Proteomic Expression Profiling Research Articles

Proteome profiling in patients with peripartum cardiomyopathy according to ethnicity a biomarker study on the EORP cohort

Abstract Background Peripartum cardiomyopathy (PPCM) is a pregnancy-associated form of heart failure, which occurs in previously healthy women towards the end of pregnancy and in the first months postpartum. Previous reports showed a varying prevalence of PPCM across different regions and potentially a higher incidence in patients with black African ethnicity. The correct and timely diagnosis remains challenging and there is a need for novel disease-specific biomarkers. Accuracy in diagnosing PPCM can be improved by using serum-protein biomarkers such as QSOX1, adiponectin and ITIH3 in addition to NT-proBNP. However, it still needs to be ascertained whether there are ethnic differences in proteomic profiles amongst patients with PPCM with different ethnicities. Aims To delineate possible differences in serum protein biomarker profiles across different ethnic groups within the EURObservation Research Programme (EORP) multi-national cohort of women with PPCM. Methods Demographic and clinical data, as well as serum samples were collected from 84 patients with PPCM from seven EORP participating countries. Serum proteomic profiling was conducted using DIA-based label-free quantitative (LFQ) LC-MS at the time of diagnosis from depleted serum samples. Mass spectrometry data were analyzed by Spectronaut v15 using a study-specific spectral library. From the 84 patients in the EORP PPCM registry on whom we performed proteomic analyses, 82 patients self-declared their ethnicity. These 82 patients were assessed for any ethnical differences in their proteomic expression profile using unsupervised principal component analysis (PCA). Results In this cohort of 82 women with PPCM, the mean age was 30.5±6.7 years (Table 1). Three quarters of this cohort had no hypertension during pregnancy and only 13.8% had a prior diagnosis of PPCM. The mean left ventricular ejection fraction (LVEF) was 35% at time of first diagnosis, with no difference between the ethnic groups. However, women of Middle Eastern decent had more severe LV dilatation (LVEDD: 64.0 (62.0-65.0) mm). Three hundred and twenty-nine (329) proteins were identified in the serum samples. As depicted in Figure 1, PCA did not yield a distinct separation between the different ethnic groups. Principal component 1 (PC1) accounted for 15.2% of the total variability in protein expression among ethnic groups, PC2 explained a comparatively lower percentage at 12%. Conclusion The protein biomarkers identified in PPCM patients showed no discernible racial differences, demonstrating consistent performance across all ethnic groups.

Proteomics Reveals Divergent Cardiac Inflammatory and Metabolic Responses After Inhalation of Ambient Particulate Matter With or Without Ozone.

Inhalation of ambient particulate matter (PM) and ozone (O3) has been associated with increased cardiovascular morbidity and mortality. However, the interactive effects of PM and O3 on cardiac dysfunction and disease have not been thoroughly examined, especially at a proteomic level. The purpose of this study was to identify and compare proteome changes in spontaneously hypertensive (SH) rats co-exposed to concentrated ambient particulates (CAPs) and O3, with a focus on investigating inflammatory and metabolic pathways, which are the two major ones implicated in the pathophysiology of cardiac dysfunction. For this, we measured and compared changes in expression status of 9 critical pro- and anti-inflammatory cytokines using multiplexed ELISA and 450 metabolic proteins involved in ATP production, oxidative phosphorylation, cytoskeletal organization, and stress response using two-dimensional electrophoresis (2-DE) and mass spectrometry (MS) in cardiac tissue of SH rats exposed to CAPs alone, O3 alone, and CAPs + O3. Proteomic expression profiling revealed that CAPs alone, O3 alone, and CAPs + O3 differentially altered protein expression patterns, and utilized divergent mechanisms to affect inflammatory and metabolic pathways and responses. Ingenuity Pathway Analysis (IPA) of the proteomic data demonstrated that the metabolic protein network centered by gap junction alpha-1 protein (GJA 1) was interconnected with the inflammatory cytokine network centered by nuclear factor kappa beta (NF-kB) potentially suggesting inflammation-induced alterations in metabolic pathways, or vice versa, collectively contributing to the development of cardiac dysfunction in response to CAPs and O3 exposure. These findings may enhance understanding of the pathophysiology of cardiac dysfunction induced by air pollution and provide testable hypotheses regarding mechanisms of action.

