-
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 -
Cancers Jun 2021Cancer is one of the foremost causes of death worldwide. Cancer develops because of mutation in genes that regulate normal cell cycle and cell division, thereby... (Review)
Review
Cancer is one of the foremost causes of death worldwide. Cancer develops because of mutation in genes that regulate normal cell cycle and cell division, thereby resulting in uncontrolled division and proliferation of cells. Various drugs have been used to treat cancer thus far; however, conventional chemotherapeutic drugs have lower bioavailability, rapid renal clearance, unequal delivery, and severe side effects. In the recent years, nanotechnology has flourished rapidly and has a multitude of applications in the biomedical field. Bio-mediated nanoparticles (NPs) are cost effective, safe, and biocompatible and have got substantial attention from researchers around the globe. Due to their safe profile and fewer side effects, these nanoscale materials offer a promising cure for cancer. Currently, various metallic NPs have been designed to cure or diagnose cancer; among these, silver (Ag), gold (Au), zinc (Zn) and copper (Cu) are the leading anti-cancer NPs. The anticancer potential of these NPs is attributed to the production of reactive oxygen species (ROS) in cellular compartments that eventually leads to activation of autophagic, apoptotic and necrotic death pathways. In this review, we summarized the recent advancements in the biosynthesis of Ag, Au, Zn and Cu NPs with emphasis on their mechanism of action. Moreover, nanotoxicity, as well as the future prospects and opportunities of nano-therapeutics, are also highlighted.
PubMed: 34198769
DOI: 10.3390/cancers13112818 -
Journal of Proteome Research Jul 2017Abdominal aortic aneurysm (AAA) is a complex disease posing diagnostic and therapeutic challenges. Metabonomics may aid in the diagnosis of AAA, determination of... (Review)
Review
Abdominal aortic aneurysm (AAA) is a complex disease posing diagnostic and therapeutic challenges. Metabonomics may aid in the diagnosis of AAA, determination of individualized risk, discovery of therapeutic targets, and improve understanding of pathogenesis. A systematic review of the diversity and outcomes of existing AAA metabonomic research has been performed. Original research studies applying metabonomics to human aneurysmal disease are included. Seven relevant articles were identified: four studies were based on plasma/serum metabolite profiling, and three studies examined aneurysmal tissue. Aminomalonic acid, guanidinosuccinic acid, and glycerol emerge as potential plasma biomarkers of large aneurysm. Lipid profiling improves predictive models of aneurysm presence. Patterns of metabolite variation associated with AAA relate to carbohydrate and lipid metabolism. Perioperative perturbations in metabolites suggest differential systemic inflammatory responses to surgery, generating hypotheses for adjunctive perioperative therapy. Significant limitations include small study sizes, lack of correction for multiple testing false discovery rates, and single time-point sampling. Metabolic profiling carries the potential to identify biomarkers of AAA and elucidate pathways underlying aneurysmal disease. Statistically and methodologically robust studies are required for validation, addressing the hiatus in understanding mechanisms of aneurysm growth and developing effective treatment strategies.
Topics: Aortic Aneurysm, Abdominal; Biomarkers; Disease Progression; Glycerol; Guanidines; Humans; Lipoxins; Malonates; Metabolome; Metabolomics; Prognosis; Succinates; Thromboxane B2
PubMed: 28287739
DOI: 10.1021/acs.jproteome.6b00894 -
EClinicalMedicine Apr 2024Knowledge of gestational age (GA) is key in clinical management of individual obstetric patients, and critical to be able to calculate rates of preterm birth and small...
BACKGROUND
Knowledge of gestational age (GA) is key in clinical management of individual obstetric patients, and critical to be able to calculate rates of preterm birth and small for GA at a population level. Currently, the gold standard for pregnancy dating is measurement of the fetal crown rump length at 11-14 weeks of gestation. However, this is not possible for women first presenting in later pregnancy, or in settings where routine ultrasound is not available. A reliable, cheap and easy to measure GA-dependent biomarker would provide an important breakthrough in estimating the age of pregnancy. Therefore, the aim of this study was to determine the accuracy of prenatal and postnatal biomarkers for estimating gestational age (GA).
