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1.
Physiol Plant ; 174(1): e13605, 2022 Jan.
Article in English | MEDLINE | ID: mdl-34837239

ABSTRACT

Salinity stress poses a significant risk to plant development and agricultural yield. Therefore, elucidation of stress-response mechanisms has become essential to identify salt-tolerance genes in plants. In the present study, two genotypes of pearl millet (Pennisetum glaucum L.) with contrasting tolerance for salinity exhibited differential morpho-physiological and proteomic responses under 150 mM NaCl. The genotype IC 325825 was shown to withstand the stress better than IP 17224. The salt-tolerance potential of IC 325825 was associated with its ability to maintain intracellular osmotic, ionic, and redox homeostasis and membrane integrity under stress. The IC 325825 genotype exhibited a higher abundance of C4 photosynthesis enzymes, efficient enzymatic and non-enzymatic antioxidant system, and lower Na+ /K+ ratio compared with IP 17224. Comparative proteomics analysis revealed greater metabolic perturbation in IP 17224 under salinity, in contrast to IC 325825 that harbored pro-active stress-responsive machinery, allowing its survival and better adaptability under salt stress. The differentially abundant proteins were in silico characterized for their functions, subcellular-localization, associated pathways, and protein-protein interaction. These proteins were mainly involved in photosynthesis/response to light stimulus, carbohydrate and energy metabolism, and stress responses. Proteomics data were validated through expression profiling of the selected genes, revealing a poor correlation between protein abundance and their relative transcript levels. This study has provided novel insights into salt adaptive mechanisms in P. glaucum, demonstrating the power of proteomics-based approaches. The critical proteins identified in the present study could be further explored as potential objects for engineering stress tolerance in salt-sensitive major crops.


Subject(s)
Pennisetum , Gene Expression Regulation, Plant , Genotype , Pennisetum/genetics , Pennisetum/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Proteomics , Salinity , Stress, Physiological
2.
Arch Biochem Biophys ; 713: 109060, 2021 11 30.
Article in English | MEDLINE | ID: mdl-34666048

ABSTRACT

Catabolite repressor activator (Cra) is a member of the LacI family transcriptional regulator distributed across a wide range of bacteria and regulates the carbon metabolism and virulence gene expression. In numerous studies to crystallize the apo form of the LacI family transcription factor, the N-terminal domain (NTD), which functions as a DNA-binding domain, has been enigmatically missing from the final resolved structures. It was speculated that the NTD is disordered or unstable and gets cleaved during crystallization. Here, we have determined the crystal structure of Cra from Escherichia coli (EcCra). The structure revealed a well-defined electron density for the C-terminal domain (CTD). However, electron density was missing for the first 56 amino acids (NTD). Our data reveal for the first time that EcCra undergoes a spontaneous cleavage at the conserved Asn 50 (N50) site, which separates the N-terminal DNA binding domain from the C-terminal effector molecule binding domain. With the site-directed mutagenesis, we confirm the involvement of residue N50 in the spontaneous cleavage phenomenon. Furthermore, the Isothermal titration calorimetry (ITC) assay of the EcCra-NTD with DNA showed EcCra-NTD is in a functional conformation state and retains its DNA binding activity.


Subject(s)
Bacterial Proteins/metabolism , Escherichia coli Proteins/metabolism , Repressor Proteins/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Crystallography, X-Ray , DNA/metabolism , Escherichia coli/chemistry , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , Mutagenesis, Site-Directed , Mutation , Protein Domains , Proteolysis , Repressor Proteins/chemistry , Repressor Proteins/genetics
3.
Plant J ; 100(6): 1176-1192, 2019 12.
Article in English | MEDLINE | ID: mdl-31437324