Hippophae Rhamnoides-derived Phytomedicine Nano-System Modulates Bax/Fas Pathways to Reduce Proliferation in Triple-Negative Breast Cancer.

Triple-negative breast cancer (TNBC) is the most common primary tumor of the breast with limited effectual drug availability. Therefore, the aim of the study is to develop an innovative phyto-nanomedicine (PNM) to cure TNBC with the least genotoxicity. Hereinafter, the sea buckthorn' extracted polyphenols (SBP), combine with metformin (MET), are synthesized as a novel PNM to evaluate its anti-tumor properties, effectiveness, and mechanism of action in TNBC in vitro and in vivo models. The SBP exhibits 16 new kinds of polyphenols that are been reported earlier which regulated cell development, proliferation, and programmed cell death (PCD) effectively. SBP-MET PNM inhibits MDA-MB-231 (47%), MDA-MB-436 (46%), and 4T1 (46%) cell proliferation but does not affect L929 normal murine cell development and successfully induce PCD (73.19%) in MDA-MB-231 cells. Mechanistically, in vivo SBP-MET proteome expression profiling reveals upregulation of proapoptotic Bax protein and activation of Fas signaling pathways convince downstream Daxx and FADD proteins, which further triggers Caspase-3 that prompts apoptosis in human TNBC cells by cleaving PARP-1 protein. Current findings establish innovative highly biocompatible phyto-nanomedicine that has significant potential to inhibit TNBC cell growth and induce regulated cell death (RCD) in vivo model, thereby opening a new arena for TNBC therapy.

Mapping dynamic molecular changes in hippocampal subregions after traumatic brain injury through spatial proteomics

BackgroundTraumatic brain injury (TBI) often results in diverse molecular responses, challenging traditional proteomic studies that measure average changes at tissue levels and fail to capture the complexity and heterogeneity of the affected tissues. Spatial proteomics offers a solution by providing insights into sub-region-specific alterations within tissues. This study focuses on the hippocampal sub-regions, analyzing proteomic expression profiles in mice at the acute (1 day) and subacute (7 days) phases of post-TBI to understand subregion-specific vulnerabilities and long-term consequences.MethodsThree mice brains were collected from each group, including Sham, 1-day post-TBI and 7-day post-TBI. Hippocampal subregions were extracted using Laser Microdissection (LMD) and subsequently analyzed by label-free quantitative proteomics.ResultsThe spatial analysis reveals region-specific protein abundance changes, highlighting the elevation of FN1, LGALS3BP, HP, and MUG-1 in the stratum moleculare (SM), suggesting potential immune cell enrichment post-TBI. Notably, established markers of chronic traumatic encephalopathy, IGHM and B2M, exhibit specific upregulation in the dentate gyrus bottom (DG2) independent of direct mechanical injury. Metabolic pathway analysis identifies disturbances in glucose and lipid metabolism, coupled with activated cholesterol synthesis pathways enriched in SM at 7-Day post-TBI and subsequently in deeper DG1 and DG2 suggesting a role in neurogenesis and the onset of recovery. Coordinated activation of neuroglia and microtubule dynamics in DG2 suggest recovery mechanisms in less affected regions. Cluster analysis revealed spatial variations post-TBI, indicative of dysregulated neuronal plasticity and neurogenesis and further predisposition to neurological disorders. TBI-induced protein upregulation (MUG-1, PZP, GFAP, TJP, STAT-1, and CD44) across hippocampal sub-regions indicates shared molecular responses and links to neurological disorders. Spatial variations were demonstrated by proteins dysregulated in both or either of the time-points exclusively in each subregion (ELAVL2, CLIC1 in PL, CD44 and MUG-1 in SM, and SHOC2, LGALS3 in DG).ConclusionsUtilizing advanced spatial proteomics techniques, the study unveils the dynamic molecular responses in distinct hippocampal subregions post-TBI. It uncovers region-specific vulnerabilities and dysregulated neuronal processes, and potential recovery-related pathways that contribute to our understanding of TBI’s neurological consequences and provides valuable insights for biomarker discovery and therapeutic targets.

Comparison of Novel Proteomic Expression Profiles for Radiation Exposure in Male and Female C57BL6 Mice.

