechanisms in place. Similarly, many DEPs related to biomacromolecule modification were down-regulated, possibly influenced by the decrease in proteins involved in photosynthesis and stress resistance. Some DEPs containing iron were up-regulated, indicating that iron was mainly used to synthesize heme and ferritin instead of Chl. Additionally, several DEPs related to sulfur or sulfate were up-regulated, implying strengthened respiration. Expansin-A4 and pectinesterase displayed up-regulation, coinciding with the emergence of a rough and bright surface in the white area, indicative of the elongation and gelation processes in cell walls. These findings provide new insights that could be utilized by future studies to explore the mechanism of color formation in WV leaves.

The intricate relationship between genomic mutations and proteomic network topology represents a frontier in understanding cellular resilience and disease mechanisms. This study presents a novel approach to analyzing how proteomic topological structures evolve and potentially break down in response to accumulating genomic mutations, offering insights into the complex interplay between genetic alterations and protein interaction networks. We developed a computational model simulating a network of ten key proteins (A-J) over 20 discrete time points, each representing a state of increasing genomic mutation load. Our model incorporates dynamic protein interaction strengths that fluctuate in response to simulated genomic alterations and a topological representation of the protein network, allowing for visualization of structural changes. Not forgetting a quantitative measure of network integrity, correlating with the system's ability to maintain function under mutational stress. Our Key findings include: visualization of proteomic network evolution through a series of topological graphs, revealing how genomic mutations progressively alter protein interaction patterns and identification of a critical "breakage point" in the network topology, signifying a threshold where genomic mutations overwhelm the protein network's ability to maintain its functional structure. And also quantification of network properties, including interaction strengths and overall network density, demonstrating the non-linear relationship between genomic mutations and proteomic topological integrity.The observed breakage point may represent a critical threshold in disease progression, where the accumulation of genomic mutations leads to a collapse in the proteomic interaction network, potentially triggering pathological states. This methodology offers a new perspective on the genotype-phenotype relationship, viewing it through the lens of protein network topology. Our approach provides a framework for future studies to analyze how specific genomic mutations might impact proteomic structures, potentially leading to new insights in cancer research, neurodegenerative disorders, and other mutation-driven diseases. It also suggests that maintaining proteomic topological integrity could be a key factor in cellular resilience against genomic instability.

Keywords: cranberry, exercise, proteomics, oxylipins, gut microbiome, metabolomics, immunity

Hepatocellular carcinoma (HCC) is a liver cancer that originates from hepatocytes. It is a primary health issue and one of the most common malignant tumors. The US FDA approved Sorafenib as the first-line anti-cancer drug for advanced HCC patients. A few patients with advanced HCC may benefit from Sorafenib treatment, but most of the patients eventually develop resistance to Sorafenib, which leads to its poor prognosis. Long-noncoding RNAs (lncRNA) have been found to play a critical role in tumorigenesis and the development of HCC, as well as various cancers. It also plays a vital role in tumor drug resistance, while the mechanisms of LncRNAs in HCC sorafenib resistance have not been characterized yet. In this review article, we summarized the molecular mechanisms, such as the involvement of transporters, receptors, cell death regulation, and other factors impacting sorafenib resistance in HCC.

Dual-fraction proteomics reveals a novel class of proteins impacted by nanoparticle exposure. Background: Nanoparticles (NPs) interact with cellular proteomes, altering biological processes. Understanding these interactions requires comprehensive analyses beyond solely characterizing the NP corona. Methods: We utilized a dual-fraction mass spectrometry (MS) approach analyzing both NP-bound and unbound proteins in Saccharomyces cerevisiae sp. protein extracts exposed to silica nanoparticles (SiNPs). We identified unique protein signatures for each fraction and quantified protein abundance changes using spectral counts. Results: Strong correlations were observed between protein profiles in each fraction and non-exposed controls, while minimal correlation existed between the fractions themselves. Linear models demonstrated equal contributions from both fractions in predicting control sample abundance. Combining both fractions revealed a larger proteomic response to SiNP exposure compared to single-fraction analysis. We identified 302/56 proteins bound/unbound to SiNPs and an additional 196 "impacted" proteins demonstrably affected by SiNPs. Conclusion: This dual-fraction MS approach provides a more comprehensive understanding of nanoparticle interactions with cellular proteomes. It reveals a novel class of "impacted" proteins, potentially undergoing conformational changes or aggregation due to NP exposure. Further research is needed to elucidate their biological functions and the mechanisms underlying their impact.

New chemicals including nanomaterials are being created and spread at high speed. In the E.U., REACH compliance imposes to manufacturers some tests but they are limited. Often, they cannot detect anything if the cells or organisms are able to overcome the toxic effect at the macroscopic level, preventing the suspicion of a potential long-term effect. Concerning bacteria that are essential for ecosystems and human health (microbiota), they are often considered as a whole in a consortium and only global parameters are measured. To overcome these limitations, we performed a study on the essential soil bacterium Bacillus subtilis. Two types of biofilm that are closer to its natural growth mode (particularly around plant roots) than the usual liquid type culture have been assayed: pellicle biofilm and swarming. We then used the power of shotgun proteomics to analyze in details these two somehow similar modes of cultures. Several physiological and metabolic patterns including proteins implicated in sporulation have shown significant differences. The effect of two types of nanoparticles (silicon and cerium oxide nanoparticles) has then been studied in the same way. This allowed us to investigate in details the response of the bacteria and focus on the differences observed depending on the biofilm type. This clearly highlighted the importance of testing several growth conditions and pinpointed the power of proteomics.