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Autoimmunity Reviews Dec 2021Identification of differentially expressed proteins in antiphospholipid syndrome (APS) is a developing area of research for unique profiles of this pathology. Advances... (Review)
Review
Identification of differentially expressed proteins in antiphospholipid syndrome (APS) is a developing area of research for unique profiles of this pathology. Advances in technologies of mass spectrometry brings improvements in proteomics and results in assessment of soluble or cellular proteins which could be candidates for clinical biomarkers of primary APS. The use of blood as a source of proteins ease the acquisition of samples for proteomics analyses and later for disease diagnosis. We performed a systematic review to explore the proteomics studies carried out in circulating released proteins (serum, plasma) or cellular proteins (monocytes and platelets) of APS patients. The study groups differentiate among clinical APS cases with the aim to translate molecular findings to disease stratification and to improve APS diagnosis and prognosis. These studies also include the unravelling of new autoantibodies in non-criteria APS or how post-translational protein modifications provides clues about the pathological mechanisms of antigen-autoantibody recognition. Herein, we identified 82 proteins that were dysregulated in APS across eleven studies. Enrichment analysis revealed its connection to cellular activation and degranulation that eventually leads to thrombosis as the main biological process highlighted by these studies. Validation of APS-relevant proteins by functional and mechanistic studies will be essential for patient stratification and the development of targeted therapies for every clinical subtype of APS.
Topics: Antiphospholipid Syndrome; Biological Phenomena; Biomarkers; Humans; Proteomics; Thrombosis
PubMed: 34718168
DOI: 10.1016/j.autrev.2021.102982 -
Eye (London, England) Jul 2023Corneal and ocular surface diseases (OSDs) carry significant psychosocial and economic burden worldwide. We set out to review the literature on the application of... (Review)
Review
Corneal and ocular surface diseases (OSDs) carry significant psychosocial and economic burden worldwide. We set out to review the literature on the application of artificial intelligence (AI) and bioinformatics for analysis of biofluid biomarkers in corneal and OSDs and evaluate their utility in clinical decision making. MEDLINE, EMBASE, Cochrane and Web of Science were systematically queried for articles using AI or bioinformatics methodology in corneal and OSDs and examining biofluids from inception to August 2021. In total, 10,264 articles were screened, and 23 articles consisting of 1058 individuals were included. Using various AI/bioinformatics tools, changes in certain tear film cytokines that are proinflammatory such as increased expression of apolipoprotein, haptoglobin, annexin 1, S100A8, S100A9, Glutathione S-transferase, and decreased expression of supportive tear film components such as lipocalin-1, prolactin inducible protein, lysozyme C, lactotransferrin, cystatin S, and mammaglobin-b, proline rich protein, were found to be correlated with pathogenesis and/or treatment outcomes of dry eye, keratoconus, meibomian gland dysfunction, and Sjögren's. Overall, most AI/bioinformatics tools were used to classify biofluids into diseases subgroups, distinguish between OSD, identify risk factors, or make predictions about treatment response, and/or prognosis. To conclude, AI models such as artificial neural networks, hierarchical clustering, random forest, etc., in conjunction with proteomic or metabolomic profiling using bioinformatics tools such as Gene Ontology or Kyoto Encylopedia of Genes and Genomes pathway analysis, were found to inform biomarker discovery, distinguish between OSDs, help define subgroups with OSDs and make predictions about treatment response in a clinical setting.
Topics: Humans; Artificial Intelligence; Proteomics; Dry Eye Syndromes; Cornea; Tears
PubMed: 36380089
DOI: 10.1038/s41433-022-02307-9 -
Biomolecules Mar 2022Proteases and protease inhibitors (P/PIs) are involved in many biological processes in human skin, yet often only specific families or related groups of P/PIs are...