There is a need for point-of-care diagnostics for future mass casualty events involving radiation exposure. The development of radiation exposure and dose prediction algorithms for biodosimetry is needed for screening of large populations during these scenarios, and exploration of the potential effects which sex, age, genetic heterogeneity, and physiological comorbidities may have on the utility of biodosimetry diagnostics is needed. In the current study, proteomic profiling was used to examine sex-specific differences in age-matched C57BL6 mice on the blood proteome after radiation exposure, and the usefulness of development and application of biodosimetry algorithms using both male and female samples. Male and female mice between 9-11 weeks of age received a dose of total-body irradiation (TBI) of either 2, 4 or 8 Gy and plasma was collected at days 1, 3 and 7 postirradiation. Plasma was then screened using the SomaScan v4.1 assay for ∼7,000 protein analytes. A subset panel of protein biomarkers demonstrated significant (FDR < 0.05 and |logFC| > 0.2) changes in expression after radiation exposure. All proteins were used for feature selection to build predictive models of radiation exposure using different sample and sex-specific cohorts. Both binary (prediction of any radiation exposure) and multidose (prediction of specific radiation dose) model series were developed using either female and male samples combined or only female or only male samples. The binary series (models 1, 2 and 3) and multidose series (models 4, 5 and 6) included female/male combined, female only and male only respectively. Detectable values were obtained for all ∼7,000 proteins included in the SomaScan assay for all samples. Each model algorithm built using a unique sample cohort was validated with a training set of samples and tested with a separate new sample series. Overall predictive accuracies in the binary model series was ∼100% at the model training level, and when tested with fresh samples, 97.9% for model 1 (female and male) and 100% for model 2 (female only) and model 3 (male only). When sex-specific models 2 and 3 were tested with the opposite sex, the overall predictive accuracy rate dropped to 62.5% for model 2 and remained 100% for model 3. The overall predictive accuracy rate in the multidose model series was 100% for all models at the model training level and, when tested with fresh samples, 83.3%, 75% and 83.3% for Multidose models 4-6, respectively. When sex-specific model 5 (female only) and model 6 (male only) were tested with the opposite sex, the overall predictive accuracy rate dropped to 52.1% and 68.8%, respectively. These models represent novel predictive panels of radiation-responsive proteomic biomarkers and illustrate the utility and necessity of considering sex-specific differences in development of radiation biodosimetry prediction algorithms. As sex-specific differences were observed in this study, and as use of point-of-care radiation diagnostics in future mass casualty settings will necessarily include persons of both sexes, consideration of sex-specific variation is essential to ensure these diagnostic tools have practical utility in the field.

Proteomic analysis of meropenem-induced outer membrane vesicles released by carbapenem-resistant Klebsiella pneumoniae.

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an important multidrug resistance (MDR) pathogen that threatens human health and is the main source of hospital-acquired infection. Outer membrane vesicles (OMVs) are extracellular vesicles derived from Gram-negative bacteria and contain materials involved in bacterial survival and pathogenesis. They also contribute to cellular communication to nearby or distant recipient cells and influence their functions and phenotypes. In this study, we sought to understand the mechanism of bacterial response to meropenem pressure and explore the relationship between pathogenic proteins and the high pathogenicity of bacteria. We performed whole-genome PacBio sequencing on a clinical CRKP strain, and its OMVs were characterized using nanoparticle tracking analysis, transmission electron microscopy, and proteomic analysis. Thousands of vesicle proteins have been identified in mass spectrometry-based high-throughput proteomics analyses of K. pneumoniae OMVs. Protein functionality analysis showed that the OMVs were predominantly involved in metabolic, intracellular compartments, nucleic acid binding, survival, defense, and antibiotic resistance, such as Chromosome partition protein MukB, 3-methyl-2-oxobutanoate hydroxymethyltransferase, methionine-tRNA ligase, Heat shock protein 60 family chaperone GroEL, and Gamma-glutamyl phosphate reductase. Additionally, a protein-protein interaction network demonstrated that OMVs from meropenem-treated K. pneumoniae showed the highest connectivity in DNA polymerase I, phenylalanine-tRNA ligase beta subunit, DNA-directed RNA polymerase subunit beta, methionine-tRNA ligase, DNA-directed RNA polymerase subunit beta, and DNA-directed RNA polymerase subunit alpha. The OMVs proteome expression profile indicates increased secretion of stress proteins released from meropenem-treated K. pneumoniae, which provides clues for revealing the biogenesis and pathophysiological functions of Gram-negative bacteria OMVs. The significant differentially expressed proteins identified in this study are of great significance for exploring effective control strategies for CRKP infection.IMPORTANCEMeropenem is one of the main antibiotics used in the clinical treatment of carbapenem-resistant Klebsiella pneumoniae (CRKP). This study demonstrated that some important metabolic changes occurred in meropenem-induced CRKP-outer membrane vesicles (OMVs), The OMVs proteome expression profile indicates increased secretion of stress proteins released from meropenem-induced Klebsiella pneumoniae. Furthermore, this is the first study to discuss the protein-protein interaction network of the OMVs released by CRKP, especially under antibiotic stress.

