Relationship Of Proteins Research Articles

Proteomic exploration of potential blood biomarkers in haemophilic arthropathy.

The pathophysiology of haemophilic arthropathy (HA) is complex and largely undefined. Proteomic analyses provide insights into the intricate mechanisms of the HA.Our study aimed to identify differentially expressed proteins in relation to the severity of HA, explore their pathophysiological roles, and evaluate their potential as HA biomarkers. Our cross-sectional observational study encompassed 30 HA patients and 15 healthy subjects. Plasma samples were pooled into three groups of 15 samples from those with severe haemophilic arthropathy (sHA), mild haemophilic arthropathy (mHA) and healthy controls. Proteomic analysis was performed using liquid chromatography-mass spectrometry. The severity of HA was assessed using the World Federation of Haemophilia Physical Examination Score and ultrasonography following the Haemophilia Early Arthropathy Detection with Ultrasound (HEAD-US) guidelines. A total of 788 proteins were identified, with 97% of the uniquely identified proteins being expressed in all analysed groups. We identified several up and downregulated proteins across the groups that were mainly related to inflammatory and immunity-modulating processes, as well as joint degeneration. We highlighted ten proteins relevant for the development of HA: cathepsin G, endoplasmic reticulum aminopeptidase 2, S100-A9, insulin-like growth factor I, apolipoprotein (a), osteopontin, pregnancy zone protein, cartilage oligomeric matrix protein, CD44, and cadherin-related family member 2. Our analysis identified several proteins that shed further light on the distinctive pathogenesis of HA and could serve for biomarker research. However, these results need to be validated on a larger patient group.

The role of inflammatory proteins in regulating the impact of lipid specifications on deep venous thrombosis: a two sample and mediated Mendelian randomization study.

To investigate the potential mediating role of inflammatory proteins in the association between lipid species and Deep Venous Thrombosis (DVT). A comprehensive analysis was conducted using pooled data from genome-wide association studies (GWAS), incorporating double-sample and reverse Mendelian randomization (MR) techniques, to identify the specific inflammatory proteins that act as intermediaries among 91 screened proteins in relation to deep vein thrombosis (DVT). Furthermore, a two-step MR approach was employed to quantify the proportion of DVT risk attributed to lipid effects mediated by these inflammatory proteins. The MR Analysis revealed that the two inflammatory proteins, as predicted by genetics, served as mediating factors in the impact of five lipids on DVT. No reverse effect of DVT was observed on 179 lipid species and 91 inflammatory proteins. In the case of TAG(58:7) and its influence on DVT, CCL20 played an intermediary role with an estimated proportion of 12.51% (ranging from 12% to 13%). SIRT2 exhibited a masking effect on DVT for PC(17:0/20:4) and PC(18:0/20:4), while CCL20 masked the impact of DVT on PC(14:0/18:2), PC(15:0/18:2), and PC(18:0/20:5). In our study, we identified CCL20 as a crucial mediator in the association between TAG(58:7) and DVT, with a mediating proportion of 12.51% (12%-13%). Further investigations are warranted to explore other potential risk factors acting as mediators.

Age-associated proteins explain the role of medial temporal lobe networks in Alzheimer's disease.

The structural connectivity (SC) of the medial temporal lobe and its associated cortical anterior temporal and posterior medial networks (MTL-AT-PM) is linked to pathologies and memory decline in Alzheimer's disease (AD). However, neuroimaging analyses cannot tell us how SC changes occur in AD at the molecular level and do not provide a means of intervening to slow/prevent pathology-related changes in MTL-AT-PM SC. The current study aimed to understand how and where AD-related changes occur within MTL-AT-PM using proteomics. We used a 4-step approach in 101 older adults froma local sample, aiming to understand how proteins and SC in combination at the multivariate level predict AD pathology, and to identify specific proteins related to SC and AD pathology. Separately, we validated the discovered proteins in relation to SC and AD pathology using ADNI sample. We identified 12 latent factors linking proteins and SC; five showed significant relationships with AD pathology and/or episodic memory. Insulin-like growth factor binding proteins and tumor necrosis factor receptors, and hippocampal/parahippocampal edges contributed most to AD-related latent factors. Fast causal inference found protein-protein, protein-SC, and protein-pathology pathways, with seven proteins showing directional links to SC and AD-related neurodegeneration. We validated these results by identifying significant relationships between six available proteins with SC and amyloid-beta and phosphorylated tau in ADNI. We identified multivariate relationships between proteins and MTL-AT-PM networks that add to our understanding of AD pathology and suggest specific non-pathological proteins that warrant further study in relation to brain networks and AD pathology as possible therapeutic targets.