Proteases and protease inhibitors (P/PIs) are involved in many biological processes in human skin, yet often only specific families or related groups of P/PIs are investigated. Proteomics approaches, such as mass spectrometry, can define proteome signatures (including P/PIs) in tissues; however, they struggle to detect low-abundance proteins. To overcome these issues, we aimed to produce a comprehensive proteome of all P/PIs present in normal and diseased human skin, in vivo, by carrying out a modified systematic review using a list of P/PIs from MEROPS and combining this with key search terms in Web of Science. Resulting articles were manually reviewed against inclusion/exclusion criteria and a dataset constructed. This study identified 111 proteases and 77 protease inhibitors in human skin, comprising the serine, metallo-, cysteine and aspartic acid catalytic families of proteases. P/PIs showing no evidence of catalytic activity or protease inhibition, were designated non-peptidase homologs (NPH), and no reported protease inhibitory activity (NRPIA), respectively. MMP9 and TIMP1 were the most frequently published P/PIs and were reported in normal skin and most skin disease groups. Normal skin and diseased skin showed significant overlap with respect to P/PI profile; however, MMP23 was identified in several skin disease groups, but was absent in normal skin. The catalytic profile of P/PIs in wounds, scars and solar elastosis was distinct from normal skin, suggesting that a different group of P/PIs is responsible for disease progression. In conclusion, this study uses a novel approach to provide a comprehensive inventory of P/PIs in normal and diseased human skin reported in our database. The database may be used to determine either which P/PIs are present in specific diseases or which diseases individual P/PIs may influence.
Topics: Antiviral Agents; Humans; Peptide Hydrolases; Protease Inhibitors; Proteome; Proteomics
PubMed: 35327667
DOI: 10.3390/biom12030475 -
International Journal of Molecular... Jul 2023Temporal lobe epilepsy (TLE) is the most common form of epilepsy in adults. Tissue reorganization at the site of the epileptogenic focus is accompanied by changes in the... (Review)
Review
Temporal lobe epilepsy (TLE) is the most common form of epilepsy in adults. Tissue reorganization at the site of the epileptogenic focus is accompanied by changes in the expression patterns of protein molecules. The study of mRNA and its corresponding proteins is crucial for understanding the pathogenesis of the disease. Protein expression profiles do not always directly correlate with the levels of their transcripts; therefore, it is protein profiling that is no less important for understanding the molecular mechanisms and biological processes of TLE. The study and annotation of proteins that are statistically significantly different in patients with TLE is an approach to search for biomarkers of this disease, various stages of its development, as well as a method for searching for specific targets for the development of a further therapeutic strategy. When writing a systematic review, the following aggregators of scientific journals were used: MDPI, PubMed, ScienceDirect, Springer, and Web of Science. Scientific articles were searched using the following keywords: "proteomic", "mass-spectrometry", "protein expression", "temporal lobe epilepsy", and "biomarkers". Publications from 2003 to the present have been analyzed. Studies of brain tissues, experimental models of epilepsy, as well as biological fluids, were analyzed. For each of the groups, aberrantly expressed proteins found in various studies were isolated. Most of the studies omitted important characteristics of the studied patients, such as: duration of illness, type and response to therapy, gender, etc. Proteins that overlap across different tissue types and different studies have been highlighted: DPYSL, SYT1, STMN1, APOE, NME1, and others. The most common biological processes for them were the positive regulation of neurofibrillary tangle assembly, the regulation of amyloid fibril formation, lipoprotein catabolic process, the positive regulation of vesicle fusion, the positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway, removal of superoxide radicals, axon extension, and the regulation of actin filament depolymerization. MS-based proteomic profiling for a relevant study must accept a number of limitations, the most important of which is the need to compare different types of neurological and, in particular, epileptic disorders. Such a criterion could increase the specificity of the search work and, in the future, lead to the discovery of biomarkers for a particular disease.
Topics: Adult; Humans; Epilepsy, Temporal Lobe; Epilepsy; Proteins; Mass Spectrometry; Biomarkers; Temporal Lobe
PubMed: 37446307
DOI: 10.3390/ijms241311130 -
Clinical Oral Investigations Feb 2020To present a systematic review that provides updated information about proteins found in salivary fluid extracted strictly from ducts.
OBJECTIVE
To present a systematic review that provides updated information about proteins found in salivary fluid extracted strictly from ducts.
METHODS
The systematic review probing strategy was based on electronic databases word search (PubMed, EMBASE, LILACS, Web of Science, and Scopus). Risk of bias was assessed based on Joanna Briggs Institute Critical Appraisal Checklist for Studies Reporting Prevalence Data.
RESULTS
After 2 rounds of scrutiny, 12 articles were included, totaling 231 individuals (125 were healthy, 41 were elder individuals with radicular caries, 56 had primary Sjögren's syndrome, and 9 were patients who had received radiotherapy for head and neck cancer). The selected studies had no similarities among proteins found, demonstrating the need of standard reference in experimental methodology to obtain a thorough coverage of proteins.