Molecular mechanism of acid stress response of Alicyclobacillus acidoterrestris DSM 3922T under sublethal pH

Alicyclobacillus acidoterrestris (A. acidoterrestris) causes the spoilage of pasteurized acidic fruit juice due to its unique thermoacidophilic properties, which caused economic losses to fruit juice industry. To reveal the molecular regulatory mechanism of how A. acidoterrestris responded to acid stress is the key to hazard control of this microbe. Herein, acid-responsive proteome expression profiles of A. acidoterrestris were analyzed using label-free quantitative mass spectrometry to investigate its acid resistance mechanism at sublethal pH. Totally, 325 differential expression proteins were identified during acid stress (pH 2.5, 15 min duration), of which the expressions of 83 proteins were up-regulated and the other 242 protein expressions were down-regulated. The identified differentially expressed proteins were mainly involved in small molecule metabolism, organic nitrogen compounds metabolism, organic acid metabolism, and signal transduction. Overall, they were mapped into 97 metabolic pathways. Combination of KEGG pathway analysis and protein functional analysis suggested that the pH homeostasis system variation and relevant changes in metabolic pathways, cell membrane permeability and DNA repair are the main acid resistance mechanisms of A. acidoterrestris. Our finding implied that A. acidoterrestris might sense and transmit pH signals from the external environment through NhaB protein which holds histidine-dependent acid resistance system, initiating a series of acid tolerance reactions. Taken together, our study demonstrated global physiological response of A. acidoterrestris to sublethal pH, which provided a better understanding of acid adaption mechanism of A. acidoterrestris.

Colony-forming endothelial cells – candidate culture for tissue vascular engineering: the gene and proteomic profile

Aim. To validate ECFC culture as a candidate culture for vascular tissue engineering using comparative analysis of the proteomic and gene expression profiles in comparison with cultures of human umbilical vein endothelial cells (HUVEC) and human coronary artery endothelial cells (HCAEC).Materials and Methods. ECFC culture was obtained by cultivating peripheral blood mononuclear cells of patients with coronary artery disease. Commercial HCAECs produced by Cell Applications, and HUVECs cultured according to the modified protocol of Jaffe were used as controls.The cells were lysed with TRIzol, and total RNA was isolated using a Purelink RNA Micro Scale Kit with concomitant DNase treatment. Next, rRNA depletion was carried out, followed by the creation of DNA libraries. DNA libraries were quantified using quantitative polymerase chain reaction on a CFX96 Touch Bio-Rad amplifier. DNA libraries were equimolarly mixed and sequenced on HiSeq 2000 (Illumina) with a paired-end reads of 2x125 nucleotides.Conventional western blotting was performed using pan-endothelial markers CD31, vWF, VEG-FR2/KDR, marker of endothelial progenitor cells CD34, markers of epithelial-mesenchymal transition Snail and Slug, and markers of endothelial specification: arterial HEY2, venous COUP-TFII and lymphatic LYVE1, VEGFR2. Dot blotting against 55 angiogenesis-related proteins was performed using Proteome Profiler Human Angiogenesis Array Kit in accordance with the manufacturer's protocol.Results. ECFC overexpresses markers of all three endothelial lineages (KDR, VWF, CD34, NRP2, FLT4 and LYVE1 compared to HCAEC; NOTCH4, DLL2) and LYVE1 compared to HUVEC. Proteomic profiling indicated ECFC as an intermediate population between HCAEC and HU-VEC in term of the expression of HEY2, LYVE1, VEGFR3, Snail and Slug. 261 DEGs were detected between ECFC and HUVEC, and 470 DEGs between ECFC and HCAEC.Conclusion. The gene expression profile of endothelial colony-forming cells corresponds to mature endothelial cells and indicates ECFC as an intermediate population between HCAEC and HUVEC. ECFC culture can be recommended for tissue vascular engineering.