Genetically predicted 91 circulating inflammatory proteins in relation to risk of urological malignancies: a Mendelian randomization study.

Urological malignancies, including kidney, bladder, and prostate cancer, are major health concerns worldwide. Inflammation has been implicated in the pathogenesis of these cancers, and circulating inflammatory proteins may play a role in their development. However, the causal relationship between specific plasma proteins and urological malignancies remains unclear. We performed a two-sample Mendelian randomization (MR) analysis using summary statistics from genome-wide association studies (GWAS). Instrumental variables representing genetic variants associated with circulating inflammatory proteins were used to infer causality on the risk of kidney, bladder, and prostate cancer. Four MR methods were utilized to provide robust effect estimates. Our analysis identified several plasma proteins associated with a lower risk of kidney and bladder cancer, including Eukaryotic translation initiation factor 4E-binding protein 1, Caspase 8, Natural killer cell receptor 2B4, and Tumor necrosis factor ligand superfamily member 12. However, after adjusting for multiple testing, these associations did not remain statistically significant. For prostate cancer, CUB domain-containing protein 1 and Interleukin-10 receptor subunit beta were found to be protective, while Glial cell line-derived neurotrophic factor and SIR2-like protein 2 were identified as risk factors. After FDR adjustment, none of the inflammatory proteins were found to be significantly associated with a lower risk of prostate cancer. Our findings suggest that certain plasma proteins may be involved in the development of urological malignancies. Mendelian randomization provides a useful framework for investigating causal relationships between inflammatory proteins and urological cancers, offering potential insights into their underlying biology and therapeutic targets.

SARS-CoV-2 Protein Nsp9 Is Involved in Viral Evasion through Interactions with Innate Immune Pathways.

The suppression of the host's innate antiviral immune response by SARS-CoV-2, a contributing factor to the severity of disease, has been considerably studied in recent years. Many of these studies have focused on the actions of the structural proteins of the virus because of their accessibility to host immunological components. However, less is known about SARS-CoV-2 nonstructural and accessory proteins in relation to viral evasion. Herein, we study SARS-CoV-2 nonstructural proteins Orf3a, Orf6, and Nsp9 in a mimicked virus-infected state using poly(I:C), a synthetic analog of viral dsRNA, that elicits the antiviral immune response. Through genome-wide expression profiling, we determined that Orf3a, Orf6, and Nsp9 all modulate the host antiviral signaling transcriptome to varying extents, uniquely suppressing aspects of innate immune signaling. Our data suggest that SARS-CoV-2 Nsp9 hinders viral detection through suppression of RIG-I expression and antagonizes the interferon antiviral cascade by downregulating NF-kB and TBK1. Our data point to unique molecular mechanisms through which the different SARS-CoV-2 proteins suppress immune signaling and promote viral evasion. Nsp9 in particular acts on major elements of the host antiviral pathways to impair the antiviral immune response.

Differential Cytokine Responses of APOE3 and APOE4 Blood-brain Barrier Cell Types to SARS-CoV-2 Spike Proteins.