ABSTRACT

Apple (Malus sp.) and other genera belonging to the sub-tribe Malinae of the Rosaceae family produce unique benzoic acid-derived biphenyl phytoalexins. Cell cultures of Malus domestica cv. 'Golden Delicious' accumulate two biphenyl phytoalexins, aucuparin and noraucuparin, in response to the addition of a Venturia inaequalis elicitor (VIE). In this study, we isolated and expressed a cinnamate-CoA ligase (CNL)-encoding sequence from VIE-treated cell cultures of cv. 'Golden Delicious' (M. domestica CNL; MdCNL). MdCNL catalyses the conversion of cinnamic acid into cinnamoyl-CoA, which is subsequently converted to biphenyls. MdCNL failed to accept benzoic acid as a substrate. When scab-resistant (cv. 'Shireen') and moderately scab-susceptible (cv. 'Golden Delicious') apple cultivars were challenged with the V. inaequalis scab fungus, an increase in MdCNL transcript levels was observed in internodal regions. The increase in MdCNL transcript levels could conceivably correlate with the pattern of accumulation of biphenyls. The C-terminal signal in the MdCNL protein directed its N-terminal reporter fusion to peroxisomes in Nicotiana benthamiana leaves. Thus, this report records the cloning and characterisation of a cinnamoyl-CoA-forming enzyme from apple via a series of in vivo and in vitro studies. Defining the key step of phytoalexin formation in apple provides a biotechnological tool for engineering elite cultivars with improved resistance.


Subject(s)
Benzoates/metabolism , Cinnamates/metabolism , Ligases/metabolism , Malus/metabolism , Amino Acid Sequence , Ascomycota/pathogenicity , Biphenyl Compounds , Cell Culture Techniques , Gene Expression Regulation, Plant , Genes, Plant , Ligases/chemistry , Malus/genetics , Models, Molecular , Molecular Docking Simulation , Plant Diseases/microbiology , Plant Leaves , Protein Conformation , Sequence Alignment , Sesquiterpenes , Nicotiana , Phytoalexins
4.
Prep Biochem Biotechnol ; 50(1): 18-27, 2020.
Article in English | MEDLINE | ID: mdl-31453751

ABSTRACT

We report on the development of a functionalized membrane-based technology for selective enrichment of milk fat globules from raw bovine milk. Functionalization was conducted by in situ polymerization of acrylic acid within a polyvinylidene fluoride membrane, followed by the electrostatic attachment of a cationic polymer to impart a net positive charge. The functionalized membrane-based technology enabled a one-step method of selective separation of globules directly from milk-based on size and charge. The presence of globules in the eluate was confirmed by fluorescence microscopy. Quantification of the extracted phospholipids from globules in the eluant revealed a significantly higher amount of polar lipids than the permeate. Our study describes a comprehensive analysis of selective enrichment of fat globules using a functionalized membrane and demonstrates the beneficial effect of extracted phospholipids from enriched fat globules.


Subject(s)
Glycolipids/isolation & purification , Glycoproteins/isolation & purification , Membranes, Artificial , Milk/chemistry , Polyvinyls/chemistry , Animals , Cattle , Chemical Fractionation/methods , Glycolipids/analysis , Glycoproteins/analysis , Lipid Droplets , Phospholipids/analysis
5.
J Biol Chem ; 293(35): 13377-13388, 2018 08 31.
Article in English | MEDLINE | ID: mdl-30002121

ABSTRACT

Acinetobacter baumannii is a Gram-negative nosocomial pathogen that causes soft tissue infections in patients who spend a long time in intensive care units. This recalcitrant bacterium is very well known for developing rapid drug resistance, which is a combined outcome of its natural competence and mobile genetic elements. Successful efforts to treat these infections would be aided by additional information on the physiology of A. baumannii Toward that end, we recently reported on a small RNA (sRNA), AbsR25, in this bacterium that regulates the genes of several efflux pumps. Because sRNAs often require the RNA chaperone Hfq for assistance in binding to their cognate mRNA targets, we identified and characterized this protein in A. baumannii The homolog in A. baumannii is a large protein with an extended C terminus unlike Hfqs in other Gram-negative pathogens. The extension has a compositional bias toward glycine and, to a lower extent, phenylalanine and glutamine, suggestive of an intrinsically disordered region. We studied the importance of this glycine-rich tail using truncated versions of Hfq in biophysical assays and complementation of an hfq deletion mutant, finding that the tail was necessary for high-affinity RNA binding. Further tests implicate Hfq in important cellular processes of A. baumannii like metabolism, drug resistance, stress tolerance, and virulence. Our findings underline the importance of the glycine-rich C terminus in RNA binding, ribo-regulation, and auto-regulation of Hfq, demonstrating this hitherto overlooked protein motif to be an indispensable part of the A. baumannii Hfq.