POLARIZED MACROPHAGE-DERIVED EXTRACELLULAR VESICLES AS POTENTIAL MEDIATORS OF TENDON REPAIR

Macrophages play a critical role in innate immunity by promoting or inhibiting tissue inflammation and repair. Classically, macrophages can differentiate into either pro-inflammatory (M1) or pro-reparative (M2) phenotypes in response to various stimuli. Therefore, this study aimed to address how extracellular vesicles (EVs) derived from polarized macrophages can affect the inflammatory response of tendon cells.For that purpose, human THP-1 cells were stimulated with lipopolysaccharide (LPS), and interleukins -4 and -13 (IL- 4, IL-13), to induce macrophages polarization into M1, M2, and hybrid M1/M2 phenotypes. Subsequently, the EVs were isolated from the culture medium by ultracentrifugation. The impact of these nanovesicles on the inflammation and injury scenarios of human tendon-derived cells (hTDCs), which had previously been stimulated with interleukin- 1 beta (IL-1ß) to mimic an inflammatory scenario, was assessed.We were able to isolate three different nanovesicles populations, showing the typical shape, size and surface markers of EVs. By extensively analyzing the proteomic expression profiles of M1, M2, and M1/M2, distinct proteins that were upregulated in each type of macrophage-derived EVs were identified. Notably, most of the detected pro- inflammatory cytokines and chemokines had higher expression levels in M1-derived EVs and were mostly absent in M2-derived EVs. Hence, by acting as a biological cue, we observed that M2 macrophage-derived EVs increased the expression of the tendon-related marker tenomodulin (TNMD) and tended to reduce the presence of pro-inflammatory markers in hTDCs. Overall, these preliminary results show that EVs derived from polarized macrophages might be a potential tool to modulate the immune system responses becoming a valuable asset in the tendon repair and regeneration fields worthy to be further explored.

4P Immune exoproteome, soluble proteome and immune-related gene expression profiles of anti-PD-1 therapy in stage IIIB/IV non-small cell lung cancer: Relevance of immunosuppressive factors

4P Immune exoproteome, soluble proteome and immune-related gene expression profiles of anti-PD-1 therapy in stage IIIB/IV non-small cell lung cancer: Relevance of immunosuppressive factors

Disclosing Potential Therapeutic Targets Associated With Osimertinib Resistance in the Non-small Cell Lung Cancer Cell Line H1975.

Osimertinib, a third-generation epidermal growth factor receptor tyrosine kinase inhibitor, is a highly effective and valuable treatment option for advanced non-small cell lung cancer (NSCLC) patients with EGFR mutations, such as T790M. However, acquired resistance ultimately limits its clinical application. In this study, we aimed to identify potential targets for overcoming osimertinib resistance. The H1975/OSI cell line was induced in vitro through intermittent induction. Cell activity was measured using a cell counting kit-8 assay. Uni-omics and multi-omics analyses were conducted on the transcriptomic and proteomic (4D label-free) expression profiles, which involved differential expression analysis, GO functional annotation and KEGG pathway enrichment analysis, as well as correlation analysis of transcription factors and PPI network. H1975/OSI cells showed resistance towards osimertinib with IC50 values approximately 5.25-fold higher than H1975 cells. A total of 2519 genes were found to be differentially expressed genes (DEGs) and 1533 proteins were found to be differentially abundant proteins (DAPs). Furthermore, 147 genes that were differentially expressed at both the transcription and protein levels (TPGs) were identified as being differentially expressed in both the transcriptome and proteome. It was revealed that many pathways related to the structure and function of ribosomes, as well as metabolites, were altered. The highest connectivity genes of 147 TPGs included NOP56, DDX21, PDCD11, CCNB1, and TOP2A. The hub genes of the transcriptional regulatory network included DDX21, KPNA2, DDX5, BRCA1, LMNB1, and HIF1A. Collectively, our high-throughput analysis uncovered functional properties that interacted with gene signatures of H1975/OSI cells, and highlighted certain pathways and eleven hub genes that may be the potential targets for improving clinical osimertinib resistance.