SARS-CoV-2 spike proteins have been shown to cross the blood-brain barrier (BBB) in mice and affect the integrity of human BBB cell models. However, the effects of SARS-CoV-2 spike proteins in relation to sporadic, late onset, Alzheimer's disease (AD) risk have not been extensively investigated. Here we characterized the individual and combined effects of SARS-CoV-2 spike protein subunits S1 RBD, S1 and S2 on BBB cell types (induced brain endothelial-like cells (iBECs) and astrocytes (iAstrocytes)) generated from induced pluripotent stem cells (iPSCs) harboring low (APOE3 carrier) or high (APOE4 carrier) relative Alzheimer's risk. We found that treatment with spike proteins did not alter iBEC integrity, although they induced the expression of several inflammatory cytokines. iAstrocytes exhibited a robust inflammatory response to SARS-CoV-2 spike protein treatment, with differences found in the levels of cytokine secretion between spike protein-treated APOE3 and APOE4 iAstrocytes. Finally, we tested the effects of potentially anti-inflammatory drugs during SARS-CoV-2 spike protein exposure in iAstrocytes, and discovered different responses between spike protein treated APOE4 iAstrocytes and APOE3 iAstrocytes, specifically in relation to IL-6, IL-8 and CCL2 secretion. Overall, our results indicate that APOE3 and APOE4 iAstrocytes respond differently to anti-inflammatory drug treatment during SARS-CoV-2 spike protein exposure with potential implications to therapeutic responses.

LKB1 Loss Correlates with STING Loss and, in Cooperation with β-Catenin Membranous Loss, Indicates Poor Prognosis in Patients with Operable Non-Small Cell Lung Cancer.

To investigate the incidence and prognostically significant correlations and cooperations of LKB1 loss of expression in non-small cell lung cancer (NSCLC), surgical specimens from 188 metastatic and 60 non-metastatic operable stage I-IIIA NSCLC patients were analyzed to evaluate their expression of LKB1 and pAMPK proteins in relation to various processes. The investigated factors included antitumor immunity response regulators STING and PD-L1; pro-angiogenic, EMT and cell cycle targets, as well as metastasis-related (VEGFC, PDGFRα, PDGFRβ, p53, p16, Cyclin D1, ZEB1, CD24) targets; and cell adhesion (β-catenin) molecules. The protein expression levels were evaluated via immunohistochemistry; the RNA levels of LKB1 and NEDD9 were evaluated via PCR, while KRAS exon 2 and BRAFV600E mutations were evaluated by Sanger sequencing. Overall, loss of LKB1 protein expression was observed in 21% (51/248) patients and correlated significantly with histotype (p < 0.001), KRAS mutations (p < 0.001), KC status (concomitant KRAS mutation and p16 downregulation) (p < 0.001), STING loss (p < 0.001), and high CD24 expression (p < 0.001). STING loss also correlated significantly with loss of LKB1 expression in the metastatic setting both overall (p = 0.014) and in lung adenocarcinomas (LUACs) (p = 0.005). Additionally, LKB1 loss correlated significantly with a lack of or low β-catenin membranous expression exclusively in LUACs, both independently of the metastatic status (p = 0.019) and in the metastatic setting (p = 0.007). Patients with tumors yielding LKB1 loss and concomitant nonexistent or low β-catenin membrane expression experienced significantly inferior median overall survival of 20.50 vs. 52.99 months; p < 0.001 as well as significantly greater risk of death (HR: 3.32, 95% c.i.: 1.71-6.43; p <0.001). Our findings underscore the impact of the synergy of LKB1 with STING and β-catenin in NSCLC, in prognosis.

The plasma proteome is linked with left ventricular and left atrial function parameters in patients with chronic heart failure.

Examining the systemic biological processes in the heterogeneous syndrome of heart failure with reduced ejection fraction (HFrEF), as reflected by circulating proteins, in relation to echocardiographic characteristics, may provide insights into HF pathophysiology. We investigated the link of 4210 repeatedly measured circulating proteins with repeatedly measured echocardiographic parameters, as well as with elevated left atrial pressure (LAP), in HFrEF patients, to provide insights into underlying mechanisms. In 173 HFrEF patients, we performed six-monthly echocardiography and trimonthly blood sampling during a median follow-up of 2.7(IQR:2.5-2.8) years. We investigated circulating proteins in relation to echocardiographic parameters of left ventricular (left ventricular ejection fraction[LVEF], global longitudinal strain[GLS]), and left atrial function (left atrial reservoir strain[LASr]) and elevated LAP(E/e' ratio >15), and used gene enrichment analyses to identify underlying pathophysiological processes. We found 723, 249, 792 and 427 repeatedly measured proteins, with significant associations with LVEF, GLS, LASr and E/e' ratio, respectively. Proteins associated with LASr reflected pathophysiological mechanisms mostly related to the extracellular matrix (ECM). Proteins associated with GLS reflected cardiovascular biological processes and diseases, whereas those associated with LVEF reflected processes involved in the sympathetic nervous system. Moreover, 49 proteins were associated with elevated LAP; after correction for LVEF, three proteins remained: Cystatin-D, Fibulin-5 and HSP40. Circulating proteins show varying associations with different echocardiographic parameters in HFrEF patients. These findings suggest that pathways involved in atrial and ventricular dysfunction, as reflected by the plasma proteome, are distinct.