Subject(s)
Acinetobacter baumannii/physiology , Bacterial Proteins/metabolism , Glycine/metabolism , Host Factor 1 Protein/metabolism , RNA, Bacterial/metabolism , Acinetobacter Infections/microbiology , Acinetobacter baumannii/chemistry , Acinetobacter baumannii/growth & development , Amino Acid Motifs , Bacterial Proteins/chemistry , Glycine/chemistry , Host Factor 1 Protein/chemistry , Humans , Protein Stability , Protein Structure, Secondary , RNA, Small Untranslated/metabolism , Stress, Physiological
6.
Crit Rev Microbiol ; 45(1): 82-102, 2019 Feb.
Article in English | MEDLINE | ID: mdl-30632429

ABSTRACT

Protein glycosylation systems in many bacteria are often associated with crucial biological processes like pathogenicity, immune evasion and host-pathogen interactions, implying the significance of protein-glycan linkage. Similarly, host protein glycosylation has been implicated in antimicrobial activity as well as in promoting growth of beneficial strains. In fact, few pathogens notably modulate host glycosylation machineries to facilitate their survival. To date, diverse chemical and biological strategies have been developed for conjugate vaccine production for disease control. Bioconjugate vaccines, largely being produced by glycoengineering using PglB (the N-oligosaccharyltransferase from Campylobacter jejuni) in suitable bacterial hosts, have been highly promising with respect to their effectiveness in providing protective immunity and ease of production. Recently, a novel method of glycoconjugate vaccine production involving an O-oligosaccharyltransferase, PglL from Neisseria meningitidis, has been optimized. Nevertheless, many questions on defining antigenic determinants, glycosylation markers, species-specific differences in glycosylation machineries, etc. still remain unanswered, necessitating further exploration of the glycosylation systems of important pathogens. Hence, in this review, we will discuss the impact of bacterial protein glycosylation on its pathogenesis and the interaction of pathogens with host protein glycosylation, followed by a discussion on strategies used for bioconjugate vaccine development.


Subject(s)
Bacteria/metabolism , Bacterial Proteins/metabolism , Glycosylation , Host-Pathogen Interactions , Bacteria/pathogenicity , Bacterial Vaccines/chemistry , Bacterial Vaccines/immunology
7.
FASEB J ; 32(9): 4889-4898, 2018 09.
Article in English | MEDLINE | ID: mdl-29634368

ABSTRACT

Fibulin-7 (Fbln7) has been identified as the latest member of the fibulin family of secreted glycoproteins in developing teeth, functioning as a cell adhesion molecule and interacting with other matrix proteins, receptors, and growth factors. More recently, we have shown that the C-terminal Fbln7 fragment (Fbln7-C) has antiangiogenic activity in vitro. Fbln7 is also expressed in immune-privileged tissues, such as eye and placenta, but its functional significance is unknown. In the current study, we show that human monocytes adhere to both full-length Fbln7 (Fbln7-FL) and Fbln7-C, in part, via integrins α5ß1 and α2ß1. Morphologic studies and surface expression analyses of CD14, mannose receptor (CD206), major histocompatibility complex II, and CD11b receptors revealed that both Fbln7-FL and Fbln7-C inhibit M-CSF-induced monocyte differentiation. Fbln7-C had significantly greater negative effects on cell spreading and stress fiber formation, including the production of IL-6 and metalloproteinase-1/-9 compared with Fbln7-FL. Furthermore, in an LPS-induced systemic inflammation model, Fbln7-C and Fbln7-FL reduced the infiltration of immune cells, such as neutrophils and macrophages, to the inflamed peritoneum. Thus, these results suggest that Fbln7 and Fbln7-C could modulate the activity of immune cells and have therapeutic potential for inflammatory diseases.-Sarangi, P. P., Chakraborty, P., Dash, S. P., Ikeuchi, T., de Vega, S., Ambatipudi, K., Wahl, L., Yamada, Y. Cell adhesion protein fibulin-7 and its C-terminal fragment negatively regulate monocyte and macrophage migration and functions in vitro and in vivo.