METHODS
Systematic review prospectively registered with PROSPERO (CRD42020167727) and reported in accordance with the PRISMA-DTA. Medline, Embase, CINAHL, LILACS, and other databases were searched from inception until September 2023 for cohort or cross-sectional studies that reported on the accuracy of prenatal and postnatal biomarkers for estimating GA. In addition, we searched Google Scholar and screened proceedings of relevant conferences and reference lists of identified studies and relevant reviews. There were no language or date restrictions. Pooled coefficients of correlation and root mean square error (RMSE, average deviation in weeks between the GA estimated by the biomarker and that estimated by the gold standard method) were calculated. The risk of bias in each included study was also assessed.
FINDINGS
Thirty-nine studies fulfilled the inclusion criteria: 20 studies (2,050 women) assessed prenatal biomarkers (placental hormones, metabolomic profiles, proteomics, cell-free RNA transcripts, and exon-level gene expression), and 19 (1,738,652 newborns) assessed postnatal biomarkers (metabolomic profiles, DNA methylation profiles, and fetal haematological components). Among the prenatal biomarkers assessed, human chorionic gonadotrophin measured in maternal serum between 4 and 9 weeks of gestation showed the highest correlation with the reference standard GA, with a pooled coefficient of correlation of 0.88. Among the postnatal biomarkers assessed, metabolomic profiling from newborn blood spots provided the most accurate estimate of GA, with a pooled RMSE of 1.03 weeks across all GAs. It performed best for term infants with a slightly reduced accuracy for preterm or small for GA infants. The pooled RMSEs for metabolomic profiling and DNA methylation profile from cord blood samples were 1.57 and 1.60 weeks, respectively.
INTERPRETATION
We identified no antenatal biomarkers that accurately predict GA over a wide window of pregnancy. Postnatally, metabolomic profiling from newborn blood spot provides an accurate estimate of GA, however, as this is known only after birth it is not useful to guide antenatal care. Further prenatal studies are needed to identify biomarkers that can be used in isolation, as part of a biomarker panel, or in combination with other clinical methods to narrow prediction intervals of GA estimation.
FUNDING
The research was funded by the Bill and Melinda Gates Foundation (INV-000368). ATP is supported by the Oxford Partnership Comprehensive Biomedical Research Centre with funding from the NIHR Biomedical Research Centre funding scheme. The views expressed are those of the authors and not necessarily those of the UK National Health Service, the NIHR, the Department of Health, or the Department of Biotechnology. The funders of this study had no role in study design, data collection, analysis or interpretation of the data, in writing the paper or the decision to submit for publication.
PubMed: 38495518
DOI: 10.1016/j.eclinm.2024.102498 -
BMC Oral Health Jun 2023The application of rubber dams is a widely accepted method of tooth isolation in dental practice. Placement of the rubber dam clamp might be associated with levels of... (Meta-Analysis)
Meta-Analysis
BACKGROUND
The application of rubber dams is a widely accepted method of tooth isolation in dental practice. Placement of the rubber dam clamp might be associated with levels of pain and discomfort, especially in younger patients. The purpose of the present systematic review is to evaluate the efficacy of the methods for reducing pain and discomfort associated with rubber dam clamp placement in children and adolescents.
MATERIALS AND METHODS
English-language literature from inception until September 6, 2022 was searched in MEDLINE (via PubMed), SCOPUS, Web of Science, Cochrane, EMBASE, and ProQuest Dissertations & Theses Database Global for articles. Randomized controlled trials (RCTs) comparing methods of reducing the pain and/or discomfort associated with rubber dam clamp placement in children and adolescents were retrieved. Risk of bias assessment was performed using a Cochrane risk of bias-2 (RoB-2) risk assessment tool and the certainty of evidence was assessed using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) evidence profile. Studies were summarized and pooled estimates of pain intensity scores and incidence of pain were calculated. The meta-analysis was conducted in the following groups according to type of interventions (LA, audiovisual (AV) distraction, behavior management (BM), electronic dental anesthesia (EDA), mandibular infiltration, inferior alveolar nerve block (IANB), TA), outcome (intensity or incidence of pain), and assessment tool (face - legs - activity - cry - consolability (FLACC), color scale, sounds - motor - ocular changes, and faces pain scale (FPS)): (a) pain intensity using (LA + AV) vs (LA + BM), (b) pain intensity using EDA vs LA (c) presence or absence of pain using EDA vs LA (d) presence or absence of pain using mandibular infiltration vs IANB (e) Comparing pain intensity using TA vs placebo (f) Presence or absence of pain using TA vs placebo. Meta-analysis was conducted using StataMP software, version 17.0 (StataCorp, College Station, Texas). Restricted maximum-likelihood random effect model (REML), Mean difference (MD) with 95% confidence interval, and log odds ratio (OR) with 95% CI were calculated were calculated.