Plasma proteins and persistent postsurgical pelvic pain among adolescents and young adults with endometriosis

Noninvasive biomarkers that predict surgical treatment response would inform personalized treatments and provide insight into potential biologic pathways underlying endometriosis-associated pain and symptom progression. To use plasma proteins in relation to the persistence of pelvic pain following laparoscopic surgery in predominantly adolescents and young adults with endometriosis using a multiplex aptamer-based proteomics biomarker discovery platform. We conducted a prospective analysis including 142 participants with laparoscopically-confirmed endometriosis from the Women's Health Study: From Adolescence to Adulthood observational longitudinal cohort with study enrollment from 2012-2018. Biologic samples and patient data were collected with modified World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonization Project tools. In blood collected before laparoscopic ablation or excision of endometriosis, we simultaneously measured 1305 plasma protein levels, including markers for immunity, angiogenesis, and inflammation, using SomaScan. Worsening or persistent postsurgical pelvic pain was defined as having newly developed, persistent (ie, stable), or worsening severity, frequency, or persistent life interference of dysmenorrhea or acyclic pelvic pain at 1-year postsurgery compared with presurgery. We calculated odds ratios and 95% confidence intervals using logistic regression adjusted for age, body mass index, fasting status, and hormone use at blood draw. We applied Ingenuity Pathway Analysis and STRING analysis to identify pathophysiologic pathways and protein interactions. The median age at blood draw was 17 years (interquartile range, 15-19 years), and most participants were White (90%). All had superficial peritoneal lesions only and were treated by excision or ablation. One-year postsurgery, pelvic pain worsened or persisted for 76 (54%) of these participants with endometriosis, whereas pelvic pain improved for 66 (46%). We identified 83 proteins associated with worsening or persistent pelvic pain 1-year postsurgery (nominal P<.05). Compared with those with improved pelvic pain 1-year postsurgery, those with worsening or persistent pelvic pain had higher plasma levels of CD63 antigen (odds ratio, 2.98 [95% confidence interval, 1.44-6.19]) and CD47 (odds ratio, 2.68 [95% confidence interval, 1.28-5.61]), but lower levels of Sonic Hedgehog protein (odds ratio, 0.55 [95% confidence interval, 0.36-0.84]) in presurgical blood. Pathways related to cell migration were up-regulated, and pathways related to angiogenesis were down-regulated in those with worsening or persistent postsurgical pelvic pain compared with those with improved pain. When we examined the change in protein levels from presurgery to postsurgery and its subsequent risk of worsening or persistent postsurgical pain at 1-year follow-up, we observed increasing levels of Sonic Hedgehog protein from presurgery to postsurgery was associated with a 4-fold increase in the risk of postsurgical pain (odds ratio [quartile 4 vs 1], 3.86 [1.04-14.33]). Using an aptamer-based proteomics platform, we identified plasma proteins and pathways associated with worsening or persistent pelvic pain postsurgical treatment of endometriosis among adolescents and young adults that may aid in risk stratification of individuals with endometriosis.