Subject(s)
Cell Adhesion Molecules/metabolism , Cell Adhesion/physiology , Macrophages/metabolism , Monocytes/metabolism , Animals , Calcium-Binding Proteins/metabolism , Cell Adhesion/drug effects , Cell Movement/drug effects , Cell Movement/physiology , Cells, Cultured , Humans , Lectins, C-Type/metabolism , Lipopolysaccharides/pharmacology , Macrophages/drug effects , Mannose Receptor , Mannose-Binding Lectins/metabolism , Mice, Inbred C57BL , Monocytes/drug effects , Neutrophils/metabolism , Receptors, Cell Surface/metabolism
8.
Clin Proteomics ; 13: 8, 2016.
Article in English | MEDLINE | ID: mdl-27095950

ABSTRACT

Bovine milk and its products (e.g. cheese, yoghurt) are an important part of human diet with beneficial effects for all ages. Although analyses of different milk components (e.g. proteins, lipids) pose huge challenges, the use of mass spectrometric (MS)-based techniques is steadily improving our understanding of the complexity of the biological traits that effect milk yield and its components to meet the global demand arising from population growth. In addition, different milk constituents have various applications in veterinary research and medicine, including early disease diagnosis. The aim of the review is to present an overview of the progress made in MS-based analysis of milk, and suggest a multi-pronged MS strategy to better explore different milk components for translational and clinical utilities.

9.
J Proteomics ; 310: 105319, 2024 Sep 17.
Article in English | MEDLINE | ID: mdl-39299547

ABSTRACT

Breast cancer adaptability to the drug environment reduces the chemotherapeutic response and facilitates acquired drug resistance. Cancer-specific therapeutics can be more effective against advanced-stage cancer than standard chemotherapeutics. To extend the paradigm of cancer-specific therapeutics, clinically relevant acquired tamoxifen-resistant MCF-7 proteome was deconstructed to identify possible druggable targets (N = 150). Twenty-eight drug inhibitors were used against identified druggable targets to suppress non-resistant (NC) and resistant cells (RC). First, selected drugs were screened using growth-inhibitory response against NC and RC. Seven drugs were shortlisted for their time-dependent (10-12 days) cytotoxic effect and further narrowed to three effective drugs (e.g., cisplatin, doxorubicin, and hydroxychloroquine). The growth-suppressive effectiveness of selected drugs was validated in the complex spheroid model (progressive and regressive). In the progressive model, doxorubicin (RC: 83.64 %, NC: 54.81 %), followed by cisplatin (RC: 76.66 %, NC: 68.94 %) and hydroxychloroquine (RC: 68.70 %, NC: 61.78 %) showed a significant growth-suppressive effect. However, in fully grown regressive spheroid, after 4th drug treatment, cisplatin significantly suppressed RC (84.79 %) and NC (40.21 %), while doxorubicin and hydroxychloroquine significantly suppressed only RC (76.09 and 76.34 %). Our in-depth investigation effectively integrated the expression data with the cancer-specific therapeutic investigation. Furthermore, our three-step sequential drug-screening approach unbiasedly identified cisplatin, doxorubicin, and hydroxychloroquine as an efficacious drug to target heterogeneous cancer cell populations. SIGNIFICANCE STATEMENT: Hormonal-positive BC grows slowly, and hormonal-inhibitors effectively suppress the oncogenesis. However, development of drug-resistance not only reduces the drug-response but also increases the chance of BC aggressiveness. Further, alternative chemotherapeutics are widely used to control advanced-stage BC. In contrast, we hypothesized that, compared to standard chemotherapeutics, cancer-specific drugs can be more effective against resistant-cancer. Although cancer-specific treatment identification is an uphill battle, our work shows proteome data can be used for drug selection. We identified multiple druggable targets and, using ex-vivo methods narrowed multiple drugs to disease-condition-specific therapeutics. We consider that our investigation successfully interconnected the expression data with the functional disease-specific therapeutic investigation and selected drugs can be used for effective resistant treatment with higher therapeutic response.

10.
J Agric Food Chem ; 71(46): 17528-17542, 2023 Nov 22.
Article in English | MEDLINE | ID: mdl-37955263

ABSTRACT

The symbiosis of probiotic bacteria with humans has rendered various health benefits while providing nutrition and a suitable environment for their survival. However, the probiotics must survive unfavorable gut conditions to exert beneficial effects. The intrinsic resistance of probiotics to survive harsh conditions results from a myriad of proteins. Interaction of microbial proteins with the host is indispensable for modulating the gut microbiome, such as interaction with cell receptors and protective action against pathogens. The complex interplay of proteins should be unraveled by utilizing metaproteomic strategies. The contribution of probiotics to health is now widely accepted. However, due to the inconsistency of generalized probiotics, contemporary research toward precision probiotics has gained momentum for customized treatment. This review explores the application of metaproteomics and AI/ML algorithms in resolving multiomics data analysis and in silico prediction of microbial features for screening specific beneficial probiotic organisms. Implementing these integrative strategies could augment the potential of precision probiotics for personalized healthcare.