Exploring multisite heterogeneity of human basal cell carcinoma proteome and transcriptome.

Basal cell carcinoma (BCC) is the most common type of skin cancer. Due to multiple, potential underlying molecular tumor aberrations, clinical treatment protocols are not well-defined. This study presents multisite molecular heterogeneity profiles of human BCC based on RNA and proteome profiling. Three areas from lesions excised from 9 patients were analyzed. The focus was gene expression profiles based on proteome and RNA measurements of intra-tumor heterogeneity from the same patient and inter-tumor heterogeneity in nodular, infiltrative, and superficial BCC tumor subtypes from different patients. We observed significant overlap in intra- and inter-tumor variability of proteome and RNA expression profiles, showing significant multisite heterogeneity of protein expression in the BCC tumors. Inter-subtype analysis has also identified unique proteins for each BCC subtype. This profiling leads to a deeper understanding of BCC molecular heterogeneity and potentially contributes to developing new sampling tools for personalized diagnostics therapeutic approaches to BCC.

Serum proteomic profile of wild stump-tailed macaques (Macaca arctoides) infected with malaria parasites in Thailand.

The number of patients infected with simian malaria is gradually increasing in many countries of Southeast Asia and South America. The most important risk factor for a zoonotic spillover event of malarial infection is mostly influenced by the interaction between humans, monkeys, and vectors. In this study, we determine the protein expression profile of a wild stump-tailed macaque (Macaca arctoides) from a total of 32 blood samples collected from Prachuap Kiri Khan Province, Thailand. The malarial parasite was analyzed using nested polymerase chain reaction (PCR) assays by dividing the samples into three groups: non-infected, mono-infected, and multiple-infected. The identification and differential proteomic expression profiles were determined using liquid chromatography with tandem mass spectrometry (LC-MS/MS) and bioinformatics tools. A total of 9,532 proteins (total proteins) were identified with the filter-based selection methods analysis, and a subset of 440 proteins were found to be different between each group. Within these proteins, the GhostKOALA functional enrichment analysis indicated that 142 important proteins were associated with either of the organismal system (28.87%), genetic information processing (23.24%), environmental information processing (16.20%), metabolism (13.38%), cellular processes (11.97%), or causing human disease (6.34%). Additionally, using interaction network analysis, nine potential reporter proteins were identified. Here, we report the first study on the protein profiles differentially expressed in the serum of wild stump-tailed macaques between non, mono, and multiple malarial infected living in a natural transmission environment. Our findings demonstrate that differentially expressed proteins implicated in host defense through lipid metabolism, involved with TGF pathway were suppressed, while those with the apoptosis pathway, such as cytokines and proinflammation signals were increased. Including the parasite's response via induced hemolysis and disruption of myeloid cells. A greater understanding of the fundamental processes involved in a malarial infection and host response can be crucial for developing diagnostic tools, medication development, and therapies to improve the health of those affected by the disease.

Similar proteome expression profiles of the aggregated lymphoid nodules area and Peyer’s patches in Bactrian camel

BackgroundThe presence of Aggregated Lymphoid Nodules Area (ALNA) is a notable anatomical characteristic observed in the abomasum of Bactrian camels. This area is comprised of two separate regions, namely the Reticular Mucosal Folds Region (RMFR) and the Longitudinal Mucosal Folds Region (LMFR). The histological properties of ALNA exhibit significant similarities to those of Peyer’s patches (PPs) found in the gastrointestinal system. The functional characteristics of ALNA were examined in relation to mucosal immunity in the gastrointestinal system.ResultsWe used iTRAQ-based proteomic analysis on twelve Bactrian camels to measure the amount of proteins expressed in ALNA. In the experiment, we sampled the RMFR and LMFR separately from the ALNA and compared their proteomic quantification results with samples from the PPs. A total of 1253 proteins were identified, among which 39 differentially expressed proteins (DEPs) were found between RMFR and PPs, 33 DEPs were found between LMFR and PPs, and 22 DEPs were found between LMFR and RMFR. The proteins FLNA, MYH11, and HSPB1 were chosen for validation using the enzyme-linked immunosorbent assay (ELISA), and the observed expression profiles were found to be in agreement with the results obtained from the iTRAQ study. The InnateDB database was utilized to get data pertaining to immune-associated proteins in ALNA. It was observed that a significant proportion, specifically 76.6%, of these proteins were found to be associated with the same orthogroups as human immune-related genes. These proteins are acknowledged to be associated with a diverse range of functions, encompassing the uptake, processing and presentation of antigens, activation of lymphocytes, the signaling pathways of T-cell and B-cell receptors, and the control of actin polymerization.ConclusionsThe experimental results suggest that there are parallels in the immune-related proteins found in ALNA and PPs. Although there are variations in the structures of LMFR and RMFR, the proteins produced in both structures exhibit a high degree of similarity and perform comparable functions in the context of mucosal immune responses.