Protein and Carbohydrate Fractionation to Evaluate Perennial Ryegrass (Lolium perenne L.) Accessions

Precise information about carbohydrates and proteins in relation to their utilization in the rumen is useful for the breeding purposes of perennial ryegrass cultivars used for animal nutrition. The objective of the current study was to evaluate 20 diploid perennial ryegrass accessions from the intermediary heading stage. The ruminal kinetics of different carbohydrate and protein fractions of grasses and legumes are important for forage breeding programs. The Cornell Net Carbohydrate and Protein System (CNCPS) was used to provide such information. Accession-based variation can be observed after considering dynamic degradation processes. Variation among the 20 accessions was observed. Ruminally digested (RDC) and undigested (UDC) carbohydrate and ruminally degraded (RDP) and undegraded (UDP) protein contents, total carbohydrate and total protein contents, and carbohydrate and protein fractions for the first cut and annual averages show significant differences. Although the variation was smaller for the protein fractions, the calculated usable protein content (uCP, sum of UDP and amount of synthesized microbial protein in the rumen) in the small intestine is mainly influenced by decreasing the neutral detergent fiber (NDF) and increasing the sugar content among cultivars. Carbohydrate and protein fractionation is suitable for characterizing perennial grass accessions as it uses parameters relevant to ruminant nutrition, allowing a step forward in forage plant breeding for forage quality. To conclude, using parameters related to ruminal degradation kinetics should favor the selection of accessions with higher amounts of ruminally digested carbohydrates (RDC). The selection of accessions based on protein quality (proportion of UDP) is less favorable for achieving a higher usable protein content.

Sequential Double Immunoblotting with Peptide Antibodies.

Immunoblotting, also termed western blotting, is a powerful method for detection and characterization of proteins separated by various electrophoretic techniques. The combination of sodium dodecyl sulfate-poly acrylamide gel electrophoresis (SDS-PAGE), having high separating power, immunoblotting to synthetic membranes, and detection with highly specific peptide antibodies, is especially useful for studying individual proteins in relation to cellular processes, disease mechanisms, etc. Here, we describe a protocol for the sequential detection of various forms of an individual protein using peptide antibodies, exemplified by the characterization of antibody specificity for different forms of the protein calreticulin by double SDS-PAGE immunoblotting.

The Role of Bcl-2 Family Proteins and Sorafenib Resistance in Hepatocellular Carcinoma.

Liver cancer has been reported to be one of the most malignant diseases in the world. It is late diagnosis consequently leads to a difficult treatment, as the cancer reached an advanced stage. Hepatocellular carcinoma (HCC) is the primary type of cancer diagnosed in the liver, with deadly characteristics and a poor prognosis. The first-in-line treatment for advanced HCC is sorafenib. Sorafenib acts by inhibiting cell proliferation and by inducing apoptosis as well as blocks receptors associated with these mechanisms. Due to its constant use, sorafenib resistance has been described, especially to proteins of the Bcl-2 family, and their overexpression of Bcl-XL and Mcl-1. This review focuses on the role of the Bcl-2 proteins in relation to sorafenib resistance as a consequence of first-in-line treatment in HCC.

단백질 발현 양상 기반 생물 특성 이해를 위한 과학영재 대상 분자생물학 실험 프로그램 개발

Proteins are essential biomolecules that govern cellular activities and play a crucial role in understanding the characteristics of living organisms. A proper understanding of proteins is essential for comprehending the life sciences at the molecular level. In this study, our objective is to provide an experimental educational program for science-gifted middle school students to grasp the concepts of protein-based molecular biology. The experiments we have designed aim to analyze proteins from various organisms, helping students gain insights into their characteristics. To achieve this, we extract proteins from Escherichia coli, yeast, and human plasma/blood cells, and then separate total proteins by size using protein electrophoresis after adjusting their concentrations. Subsequently, we qualitatively determine the quantity and size of proteins through protein staining/de-staining processes. This is followed by discussions and comprehension of the major proteins in relation to biological characteristics. The entire experiment takes approximately 6 hours, allowing participants to learn diverse and universally applicable molecular experimental techniques related to protein analysis. To assess the effectiveness of this program, we conducted both a pre-test and post-test with nine participants who completed the experimental module, and we also gathered additional program feedback. The results of the experimental module showed high satisfaction among the participants, who did not encounter significant difficulties in understanding the experimental content. Furthermore, there was a slight increase in interest and career aspirations in molecular biology, and knowledge of intracellular protein roles and related molecular biology significantly improved. Therefore, This experimental program is expected to facilitate students in comprehending molecular biological concepts based on proteins and establishing a foundation for conducting molecular biology-related research, and ultimately to assist in making their informed career choices in the life sciences.