Subject(s)
Gastrointestinal Microbiome , Probiotics , Humans , Artificial Intelligence , Proteomics/methods , Delivery of Health Care
11.
Proteomics Clin Appl ; 17(6): e2300016, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37259687

ABSTRACT

Breast cancer, a multi-networking heterogeneous disease, has emerged as a serious impediment to progress in clinical oncology. Although technological advancements and emerging cancer research studies have mitigated breast cancer lethality, a precision cancer-oriented solution has not been achieved. Thus, this review will persuade the acquiescence of proteomics-based diagnostic and therapeutic options in breast cancer management. Recently, the evidence of breast cancer health surveillance through imaging proteomics, single-cell proteomics, interactomics, and post-translational modification (PTM) tracking, to construct proteome maps and proteotyping for stage-specific and sample-specific cancer subtyping have outperformed conventional ways of dealing with breast cancer by increasing diagnostic efficiency, prognostic value, and predictive response. Additionally, the paradigm shift in applied proteomics for designing a chemotherapy regimen to identify novel drug targets with minor adverse effects has been elaborated. Finally, the potential of proteomics in alleviating the occurrence of chemoresistance and enhancing reprofiled drugs' effectiveness to combat therapeutic obstacles has been discussed. Owing to the enormous potential of proteomics techniques, the clinical recognition of proteomics in breast cancer management can be achievable and therapeutic intricacies can be surmountable.


Subject(s)
Breast Neoplasms , Proteomics , Humans , Female , Proteomics/methods , Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Breast Neoplasms/diagnosis , Drug Repositioning , Protein Processing, Post-Translational , Prognosis
12.
Proteomics ; 12(19-20): 3113-20, 2012 Oct.
Article in English | MEDLINE | ID: mdl-22888089

ABSTRACT

The diagnosis of primary Sjögren's syndrome (pSS) is difficult due to the lack of specific laboratory and clinical tests. As an initial step for the global discovery of changes in the abundance of parotid salivary proteins in pSS, a pooled sample was compared to that from healthy control subjects by multidimensional protein identification technology (MudPIT). A total of 1246 proteins were identified by MudPIT. The abundance of 477 of these proteins did not change, 529 were only detected in either the pSS or HC sample, while 206 of these proteins were significantly upregulated ≥ twofold and 34 were downregulated ≤ 0.5. Ingenuity Pathway Analyses of differentially expressed proteins identified by MudPIT resulted in the identification of 100 significant pathways. The same samples were quantified in parallel using RP MS. Fifty-eight of 71 proteins identified by RP overlapped with MudPIT results. Five proteins were further analyzed by targeted label-free quantification to confirm the similar relative differential expression observed by RP and MudPIT approaches. The present study supports the use of MS for global discovery and validation of marker proteins for improved and early diagnosis of pSS.


Subject(s)
Parotid Gland/metabolism , Proteomics/methods , Saliva/chemistry , Salivary Proteins and Peptides/analysis , Sjogren's Syndrome/metabolism , Amino Acid Sequence , Biomarkers/analysis , Biomarkers/chemistry , Biomarkers/metabolism , Case-Control Studies , Chromatography, High Pressure Liquid , Databases, Protein , Female , Humans , Mass Spectrometry , Molecular Sequence Data , Parotid Gland/chemistry , Salivary Proteins and Peptides/chemistry , Salivary Proteins and Peptides/metabolism
13.
J Clin Immunol ; 32(6): 1390-9, 2012 Dec.
Article in English | MEDLINE | ID: mdl-22806177