RESULTS
Initially, 1452 articles were retrieved. Sixteen RCTs were finally included for reviewing and summarizing. Nine articles with a total of 867 patients were included for quantitative meta-analysis. The differences in pain intensity scores were not significant in any comparison groups (group a: [MD = -0.04 (95% CI = - 0.56, 0.47), P = 0.87, I = 0.00%], group b: [MD = 0.25 (95% CI = -0.08, 0.58), P = 0.14, I = 0.00%], group c [MD = -0.48 (95% CI = -1.41, 0.45), P = 0.31, I 2 = 0.00%], group d: [MD = -0.67 (95% CI = -3.17, 1.83), P = 0.60, I 2 = 0.00%], group e: [MD = -0.46 (95% CI = -l.08, 0.15), P = 0.14, I 2 = 90.67%], and group f: [MD = 0.61 (95% CI = -0.01, 1.23), P = 0.06, I 2 = 41.20%]. Eight studies were judged as having some concern for risk of bias and the remaining studies were considered as low risk for bias. The certainty of evidence was considered medium for all comparison groups.
DISCUSSION
In the present meta-analysis, a considerable difference was obtained between the included studies regarding intervention methods and pain assessment tools and the analysis was performed in groups with small numbers of the studies. Owing to the mentioned variabilities and the small number of studies, the results of the analysis should be interpreted with caution. The indistinguishability of the manifestations of pain/discomfort from fear/anxiety, particularly in children, should also be considered while using the results of the present study. Within the limitations of the current study, no significant differences were found between the proposed methods for reducing pain and discomfort associated with rubber dam clamp placement in children and adolescents. A larger number of more homogenous studies regarding intervention methods and pain assessment tools need to be conducted in order to draw stronger conclusions.
TRIAL REGISTRATION
This study was registered in PROSPERO (ID number: CRD42021274835) and research deputy of Mashhad University of Medical Sciences with ID number 4000838 ( https://research.mums.ac.ir/ ).
Topics: Child; Humans; Adolescent; Rubber Dams; Pain; Dental Instruments; Randomized Controlled Trials as Topic
PubMed: 37328861
DOI: 10.1186/s12903-023-03115-7 -
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 -
Iranian Journal of Medical Sciences Sep 2018Chronic and abnormal increase of different types of dyslipidemia leads to some important diseases, such as constriction and abstraction of vessels in various parts of... (Review)
Review
BACKGROUND
Chronic and abnormal increase of different types of dyslipidemia leads to some important diseases, such as constriction and abstraction of vessels in various parts of the body, especially in the heart. High lipid profile, such as increased total cholesterol and LDL as well as decreased HDL are recognized as cardiovascular disease risk factors. The present study aimed to estimate the prevalence of different types of dyslipidemia in Iran by a meta-analysis method.
METHODS
A literature search for studies published during 1998-2015 was carried out using both Persian and English databases (SID, Magiran, IranMedex, MedLib, PubMed, and Scopus). Keywords such as lipid, dyslipidemia, CVD, cardiovascular risk factors, hypercholesterolemia, high LDL-C, low HDL-C, and prevalence were used in the search. Random-effects model was used for the analysis using STATA (version 11.2).
RESULTS
In total, 163 articles were identified of which 49 articles fulfilled the inclusion criteria. The estimated prevalence (95% confidence interval) of eligible articles for high cholesterol ≥200 mg/dl and ≥240 mg/dl was 42% (95% CI: 38-45) and 17% (95% CI: 14-20), respectively. Moreover, the prevalence (95% confidence interval) for high LDL-C ≥130 mg/dl and ≥160 mg/dl was 40% (95% CI: 32-48) and 19% (95% CI: 16-23), respectively. The pooled prevalence estimate for low HDL-C (<40 among males, <50 among females) was 43% (95% CI: 33-53) in both sexes of the Iranian people. All types of lipid component abnormalities (hypercholesterolemia, high LDL-C, and low HDL-C) were more prevalent in women.
CONCLUSION
The results indicate that the prevalence of different types of dyslipidemia in Iran is substantial. Given the risk of complications (e.g. cardiovascular disease and control of different types of dyslipidemia) in Iranian people, it is important to reduce the burden of cardiovascular diseases.
PubMed: 30214097
DOI: No ID Found -
World Journal of Stem Cells Oct 2020The proteomic signature or profile best describes the functional component of a cell during its routine metabolic and survival activities. Additional complexity in...