CONCLUSION
Further studies are required to better determine the relative amount of proteins described in this study. It is essential to increase the number of samples, to perform similar collection techniques, to include other analyses methods such as mass spectrometry, and to perform the validation of some proteins using immunoassay techniques such as Elisa and Western blot.
CLINICAL RELEVANCE
Proteomic profile of saliva collected from ducts is essential to better understand the disease process, enabling the identification of biomarkers for specific clinical situations.
Topics: Biomarkers; Humans; Mass Spectrometry; Proteomics; Saliva; Sjogren's Syndrome
PubMed: 31832792
DOI: 10.1007/s00784-019-03165-8 -
Journal of Clinical Oncology : Official... Jun 2024Effective diagnosis, prognostication, and management of CNS malignancies traditionally involves invasive brain biopsies that pose significant risk to the patient.... (Review)
Review
Effective diagnosis, prognostication, and management of CNS malignancies traditionally involves invasive brain biopsies that pose significant risk to the patient. Sampling and molecular profiling of cerebrospinal fluid (CSF) is a safer, rapid, and noninvasive alternative that offers a snapshot of the intracranial milieu while overcoming the challenge of sampling error that plagues conventional brain biopsy. Although numerous biomarkers have been identified, translational challenges remain, and standardization of protocols is necessary. Here, we systematically reviewed 141 studies (Medline, SCOPUS, and Biosis databases; between January 2000 and September 29, 2022) that molecularly profiled CSF from adults with brain malignancies including glioma, brain metastasis, and primary and secondary CNS lymphomas. We provide an overview of promising CSF biomarkers, propose CSF reporting guidelines, and discuss the various considerations that go into biomarker discovery, including the influence of blood-brain barrier disruption, cell of origin, and site of CSF acquisition (eg, lumbar and ventricular). We also performed a meta-analysis of proteomic data sets, identifying biomarkers in CNS malignancies and establishing a resource for the research community.
Topics: Humans; Biomarkers, Tumor; Brain Neoplasms; Proteomics; Central Nervous System Neoplasms
PubMed: 38608213
DOI: 10.1200/JCO.23.01621 -
Archives of Oral Biology Apr 2022To integrate all the available data published in the English literature regarding the protein diagnostic and/or prognostic markers in salivary gland tumors identified by... (Review)
Review
OBJECTIVE
To integrate all the available data published in the English literature regarding the protein diagnostic and/or prognostic markers in salivary gland tumors identified by mass spectrometry (MS)-based discovery proteomics.
DESIGN
An extensive search was carried out using MEDLINE/PubMed, EMBASE, Web of Science, and Scopus databases. Manual searching in Google Scholar and assessment of the reference list of the included articles also was performed. The risk of bias was assessed by the Joanna Briggs Institute Critical Appraisal tool for the specific type of study.
RESULTS
A total of 1092 articles were initially retrieved within which 6 were used for data extraction, resulting in 145 cases of salivary gland tumors. The data was composted by eleven salivary gland tumor types. In total, 2136 proteins were detected by MS-based discovery proteomics in salivary gland tumors. Ninety-one proteins were proposed as potential diagnostic and/or prognostic markers. Of these, some have been identified in one or more studies, whereas fifteen were in common across studies and a total of seventy-six were non-repeat proteins.
CONCLUSION
In summary, we compiled data about the proteomic profile of potential diagnostic and/or prognostic protein markers of the salivary gland tumors detected by MS-based discovery proteomics. The proteins ANXA1, ANXA5, CAPG, CRYAB, FGB, GNB2L1, IGHG1, PPIA, S100A9, and SOD1 were proposed as the most common potential diagnostic markers of salivary gland tumors.