Differences between the wild-type and cultivated Gracilariopsis lemaneiformis revealed by quantitative proteome and gene expression profiling analysis

Abstract The seaweed Gracilariopsis lemaneiformis is widely cultivated in the southern and northern coasts of China, and is mainly used for agar extraction and abalone feed. The cultivated strain of G. lemaneiformis 981 has various advantages over the wild type such as growth rate and high-temperature tolerance. Therefore, it is necessary to investigate the differences between the wild-type and cultivated G. lemaneiformis. Here, 648 up-regulated and 837 down-regulated proteins were screened using the isobaric tags for relative and absolute quantitation (iTRAQ) technique, and these differentially expressed proteins (DEPs) were concentrated in the pathways including “Ribosome”, “Photosynthesis-antenna proteins”, “alpha-Linolenic acid metabolism”, and “Phenylpropanoid biosynthesis”. The most prominent pathway was “Ribosome”, namely, 116 out of 119 ribosome-associated proteins were up-regulated in G. lemaneiformis 981 compared to the wild type. Subsequently, multiple reaction monitoring (MRM) validated the credibility of the iTRAQ results. Finally, “Phenylpropanoid biosynthesis” and “Photosynthesis-antenna proteins” pathways were also found to be significantly changed in G. lemaneiformis 981 validated by gene expression profiling analysis. Altogether, these results, in combination with chlorophyll fluorescence parameters, unveiled the possible mechanism of differences in growth and anti-abiotic stresses between the wild-type and cultivated G. lemaneiformis, which would provide a reference for breeding of excellent seaweeds.

Identification of transition factors in myotube formation from proteome and transcriptome analyses

Muscle fibers are the main component of skeletal muscle and undergo maturation through the formation of myotubes. During early development, a population of skeletal muscle satellite cells (SSCs) proliferate into myoblasts. The myoblasts then undergo further differentiation and fusion events, leading to the development of myotubes. However, the mechanisms involved in the transition from SSCs to myotube formation remain unclear. In this study, we characterized changes in the proteomic and transcriptomic expression profiles of SSCs, myoblasts (differentiation for 2 d) and myotubes (differentiation for 10 d). Proteomic analysis identified SLMAP and STOM as potentially associated with myotube formation. In addition, some different changes in MyoD, MyoG, Myosin7 and Desmin occurred after silencing SLMAP and STOM, suggesting that they may affect changes in the myogenic marker. GO analysis indicated that the differentiation and migration factors SVIL, ENSCHIG00000026624 (AQP1) and SERPINE1 enhanced the transition from SSCs to myoblasts, accompanied by changes in the apoptotic balance. In the myoblast vs. myotube group, candidates related to cell adhesion and signal transduction were highly expressed in the myotubes. Additionally, CCN2, TGFB1, MYL2 and MYL4 were identified as hub-candidates in this group. These data enhance our existing understanding of myotube formation during early development and repair.

COX2-Inhibitory and Cytotoxic Activities of Phytoconstituents of Matricaria chamomilla L.

Chamomile tea is a popular beverage and herbal remedy with various health benefits, including antioxidant and antimicrobial activities and beneficial effects on metabolism. In this study, we investigated the inhibitory activities of secondary metabolites from Matricaria chamomile L. against COX2, an enzyme involved in inflammation and linked to cancer development. The cytotoxicity of the compounds was also evaluated on a panel of 60 cancer cell lines. Myricetin, one of the COX2-inhibiting and cytotoxic compounds in chamomile tea, was further studied to determine a proteomic expression profile that predicts the sensitivity or resistance of tumor cell lines to this compound. The expression of classical mechanisms of anticancer drug resistance did not affect the responsiveness of cancer cells to myricetin, e.g., ATP-binding cassette (ABC) transporters (ABCB, ABCB5, ABCC1, ABCG2), tumor suppressors (p53, WT1), and oncogenes (EGFR, RAS), whereas significant correlations between myricetin responsiveness and GSTP expression and cellular proliferation rates were observed. Additionally, Kaplan–Meier survival time analyses revealed that high COX2 expression is associated with a worse survival prognosis in renal clear cell carcinoma patients, suggesting a potential utility for COX2 inhibition by myricetin in this tumor type. Overall, this study provides insight into the molecular modes of action of chamomile secondary metabolites and their potential as cancer-preventive or therapeutic agents.