ABSTRACT

PURPOSE: Chronic graft-versus-host disease (cGVHD) is a severe immunological complication that occurs after allogeneic hematopoietic stem cell transplantation (HSCT). Although oral cGVHD occurs in >25% of cGVHD patients and leads to decreased quality of life, its etiology is poorly understood. The present retrospective cross-sectional analysis of oral cGVHD patients sought to (1) test the feasibility of liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify protein biomarkers of oral cGVHD and (2) to gain a clearer understanding of salivary proteins impacted by oral cGVHD. METHODS: Using unstimulated whole saliva, we compared pooled saliva from five patients with a diagnosis of moderate or severe oral cGVHD, with a gender-and age- matched pool of five cGVHD patients with no oral mucosal findings. LC-MS/MS was used to identify salivary proteins, followed by Ingenuity Pathway Analysis (IPA). Selected mass spectrometric findings, including lactotransferrin, lactoperoxidase, and albumin, were confirmed by targeted label-free quantification. RESULTS: LC-MS/MS led to confident identification of 180 proteins. Of these proteins, 102 changed in abundance at least 2 fold, including 12 proteins identified only in the No oral cGVHD group. Downregulation of ~0.4 fold was confirmed for both lactotransferrin and lactoperoxidase in Oral cGVHD saliva using targeted label-free quantification. IPA analysis implicated pathways involved in cellular metabolism and immunoregulation. CONCLUSIONS: Reduction of salivary lactoperoxidase, lactotransferrin, and several cysteine proteinase inhibitor family proteins suggests impaired oral antimicrobial host immunity in cGVHD patients. This shotgun proteomic analysis of oral cGVHD saliva using targeted label-free quantification of select proteins supports the use of mass spectrometry for future validation in a large patient population as noninvasive tests for screening, early detection, and monitoring of cGVHD.


Subject(s)
Gene Expression Regulation , Graft vs Host Disease/genetics , Hematopoietic Stem Cell Transplantation , Salivary Proteins and Peptides/genetics , Adult , Albumins/genetics , Albumins/immunology , Chromatography, Liquid , Chronic Disease , Cross-Sectional Studies , Cysteine Proteinase Inhibitors/genetics , Cysteine Proteinase Inhibitors/immunology , Female , Graft vs Host Disease/immunology , Graft vs Host Disease/pathology , Humans , Lactoferrin/genetics , Lactoferrin/immunology , Lactoperoxidase/genetics , Lactoperoxidase/immunology , Male , Middle Aged , Proteomics , Retrospective Studies , Saliva/immunology , Saliva/metabolism , Salivary Proteins and Peptides/immunology , Tandem Mass Spectrometry
14.
J Agric Food Chem ; 70(13): 3929-3947, 2022 Apr 06.
Article in English | MEDLINE | ID: mdl-35324181

ABSTRACT

Human milk, the gold standard for optimal nourishment, controls the microbial composition of infants by either enhancing or limiting bacterial growth. The milk fat globule membrane has gained interest in gut-related functions and cognitive development. The membrane proteins can directly interact with probiotic bacteria, influencing their survival and adhesion through gastrointestinal transit, whereas membrane phospholipids increase the residence time of probiotic bacteria in the gut. The commensal bacteria in milk act as the initial inoculum in building up the gut colonization of an infant, whereas oligosaccharides promote proliferation of beneficial microorganisms. Interestingly, milk extracellular vesicles are also involved in influencing the microbiota composition but are not well-explored. This review highlights the contribution of different milk components in modulating the infant gut microbiota, particularly the fat globule membrane, and the complex interplay between host- and brain-gut microbiota signaling affecting infant and adult health positively.


Subject(s)
Gastrointestinal Microbiome , Microbiota , Adult , Humans , Infant , Infant Health , Milk, Human/microbiology , Oligosaccharides
15.
J Proteomics ; 267: 104701, 2022 09 15.
Article in English | MEDLINE | ID: mdl-35995384

ABSTRACT

Triple-negative breast cancer (TNBC) is the most aggressive subtype due to the absence of hormonal receptors. Our study aimed to identify and determine the effectiveness of salivary proteins as candidate markers for metastatic TNBC subtype using parallel reaction monitoring mass spectrometry (PRM-MS). Three salivary proteins (lipocalin-1, SMR3B, and plastin-2) that showed significant differential expression in label-free quantitation (LFQ) between TNBC (N = 6) and health subjects (HS; N = 6) were selected for further validation. The developed PRM assay was used to quantify peptides GLST and NNLE (lipocalin-1), VYAL and MINL (Plastin-2) and GPYP, and IPPP (SMR3B) on a different cohort of TNBC patients (N = 20) and HS (N = 20) for evaluating their discriminating performances. Quantitative validation using PRM correlated well with the LFQ results, and 5 peptides from three proteins showed a similar up-or down-regulation. Subsequently, these proteins were validated by Western blot analysis. Compared to one protein's performance as an individual marker, the five-signature panel with salivary GLST, VYAL, MINL, GPYP, and IPPP achieved better performance in differentiating aggressive TNBC and HS with sensitivity (80%) and specificity (95%). Targeted proteomic analysis of the prioritized proteins highlights a peptide-based signature in saliva as the potential predictor to distinguish between TNBC and HS. SIGNIFICANCE OF THE STUDY: This study was designed to identify and quantify potential markers in saliva from the triple-negative breast cancer (TNBC) patients using parallel reaction monitoring assay. Three salivary proteins, Lipocalin-1 (LCN-1), Submaxillary androgen-regulated protein 3B (SMR3B), and Plastin-2 (LCP-1) selected in the discovery-phase were further quantified by targeted proteomics and Western blots. The salivary proteins successfully differentiated TNBC patients from healthy subjects with a sensitivity (80%) and specificity (95%).


