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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 -
Pharmaceuticals (Basel, Switzerland) Oct 2021Pharmacometabolomics (PMx) studies aim to predict individual differences in treatment response and in the development of adverse effects associated with specific drug... (Review)
Review
Pharmacometabolomics (PMx) studies aim to predict individual differences in treatment response and in the development of adverse effects associated with specific drug treatments. Overall, these studies inform us about how individuals will respond to a drug treatment based on their metabolic profiles obtained before, during, or after the therapeutic intervention. In the era of precision medicine, metabolic profiles hold great potential to guide patient selection and stratification in clinical trials, with a focus on improving drug efficacy and safety. Metabolomics is closely related to the phenotype as alterations in metabolism reflect changes in the preceding cascade of genomics, transcriptomics, and proteomics changes, thus providing a significant advance over other omics approaches. Nuclear Magnetic Resonance (NMR) is one of the most widely used analytical platforms in metabolomics studies. In fact, since the introduction of PMx studies in 2006, the number of NMR-based PMx studies has been continuously growing and has provided novel insights into the specific metabolic changes associated with different mechanisms of action and/or toxic effects. This review presents an up-to-date summary of NMR-based PMx studies performed over the last 10 years. Our main objective is to discuss the experimental approaches used for the characterization of the metabolic changes associated with specific therapeutic interventions, the most relevant results obtained so far, and some of the remaining challenges in this area.
PubMed: 34681239
DOI: 10.3390/ph14101015 -
PloS One 2023Periodontitis is a chronic multifactorial inflammatory disease linked to oral microbiota dysbiosis. This disease progresses to infection that stimulates a host...
CONTEXT
Periodontitis is a chronic multifactorial inflammatory disease linked to oral microbiota dysbiosis. This disease progresses to infection that stimulates a host immune/inflammatory response, with progressive destruction of the tooth-supporting structures.
OBJECTIVE
This systematic review aims to present a robust critical evaluation of the evidence of salivary protein profiles for identifying oral diseases using proteomic approaches and summarize the use of these approaches to diagnose chronic periodontitis.
DATA SOURCES
A systematic literature search was conducted from January 1st, 2010, to December 1st, 2022, based on PICO criteria following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and by searching the three databases Science Direct, Scopus, and Springer Link.
STUDY SELECTION
According to the inclusion criteria, eight studies were identified to analyze the proteins identified by proteomics.
RESULTS
The protein family S100 was identified as the most abundant in patients with chronic periodontitis. In this family, an increased abundance of S100A8 and S100A9 from individuals with the active disease was observed, which strongly relates to the inflammatory response. Moreover, the ratio S100A8/S100A9 and the metalloproteinase-8 in saliva could differentiate distinct periodontitis groups. The changes in protein profile after non-surgical periodontal therapy improved the health of the buccal area. The results of this systematic review identified a set of proteins that could be used as a complementary tool for periodontitis diagnosis using salivary proteins.
CONCLUSION
Biomarkers in saliva can be used to monitor an early stage of periodontitis and the progression of the disease following therapy.
Topics: Humans; Chronic Periodontitis; Proteomics; Saliva; Periodontium; Periodontal Ligament; Calgranulin A; Calgranulin B
PubMed: 37224160
DOI: 10.1371/journal.pone.0286079 -
Environment International Jun 2022Systematic evidence maps are increasingly used to develop chemical risk assessments. These maps can provide an overview of available studies and relevant study... (Review)
Review
BACKGROUND
Systematic evidence maps are increasingly used to develop chemical risk assessments. These maps can provide an overview of available studies and relevant study information to be used for various research objectives and applications. Environmental epidemiological studies that examine the impact of chemical exposures on various 'omic profiles in human populations provide relevant mechanistic information and can be used for benchmark dose modeling to derive potential human health reference values.
OBJECTIVES
To create a systematic evidence map of environmental epidemiological studies examining environmental contaminant exposures with 'omics in order to characterize the extent of available studies for future research needs.
METHODS
Systematic review methods were used to search and screen the literature and included the use of machine learning methods to facilitate screening studies. The Populations, Exposures, Comparators and Outcomes (PECO) criteria were developed to identify and screen relevant studies. Studies that met the PECO criteria after full-text review were summarized with information such as study population, study design, sample size, exposure measurement, and 'omics analysis.
RESULTS
Over 10,000 studies were identified from scientific databases. Screening processes were used to identify 84 studies considered PECO-relevant after full-text review. Various contaminants (e.g. phthalate, benzene, arsenic, etc.) were investigated in epidemiological studies that used one or more of the four 'omics of interest: epigenomics, transcriptomics, proteomics, and metabolomics . The epidemiological study designs that were used to explore single or integrated 'omic research questions with contaminant exposures were cohort studies, controlled trials, cross-sectional, and case-control studies. An interactive web-based systematic evidence map was created to display more study-related information.
CONCLUSIONS
This systematic evidence map is a novel tool to visually characterize the available environmental epidemiological studies investigating contaminants and biological effects using 'omics technology and serves as a resource for investigators and allows for a range of applications in chemical research and risk assessment needs.