BACKGROUND
The proteomic signature or profile best describes the functional component of a cell during its routine metabolic and survival activities. Additional complexity in differentiation and maturation is observed in stem/progenitor cells. The role of functional proteins at the cellular level has long been attributed to anatomical niches, and stem cells do not deflect from this attribution. Human dental stem cells (hDSCs), on the whole, are a combination of mesenchymal and epithelial coordinates observed throughout craniofacial bones to pulp.
AIM
To specify the proteomic profile and compare each type of hDSC with other mesenchymal stem cells (MSCs) of various niches. Furthermore, we analyzed the characteristics of the microenvironment and preconditioning changes associated with the proteomic profile of hDSCs and their influence on committed lineage differentiation.
METHODS
Literature searches were performed in PubMed, EMBASE, Scopus, and Web of Science databases, from January 1990 to December 2018. An extra inquiry of the grey literature was completed on Google Scholar, ProQuest, and OpenGrey. Relevant MeSH terms (PubMed) and keywords related to dental stem cells were used independently and in combination.
RESULTS
The initial search resulted in 134 articles. Of the 134 full-texts assessed, 96 articles were excluded and 38 articles that met the eligibility criteria were reviewed. The overall assessment of hDSCs and other MSCs suggests that differences in the proteomic profile can be due to stem cellular complexity acquired from varied tissue sources during embryonic development. However, our comparison of the proteomic profile suffered inconsistencies due to the heterogeneity of various hDSCs. We believe that the existence of a heterogeneous population of stem cells at a given niche determines the modalities of regeneration or tissue repair. Added prominences to the differences present between various hDSCs have been reasoned out.
CONCLUSION
Systematic review on proteomic studies of various hDSCs are promising as an eye-opener for revisiting the proteomic profile and in-depth analysis to elucidate more refined mechanisms of hDSC functionalities.
PubMed: 33178402
DOI: 10.4252/wjsc.v12.i10.1214 -
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 -
BMC Genomics Sep 2017Pancreatic β-cells require a constant supply of zinc to maintain normal insulin secretory function. Following co-exocytosis with insulin, zinc is replenished via the... (Review)
Review
BACKGROUND
Pancreatic β-cells require a constant supply of zinc to maintain normal insulin secretory function. Following co-exocytosis with insulin, zinc is replenished via the Zrt- and Irt-like (ZIP; SLC39A) family of transporters. However the ZIP paralogues of particular importance for zinc uptake, and associations with β-cell function and Type 2 Diabetes remain largely unexplored. We retrieved and statistically analysed publically available microarray and RNA-seq datasets to perform a systematic review on the expression of β-cell SLC39A paralogues. We complemented results with experimental data on expression profiling of human islets and mouse β-cell derived MIN6 cells, and compared transcriptomic and proteomic sequence conservation between human, mouse and rat.
RESULTS
The 14 ZIP paralogues have 73-98% amino sequence conservation between human and rodents. We identified 18 datasets for β-cell SLC39A analysis, which compared relative expression to non-β-cells, and expression in response to PDX-1 activity, cytokines, glucose and type 2 diabetic status. Published expression data demonstrate enrichment of transcripts for ZIP7 and ZIP9 transporters within rodent β-cells and of ZIP6, ZIP7 and ZIP14 within human β-cells, with ZIP1 most differentially expressed in response to cytokines and PDX-1 within rodent, and ZIP6 in response to diabetic status in human and glucose in rat. Our qPCR expression profiling data indicate that SLC39A6, -9, -13, and - 14 are the highest expressed paralogues in human β-cells and Slc39a6 and -7 in MIN6 cells.
CONCLUSIONS
Our systematic review, expression profiling and sequence alignment reveal similarities and potentially important differences in ZIP complements between human and rodent β-cells. We identify ZIP6, ZIP7, ZIP9, ZIP13 and ZIP14 in human and rodent and ZIP1 in rodent as potentially biologically important for β-cell zinc trafficking. We propose ZIP6 and ZIP7 are key functional orthologues in human and rodent β-cells and highlight these zinc importers as important targets for exploring associations between zinc status and normal physiology of β-cells and their decline in Type 2 Diabetes.
Topics: Animals; Cation Transport Proteins; Gene Expression Profiling; Humans; Insulin-Secreting Cells
PubMed: 28893192
DOI: 10.1186/s12864-017-4119-2