Sustainable Use of Organic Seaweed Fertilizer Improves the Metagenomic Function of Microbial Communities in the Soil of Rice Plants

The frequent use of chemical fertilizers in agricultural practices has developed into a serious environmental concern which urgently needs a solution to restrain their use in agricultural systems. Hence, there is an urgent need to investigate potential organic fertilizers from various natural resources to decrease the use of chemical fertilizers. Seaweed is among the natural resources with potential sustainability value. Our previous work has shown the effectiveness of seaweed fertilizer for increasing plant growth and soil beneficial microbiota. This study aims to evaluate the functional genes present in the soil of rice plants treated with seaweed fertilization. It involves amendments with reduced concentrations of chemical fertilizer in three groups: CF (only chemical fertilizer), CFSF1 (50% dose of CF + seaweed fertilizer 1 ton/ha), and CFSF2 (50% dose of CF + seaweed fertilizer 2 ton/ha). The rice plants supplemented with CFSF1 and CFSF2 were taller and faster to mature compared to CF. In addition, the primary macronutrients nitrogen (N), phosphorus (P), and potassium (K) were also significantly higher in soil supplemented with SF. Our findings showed increased ammonia-oxidizing archaea Crenarchaeota abundance in increasing SF treatments. The PICRUSt analyses indicated enriched functional genes and proteins in relation to amino acid, nucleotide, protein, and carbohydrate metabolism based on the KEGG, BioCyc, and PFAM databases. The current outcomes enhanced our understanding regarding the importance of microbial community for soil quality. Furthermore, seaweed supplementation has shown improvement in soil fertility, which significantly increases rice plant growth and productivity.

Joint association of air pollution exposure and inflammation-related proteins in relation to infant lung function

Background and aimSystemic inflammation is one potential mechanism underlying negative impact of air pollution on lung function. Levels of inflammation-related proteins have the potential to characterize infants’ susceptibility to air pollution induced lung function impairment. This study aimed to examine the interplay between air pollution exposure and inflammation-related proteins on lung function in 6-months-old infants. MethodsIn the EMIL birth cohort from Stockholm (n = 82), dynamic spirometry, along with measurement of plasma levels of 92 systemic inflammation-related proteins (Olink Proseek Multiplex Inflammation panel) have been carried out in infants aged six months. Time-weighted average exposure to particles with an aerodynamic diameter of <10 μm (PM10), <2.5 μm (PM2.5), and nitrogen dioxide (NO2) at residential addresses from birth and onwards was estimated via validated dispersion models. To characterize the abnormality of inflammation-related protein profile, for each protein in each infant, we calculated the relative deviance of the protein level from age- and sex-specific median in terms of its age- and sex-specific interquartile range (IQR), followed by computing the absolute value of the smallest relative deviance, “minimum absolute deviance”. Using linear regression models, interaction of air pollution and the abnormal inflammatory profile on lung function was estimated on the additive scale. ResultsWe found joint association of PM exposure and an abnormal inflammatory protein profile in relation to FEV0.5 and FVC. For 0.1 unit increase in minimum absolute deviance, one IQR increase in PM10 was associated with 85.9 ml (95% CI: −122.9, −48.9) additional decrease in FEV0.5, and 72.3 ml (95% CI: −121.5, −23.2) additional decrease in FVC. Similar results were obtained with PM2.5 exposure, while less apparent for NO2. ConclusionsEarly life air pollution exposure and abnormal inflammation-related protein profiles may interact synergistically towards lower lung function in infants.

The Anti-Inflammatory Action of Cannabigerol Accompanied by the Antioxidant Effect of 3-O-ethyl Ascorbic Acid in UVA-Irradiated Human Keratinocytes.