Topics: Cross-Sectional Studies; Environmental Exposure; Epidemiologic Studies; Humans; Reference Values; Risk Assessment
PubMed: 35551006
DOI: 10.1016/j.envint.2022.107243 -
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 -
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 -
Annals of the Rheumatic Diseases Sep 2012Dupuytren's disease (DD) is a common fibroproliferative disorder affecting the palmar fascia, which may lead to permanent contracture of the affected digit. Profiling... (Meta-Analysis)
Meta-Analysis Review
Dupuytren's disease (DD) is a common fibroproliferative disorder affecting the palmar fascia, which may lead to permanent contracture of the affected digit. Profiling studies investigating DD at whole-genomic, transcriptomic and proteomic levels have been carried out, from which large numbers of candidate genes potentially involved in DD have been reported. This review focuses on identifying genes reported by multiple studies or validated by multiple experimental techniques, as well as signalling pathways suggested to contribute to DD. Meta-analysis was also carried out on three microarray datasets. Twenty-one genes were found to be reported as dysregulated in multiple gene expression microarrays, seven of which have been further validated by other experimental methods. Sixty-four genes determined to be dsyregulated by meta-analysis correlate to those reported by published microarray studies. In addition, several pathways have been proposed to be involved in DD by whole-genome or global expression profiling. Further investigation in these genes and pathways, and correlating them to genotypes or environmental factors for DD, may aid in further elucidation of mechanisms involved in DD pathogenesis.
Topics: Dupuytren Contracture; Gene Expression Profiling; Genome; Humans; Oligonucleotide Array Sequence Analysis
PubMed: 22772327
DOI: 10.1136/annrheumdis-2012-201295 -
Expert Opinion on Pharmacotherapy Jun 2013The incidence of renal cell cancer (RCC) has been steadily increasing over the past decade. Advances in understanding the pathophysiology and carcinogenesis RCC have led... (Review)
Review
INTRODUCTION
The incidence of renal cell cancer (RCC) has been steadily increasing over the past decade. Advances in understanding the pathophysiology and carcinogenesis RCC have led to the development of novel therapies that target molecular pathways. Everolimus is a synthetic, orally available analogue of rapamycin that inhibits the activation of mTOR. Everolimus extended progression-free survival in RCC patients from 1.9 months (for patients receiving a placebo) to 4.9 months. Grades 3 and 4 adverse events include stomatitis, fatigue, pneumonitis, infections, asthenia, diarrhea, mucosal inflammation, dyspnea, rash, anorexia and dry skin. Grades 3 and 4 laboratory abnormalities include lymphopenia, anemia, thrombocytopenia, hyperglycemia, hypophosphatemia, hypercholesterolemia, hypertriglycemia, elevated creatinine, elevated alkaline phosphatase, elevated aspartate aminotransferase and elevated alanine aminotransferase. Studies have been conducted to evaluate any synergistic effect of combination therapies and continue to need to be further evaluated.
AREAS COVERED
A systematic review of medical literature for everolimus as a single agent or combination was completed using PubMed.
EXPERT OPINION
Everolimus has significant clinical benefit and is well tolerated with reversible side effects as second- or third-line therapy for treating RCC. The next phase of research for everolimus is determining patient selection based on mTOR profile utilizing skills such as proteomics and genomics.
Topics: Administration, Oral; Antineoplastic Agents; Carcinoma, Renal Cell; Disease-Free Survival; Drug Design; Everolimus; Humans; Kidney Neoplasms; Molecular Targeted Therapy; Patient Selection; Sirolimus; TOR Serine-Threonine Kinases
PubMed: 23578333
DOI: 10.1517/14656566.2013.791677 -
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 -
BJOG : An International Journal of... Aug 2011Being able to predict preterm birth is important, as it may allow a high-risk population to be selected for future interventional studies and help in understanding the... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Being able to predict preterm birth is important, as it may allow a high-risk population to be selected for future interventional studies and help in understanding the pathways that lead to preterm birth.
OBJECTIVE
To investigate the accuracy of novel biomarkers to predict spontaneous preterm birth in women with singleton pregnancies and no symptoms of preterm labour.
SEARCH STRATEGY
Electronic searches in PubMed, Embase, Cinahl, Lilacs, and Medion, references of retrieved articles, and conference proceedings. No language restrictions were applied.
SELECTION CRITERIA
Observational studies that evaluated the accuracy of biomarkers proposed in the last decade to predict spontaneous preterm birth in asymptomatic women. We excluded studies in which biomarkers were evaluated in women with preterm labour.
DATA COLLECTION AND ANALYSIS
Two reviewers independently extracted data on study characteristics, quality, and accuracy. Data were arranged in 2 × 2 contingency tables and synthesised separately for spontaneous preterm birth before 32, 34, and 37 weeks of gestation. We used bivariate meta-analysis to estimate pooled sensitivities and specificities, and calculated likelihood ratios (LRs).
MAIN RESULTS
A total of 72 studies, including 89,786 women and evaluating 30 novel biomarkers, met the inclusion criteria. Only three biomarkers (proteome profile and prolactin in cervicovaginal fluid, and matrix metalloproteinase-8 in amniotic fluid) had positive LRs > 10. However, each of these biomarkers was evaluated in only one small study. Four biomarkers had a moderate predictive accuracy (interleukin-6 and angiogenin, in amniotic fluid; human chorionic gonadotrophin and phosphorylated insulin-like growth factor binding protein-1, in cervicovaginal fluid). The remaining biomarkers had low predictive accuracies.
CONCLUSIONS
None of the biomarkers evaluated in this review meet the criteria to be considered a clinically useful test to predict spontaneous preterm birth. Further large, prospective cohort studies are needed to evaluate promising biomarkers such as a proteome profile in cervicovaginal fluid.
Topics: Amniotic Fluid; Biomarkers; Cervix Mucus; Chorionic Gonadotropin; Female; Humans; Insulin-Like Growth Factor Binding Proteins; Interleukin-6; Matrix Metalloproteinase 8; Pregnancy; Premature Birth; Prolactin; Proteome; Ribonuclease, Pancreatic; Tumor Suppressor Proteins
PubMed: 21401853
DOI: 10.1111/j.1471-0528.2011.02923.x