Subject(s)
Triple Negative Breast Neoplasms , Biomarkers , Humans , Lipocalin 1 , Lipocalins , Mass Spectrometry , Microfilament Proteins , Proteomics/methods , Salivary Proteins and Peptides/metabolism , Triple Negative Breast Neoplasms/metabolism
16.
J Proteomics ; 267: 104696, 2022 09 15.
Article in English | MEDLINE | ID: mdl-35995382

ABSTRACT

Milk is a biofluid with various functions, containing carbohydrates, lipids, proteins, vitamins, and minerals. Owing to its importance and availability of vast proteomics information, our research group designed a database for bovine milk proteins (N = 3159) containing the primary and secondary information called BoMiProt. Due to the gaining interest and intensively published literature in the last three years, BoMiProt has been upgraded with newer identified proteins (N = 7459) from peer-reviewed journals, significantly expanding the database from different milk fractions (e.g., whey, fat globule membranes, and exosomes). Additionally, class, architecture, topology, and homology, structural classification of proteins, known and predicted disorder, predicted transmembrane helices, and structures have been included. Each protein entry in the database is thoroughly cross-referenced, including 1392 BoMiProt defined proteins provided with secondary information, such as protein function, biochemical properties, post-translational modifications, significance in milk, domains, fold, AlphaFold predicted models and crystal structures. The proteome data in the database can be retrieved using several search parameters using protein name, accession IDs, and FASTA sequence. Overall, BoMiProt represents an extensive compilation of newer proteins, including structural, functional, and hierarchical information, to help researchers better understand mammary gland pathophysiology, including their potential application in improving the nutritional quality of dairy products.


Subject(s)
Milk Proteins , Milk , Animals , Databases, Protein , Milk/chemistry , Milk Proteins/analysis , Proteome/analysis , Proteomics
17.
iScience ; 25(1): 103592, 2022 Jan 21.
Article in English | MEDLINE | ID: mdl-35005541

ABSTRACT

Chronic graft-versus-host disease (cGVHD) targets include the oral mucosa and salivary glands after allogeneic hematopoietic stem cell transplant (HSCT). Without incisional biopsy, no diagnostic test exists to confirm oral cGVHD. Consequently, therapy is often withheld until severe manifestations develop. This proteomic study examined saliva and human salivary gland for a biomarker profile at first onset of oral cGVHD prior to initiation of topical steroid therapy. Whole saliva collected at onset of biopsy-proven oral GVHD was assessed using liquid chromatography-coupled tandem mass spectrometry with identification of 569 proteins, of which 77 significantly changed in abundance. ZG16B, a secretory lectin protein, was reduced 2-fold in oral cGVHD saliva (p <0.05), and significantly decreased in salivary gland secretory cells affected by cGVHD. Single-cell RNA-seq analysis of healthy MSG localized ZG16B expression to two discrete acinar cell populations. Reduced ZG16B expression may indicate specific cGVHD activity and possibly general salivary gland dysfunction.