Excessive daily exposure of human skin to natural UVA radiation leads to impaired redox homeostasis in epidermal keratinocytes, resulting in changes in their proteome. Commonly used antioxidants usually exhibit protection in a narrowed range, which makes it necessary to combine their effects. Therefore, the aim of this study was to analyze the protective effect of cannabigerol (CBG) and 3-O-ethyl ascorbic acid (EAA), used separately and together, on the proteomic profile of UVA irradiated keratinocytes. Proteomic analysis with the use of the Q Exactive HF mass spectrometer, combined with biostatistic tests, performed on UVA-irradiated keratinocytes indicated enhanced and lowered expression of 186 and 160 proteins, respectively. CBG treatment after UVA irradiation reduced these numbers to 110 upregulated and 49 downregulated proteins, while EAA eliminated all these changes. CBG completely eliminated the UV-induced effect on the expression of pro-inflammatory proteins and significantly increased the level of proteins responsible for cellular locomotion. On the other hand, CBG reduced the level of UVA-induced 4-hydroxynonenal protein adducts fivefold, whereas EAA had no effect on this modification. At the same time, CBG and EAA did not modify the expression/structure of proteins in relation to the nonirradiated control keratinocytes in the case of an unaccompanied use or slightly modified the protein profile when used in a mixture. The combined protective effects of CBG on protein structure and EAA on protein expression profile allowed us to obtain a wider protection of cells against UVA radiation, compared with when the compounds were used alone. SIGNIFICANCE STATEMENT: Proteomic analysis of human skin cells allows to conclude that 3-O-ethyl ascorbic acid eliminates UVA-induced changes in the expression of keratinocyte proteins, while cannabigerol significantly reduces 4-hydroxynonenal protein adducts. The combined protective effects of cannabigerol on protein structure and of 3-O-ethyl ascorbic acid on protein expression profile allowed to obtain a wider protection of cells against UVA radiation.

Prophage identification and molecular analysis in the genomes of Pseudomonas aeruginosa strains isolated from critical care patients.

Prophages are bacteriophages integrated into the bacterial host's chromosome. This research aims to analyze and characterize the existing prophages within a collection of 53 Pseudomonas aeruginosa strains from intensive care units (ICUs) in Portugal and Spain. A total of 113 prophages were localized in the collection, with 18 of them being present in more than one strain simultaneously. After annotation, five of them were discarded as incomplete, and the 13 remaining prophages were characterized. Of 13, 10 belonged to the siphovirus tail morphology group, 2 to the podovirus tail morphology group, and 1 to the myovirus tail morphology group. All prophages had a length ranging from 20,199 to 63,401 bp and a GC% between 56.2% and 63.6%. The number of open reading frames (ORFs) oscillated between 32 and 88, and in 3/13 prophages, more than 50% of the ORFs had an unknown function. With our findings, we show that prophages are present in the majority of the P. aeruginosa strains isolated from Portuguese and Spanish critically ill patients, many of them found in more than one circulating strain at the same time and following a similar clonal distribution pattern. Although a great sum of ORFs had an unknown function, number of proteins in relation to viral defense (anti-CRISPR proteins, toxin/antitoxin modules, proteins against restriction-modification systems) as well as to prophage interference into their host's quorum sensing system and regulatory cascades were found. This supports the idea that prophages have an influence in bacterial pathogenesis and anti-phage defense. IMPORTANCE Despite being known for decades, prophages remain understudied when compared to the lytic phages employed in phage therapy. This research aims to shed some light into the nature, composition, and role of prophages found within a set of circulating strains of Pseudomas aeruginosa, with special attention to high-risk clones. Given the fact that prophages can effectively influence bacterial pathogenesis, prophage basic research constitutes a topic of growing interest. Furthermore, the abundance of viral defense and regulatory proteins within prophage genomes detected in this study evidences the importance of characterizing the most frequent prophages in circulating clinical strains and in high-risk clones if phage therapy is to be used.

Quantitative proteomics analysis of bacteriocin-like substance producing Lactococcus spp. in simulated vegetable and fruit media