Topics: Annexin A5; Biomarkers; Humans; Mass Spectrometry; Proteomics; Salivary Gland Neoplasms
PubMed: 35180549
DOI: 10.1016/j.archoralbio.2022.105373 -
Nutrition Research (New York, N.Y.) May 2024Gut peptides play a role in signaling appetite control in the hypothalamus. Limited knowledge exists regarding the release of these peptides in individuals with obesity... (Review)
Review
Gut peptides play a role in signaling appetite control in the hypothalamus. Limited knowledge exists regarding the release of these peptides in individuals with obesity before and during external stimuli. We hypothesize that the expression of gut peptides is different in the fasting and postprandial states in the scenario of obesity. PubMed/MEDLINE, Scopus, and Science Direct electronic databases were searched. The meta-analysis was performed using Review Manager Software. Randomized controlled trials that measured gut peptides in both obese and lean subjects were included in the analysis. A total of 552 subjects with obesity were enrolled in 25 trials. The gut peptide profile did not show any significant difference between obese and lean subjects for glucagon-like peptide 1 (95% confidence interval [CI], -1.21 to 0.38; P = .30), peptide YY (95% CI, -1.47 to 0.18; P = .13), and cholecystokinin (95% CI, -1.25 to 1.28; P = .98). Gut peptides are decreased by an increased high-fat, high-carbohydrate diet and by decreased chewing. There is no statistically significant difference in gut peptides between individuals with obesity and leanness in a fasting state. However, the release of gut peptides is affected in individuals with obesity following external stimuli, such as dietary interventions and chewing. Further studies are necessary to investigate the relationship between various stimuli and the release of gut peptides, as well as their impact on appetite regulation in subjects with obesity.
PubMed: 38843565
DOI: 10.1016/j.nutres.2024.04.007 -
International Journal of Molecular... Nov 2022Persistent organic pollutants (POPs) are organic chemical substances that are widely distributed in environments around the globe. POPs accumulate in living organisms... (Review)
Review
Persistent organic pollutants (POPs) are organic chemical substances that are widely distributed in environments around the globe. POPs accumulate in living organisms and are found at high concentrations in the food chain. Humans are thus continuously exposed to these chemical substances, in which they exert hepatic, reproductive, developmental, behavioral, neurologic, endocrine, cardiovascular, and immunologic adverse health effects. However, considerable information is unknown regarding the mechanism by which POPs exert their adverse effects in humans, as well as the molecular and cellular responses involved. Data are notably lacking concerning the consequences of acute and chronic POP exposure on changes in gene expression, protein profile, and metabolic pathways. We conducted a systematic review to provide a synthesis of knowledge of POPs arising from proteomics-based research. The data source used for this review was PubMed. This study was carried out following the PRISMA guidelines. Of the 742 items originally identified, 89 were considered in the review. This review presents a comprehensive overview of the most recent research and available solutions to explore proteomics datasets to identify new features relevant to human health. Future perspectives in proteomics studies are discussed.
Topics: Humans; Persistent Organic Pollutants; Proteomics; Environmental Pollutants; Organic Chemicals; Reproduction
PubMed: 36430748
DOI: 10.3390/ijms232214271 -
Biomolecules Jan 2024Ocular graft-versus-host disease (oGVHD) affects ~50% of post-stem cell transplant patients and is the only form of GVHD diagnosed without a biopsy. As it must be... (Review)
Review
Ocular graft-versus-host disease (oGVHD) affects ~50% of post-stem cell transplant patients and is the only form of GVHD diagnosed without a biopsy. As it must be distinguished from other dry eye diseases, there is a need to identify oGVHD biomarkers to improve diagnosis and treatment. We conducted a systematic review of 19 scholarly articles published from 2018 to 2023 including articles focused on adult patients diagnosed with oGVHD following allogeneic hematopoietic stem cell transplant and used biomarkers as the outcome measure. Articles that were not original investigations or were not published in English were excluded. These clinical investigations explored different molecular oGVHD biomarkers and were identified on 3 October 2023 from the Scopus, PubMed, and Embase databases by using search terms including ocular graft-versus-host disease, biomarkers, cytokines, proteomics, genomics, immune response, imaging techniques, and dry-eye-related key terms. The Newcastle-Ottawa scale for case-control studies was used to assess bias. From the 19 articles included, cytokine, proteomic, lipid, and leukocyte profiles were studied in tear film, as well as ocular surface microbiota and fluorescein staining. Our findings suggest that cytokine profiling is the most studied oGVHD biomarker. Additionally, variations correlating these biomarkers with disease state may lead to a more targeted diagnosis and therapeutic approach. Limitations include language bias, publication bias, and sampling bias, as well as a lack of appropriate controls for included studies.
Topics: Adult; Humans; Proteomics; Biomarkers; Biopsy; Cytokines; Graft vs Host Disease
PubMed: 38254702
DOI: 10.3390/biom14010102