Differential proteomic expression profiles in vulvar lichen planus as compared to normal vulvar tissue, vulvar lichen sclerosus, or oral lichen planus: An exploratory study.

Vulvar lichen planus (VLP) is a chronic inflammatory disease which adversely affects patients' quality of life. The pathogenesis of VLP is unknown although Th1 immune response has been implicated. We aimed to discover specific tissue-based protein biomarkers in VLP compared to normal vulvar tissue (NVT), vulvar lichen sclerosus (VLS) and oral lichen planus (OLP). We used laser capture microdissection-liquid chromatography- tandem mass spectrometry to assess protein expression in fixed lesional mucosal specimens from patients with VLP (n = 5). We then compared proteomic profiles against those of NVT (n = 4), VLS (n = 5), OLP (n = 6) and normal oral mucosa (n = 5), previously published by our group. IL16, PTPRC, PTPRCAP, TAP1 and ITGB2 and were significantly overexpressed in VLP compared to NVT. Ingenuity pathway analysis identified antigen presentation and integrin signalling pathways. Proteins overexpressed in both VLP versus NVT and OLP versus NOM included IL16, PTPRC, PTPRCAP, TAP1, HLA-DPB1, HLA-B and HLA-DRA. This proteomic analysis revealed several overexpressed proteins in VLP that relate to Th1 autoimmunity, including IL16. Overlapping pathways, including those involving IFNγ and Th1 signalling, were observed between VLP, VLS, and OLP.

Modulation of Klebsiella pneumoniae Outer Membrane Vesicle Protein Cargo under Antibiotic Treatment.

Klebsiella pneumoniae is a nosocomial pathogen and an important propagator of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. Like other Gram-negative bacteria, they secrete outer membrane vesicles (OMVs) that distribute virulence and resistance factors. Here, we subjected a K. pneumoniae-XDR to subinhibitory concentrations of meropenem, amikacin, polymyxin B, and a combination of these agents to evaluate changes in the protein cargo of OMVs through liquid chromatography-tandem mass spectrometry (LC-MS/MS). Genome sequencing of the clinical isolate K. pneumoniae strain HCD1 (KpHCD1) revealed the presence of 41 resistance genes and 159 virulence factors. We identified 64 proteins in KpHCD1-OMVs modulated with different antibiotic treatments involved in processing genetic information, environmental information, cell envelope formation, energy metabolism, and drug resistance. The OMV proteome expression profile suggests that OMVs may be associated with pathogenicity, survival, stress response, and resistance dissemination.

The extracellular matrix landscape in salivary gland carcinomas is defined by cellular differentiation via expression of three distinct protein modules.

The extracellular matrix (ECM) is an integral part of the tumor microenvironment of carcinomas. Even though salivary gland carcinomas (SGCs) display a range of tumor cell differentiation and distinct extracellular matrices, their ECM landscape has not been characterized in depth. The ECM composition of 89 SGC primaries, 14 metastases, and 25 normal salivary gland tissues was assessed using deep proteomic profiling. Machine learning algorithms and network analysis were used to detect tumor groups and protein modules that explain specific ECM landscapes. Multimodal in situ studies to validate exploratory findings and to infer a putative cellular origin of ECM components were applied. We revealed two fundamental SGC ECM classes which align with the presence or absence of myoepithelial tumor differentiation. We describe the SGC ECM through three biologically distinct protein modules that are differentially expressed across ECM classes and cell types. The modules have a distinct prognostic impact on different SGC types. Since targeted therapy is rarely available for SGC, we used the proteomic expression profile to identify putative therapeutic targets. In summary, we provide the first extensive inventory of ECM components in SGC, a difficult-to-treat disease that encompasses tumors with distinct cellular differentiation. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.