Lactic acid bacteria (LAB) and their metabolites such as bacteriocins have gained considerable interest in terms of their bio-preservative properties to improve food safety and quality. In this study, a quantitative proteomic investigation employing stable isotope labeling by peptide demethylation was carried out to investigate changes in intracellular proteins of bacteriocin-like substance (BLS) producing Lactococcus spp. 7.17 grown in vegetable or fruit juice culture media at 10 °C for 0, 3 or 7 days. In total, 1053 proteins in vegetable medium and 1113 in fruit medium were identified and quantified. Proteins that changed more than two- fold were identified as increased or decreased ones and grouped into four clusters. Those increased proteins were involved in the events of low temperature and ROS stress responses, DNA processing, transcription and translation, central carbon metabolism, fatty acid and phospholipid metabolism, amino acid and cell wall biosynthesis. Key proteins in relation to BLS producing property were also identified suggesting that at least one bacteriocin IIa production system exists in Lactococcus spp. 7.17. These findings provide insights into protein changes of L. lactis at low temperature and lay foundations for further investigations on BLS producing LAB using targeted quantitative proteomic approaches. Significance of the researchThe inhibitory effects of Lactococcus spp. 7.17 on Listeria innocua in fruit and vegetable juice culture media were confirmed.Using a quantitative proteomic approach employing stable isotope labeling by peptide demethylation, 99 or 113 significantly changed proteins of Lactococcus spp. 7.17 grown in vegetable or fruit juice medium were determined, respectively.The significant change in protein abundance suggested an adaptive mechanism of Lactococcus spp. to culture condition at low temperatures.This research provides insights on protein changes of Lactococcus spp. which has potential application in fresh and fresh-cut fruit and vegetables at low temperature.

The expression pattern of pyruvate dehydrogenase kinases predicts prognosis and correlates with immune exhaustion in clear cell renal cell carcinoma

Renal cancer cells constitute a paradigm of tumor cells with a glycolytic reprogramming which drives metabolic alterations favouring cell survival and transformation. We studied the expression and activity of pyruvate dehydrogenase kinases (PDK1-4), key enzymes of the energy metabolism, in renal cancer cells. We analysed the expression, subcellular distribution and clinicopathological correlations of PDK1-4 by immunohistochemistry of tumor tissue microarray samples from a cohort of 96 clear cell renal cell carcinoma (ccRCC) patients. Gene expression analysis was performed on whole tumor tissue sections of a subset of ccRCC samples. PDK2 and PDK3 protein expression in tumor cells correlated with lower patient overall survival, whereas PDK1 protein expression correlated with higher patient survival. Gene expression analysis revealed molecular association of PDK2 and PDK3 expression with PI3K signalling pathway, as well as with T cell infiltration and exhausted CD8 T cells. Inhibition of PDK by dichloroacetate in human renal cancer cell lines resulted in lower cell viability, which was accompanied by an increase in pAKT. Together, our findings suggest a differential role for PDK enzymes in ccRCC progression, and highlight PDK as actionable metabolic proteins in relation with PI3K signalling and exhausted CD8 T cells in ccRCC.

Circulating proteins and peripheral artery disease risk: observational and Mendelian randomization analyses.

We conducted observational and Mendelian randomization (MR) analyses to explore the associations between blood proteins and risk of peripheral artery disease (PAD). The observational cohort analyses included data on 257 proteins estimated in fasting blood samples from 12 136 Swedish adults aged 55-94 years who were followed up for incident PAD via the Swedish Patient Register. Mendelian randomization analyses were undertaken using cis-genetic variants strongly associated with the proteins as instrumental variables and genetic association summary statistic data for PAD from the FinnGen study (11 924 cases and 288 638 controls) and the Million Veteran Program (31 307 cases and 211 753 controls). The observational analysis, including 86 individuals diagnosed with incident PAD during a median follow-up of 6.6-year, identified 13 proteins [trefoil factor two, matrix metalloproteinase-12 (MMP-12), growth differentiation factor 15, V-set and immunoglobulin domain-containing protein two, N-terminal prohormone brain natriuretic peptide, renin, natriuretic peptides B, phosphoprotein associated with glycosphingolipid-enriched microdomains one, C-C motif chemokine 15, P-selectin, urokinase plasminogen activator surface receptor, angiopoietin-2, and C-type lectin domain family five member A] associated with the risk of PAD after multiple testing correction. Mendelian randomization analysis found associations of T-cell surface glycoprotein CD4, MMP-12, secretoglobin family 3A member 2, and ADM with PAD risk. The observational and MR associations for T-cell surface glycoprotein CD4 and MMP-12 were in opposite directions. This study identified many circulating proteins in relation to the development of incident PAD. Future studies are needed to verify our findings and assess the predictive and therapeutic values of these proteins in PAD.