18.
Cancer Biol Ther ; 22(10-12): 493-512, 2021 12 02.
Article in English | MEDLINE | ID: mdl-34696706

ABSTRACT

Tumor metastasis is the leading cause of cancer mortality, often characterized by abnormal cell growth and invasion to distant organs. The cancer invasion due to epithelial to mesenchymal transition is affected by metabolic and oxygen availability in the tumor-associated micro-environment. A precise alteration in oxygen and metabolic signaling between healthy and metastatic cells is a substantial probe for understanding tumor progression and metastasis. Molecular heterogeneity in the tumor microenvironment help to sustain the metastatic cell growth during their survival shift from low to high metabolic-oxygen-rich sites and reinforces the metastatic events. This review highlighted the crucial role of oxygen and metabolites in metastatic progression and exemplified the role of metabolic rewiring and oxygen availability in cancer cell adaptation. Furthermore, we have also addressed potential applications of altered oxygen and metabolic networking with tumor type that could be a signature pattern to assess tumor growth and chemotherapeutics efficacy in managing cancer metastasis.


Subject(s)
Neoplasms , Tumor Microenvironment , Cell Proliferation , Epithelial-Mesenchymal Transition , Humans , Neoplasm Metastasis , Oxygen
19.
J Proteome Res ; 9(12): 6605-14, 2010 Dec 03.
Article in English | MEDLINE | ID: mdl-20858015

ABSTRACT

The saliva proteome includes host defense factors and specific bacterial-binding proteins that modulate microbial growth and colonization of the tooth surface in the oral cavity. A multidimensional mass spectrometry approach identified the major host-derived salivary proteins that interacted with Streptococcus mutans (strain UA159), the primary microorganism associated with the pathogenesis of dental caries. Two abundant host proteins were found to tightly bind to S. mutans cells, common salivary protein-1 (CSP-1) and deleted in malignant brain tumor 1 (DMBT1, also known as salivary agglutinin or gp340). In contrast to gp340, limited functional information is available on CSP-1. The sequence of CSP-1 shares 38.1% similarity with rat CSP-1. Recombinant CSP-1 (rCSP-1) protein did not cause aggregation of S. mutans cells and was devoid of any significant biocidal activity (2.5 to 10 µg/mL). However, S. mutans cells exposed to rCSP-1 (10 µg/mL) in saliva displayed enhanced adherence to experimental salivary pellicle and to glucans in the pellicle formed on hydroxyapatite surfaces. Thus, our data demonstrate that the host salivary protein CSP-1 binds to S. mutans cells and may influence the initial colonization of this pathogenic bacterium onto the tooth surface.


Subject(s)
Dental Pellicle/metabolism , Durapatite/metabolism , Glucans/metabolism , Salivary Proteins and Peptides/metabolism , Streptococcus mutans/metabolism , Amino Acid Sequence , Animals , Bacterial Adhesion/drug effects , Calcium-Binding Proteins , Cell Line , DNA-Binding Proteins , Dental Pellicle/drug effects , Dental Pellicle/microbiology , Electrophoresis, Polyacrylamide Gel , Humans , Intercellular Signaling Peptides and Proteins , Molecular Sequence Data , Protein Binding , Proteins/genetics , Proteins/metabolism , Proteins/pharmacology , Receptors, Cell Surface/metabolism , Recombinant Proteins/metabolism , Recombinant Proteins/pharmacology , Saliva/metabolism , Saliva/microbiology , Salivary Proteins and Peptides/genetics , Salivary Proteins and Peptides/pharmacology , Sequence Homology, Amino Acid , Streptococcus mutans/drug effects , Streptococcus mutans/growth & development , Tumor Suppressor Proteins
20.
FEMS Microbiol Ecol ; 97(1)2020 12 30.
Article in English | MEDLINE | ID: mdl-33242081

ABSTRACT

Bovine mastitis is a prototypic emerging and reemerging bacterial disease that results in cut-by-cut torture to animals, public health and the global economy. Pathogenic microbes causing mastitis have overcome a series of hierarchical barriers resulting in the zoonotic transmission from bovines to humans either by proximity or remotely through milk and meat. The disease control is challenging and has been attributed to faulty surveillance systems to monitor their emergence at the human-animal interface. The complex interaction between the pathogens, the hidden pathobionts and commensals of the bovine mammary gland that create a menace during mastitis remains unexplored. Here, we review the zoonotic potential of these pathogens with a primary focus on understanding the interplay between the host immunity, mammary ecology and the shift from symbiosis to dysbiosis. We also address the pros and cons of the current management strategies and the extent of the success in implementing the One-Health approach to keep these pathogens at bay.


Subject(s)
Bacterial Infections , Mastitis, Bovine , Animals , Bacterial Infections/veterinary , Cattle , Dysbiosis/veterinary , Female , Humans , Mammary Glands, Animal , Milk
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