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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 -
Vaccines Feb 2022Hepatitis B virus (HBV) infection remains a worldwide health problem and no eradicative therapy is currently available. Host T cell immune responses have crucial... (Review)
Review
Hepatitis B virus (HBV) infection remains a worldwide health problem and no eradicative therapy is currently available. Host T cell immune responses have crucial influences on the outcome of HBV infection, however the development of therapeutic vaccines, T cell therapies and the clinical evaluation of HBV-specific T cell responses are hampered markedly by the lack of validated T cell epitopes. This review presented a map of T cell epitopes functionally validated from HBV antigens during the past 33 years; the human leukocyte antigen (HLA) supertypes to present these epitopes, and the methods to screen and identify T cell epitopes. To the best of our knowledge, a total of 205 CD8 T cell epitopes and 79 CD4 T cell epitopes have been defined from HBV antigens by cellular functional experiments thus far, but most are restricted to several common HLA supertypes, such as HLA-A0201, A2402, B0702, DR04, and DR12 molecules. Therefore, the currently defined T cell epitope repertoire cannot cover the major populations with HLA diversity in an indicated geographic region. More researches are needed to dissect a more comprehensive map of T cell epitopes, which covers overall HBV proteome and global patients.
PubMed: 35214714
DOI: 10.3390/vaccines10020257 -
International Journal of Molecular... Jun 2023Despite the high incidence and burden of stroke, biological biomarkers are not used routinely in clinical practice to diagnose, determine progression, or prognosticate... (Review)
Review
Despite the high incidence and burden of stroke, biological biomarkers are not used routinely in clinical practice to diagnose, determine progression, or prognosticate outcomes of acute ischemic stroke (AIS). Because of its direct interface with neural tissue, cerebrospinal fluid (CSF) is a potentially valuable source for biomarker development. This systematic review was conducted using three databases. All trials investigating clinical and preclinical models for CSF biomarkers for AIS diagnosis, prognostication, and severity grading were included, yielding 22 human trials and five animal studies for analysis. In total, 21 biomarkers and other multiomic proteomic markers were identified. S100B, inflammatory markers (including tumor necrosis factor-alpha and interleukin 6), and free fatty acids were the most frequently studied biomarkers. The review showed that CSF is an effective medium for biomarker acquisition for AIS. Although CSF is not routinely clinically obtained, a potential benefit of CSF studies is identifying valuable biomarkers from the pathophysiologic microenvironment that ultimately inform optimization of targeted low-abundance assays from peripheral biofluid samples (e.g., plasma). Several important catabolic and anabolic markers can serve as effective measures of diagnosis, etiology identification, prognostication, and severity grading. Trials with large cohorts studying the efficacy of biomarkers in altering clinical management are still needed.
Topics: Humans; Ischemic Stroke; Proteomics; Stroke; Biomarkers; Fatty Acids, Nonesterified
PubMed: 37446092
DOI: 10.3390/ijms241310902 -
Toxins Nov 2023Colombia encompasses three mountain ranges that divide the country into five natural regions: Andes, Pacific, Caribbean, Amazon, and Orinoquia. These regions offer an... (Review)
Review
Colombia encompasses three mountain ranges that divide the country into five natural regions: Andes, Pacific, Caribbean, Amazon, and Orinoquia. These regions offer an impressive range of climates, altitudes, and landscapes, which lead to a high snake biodiversity. Of the almost 300 snake species reported in Colombia, nearly 50 are categorized as venomous. This high diversity of species contrasts with the small number of studies to characterize their venom compositions and natural history in the different ecoregions. This work reviews the available information about the venom composition, isolated toxins, and potential applications of snake species found in Colombia. Data compilation was conducted according to the PRISMA guidelines, and the systematic literature search was carried out in Pubmed/MEDLINE. Venom proteomes from nine Viperidae and three Elapidae species have been described using quantitative analytical strategies. In addition, venoms of three Colubridae species have been studied. Bioactivities reported for some of the venoms or isolated components-such as antibacterial, cytotoxicity on tumoral cell lines, and antiplasmodial properties-may be of interest to develop potential applications. Overall, this review indicates that, despite recent progress in the characterization of venoms from several Colombian snakes, it is necessary to perform further studies on the many species whose venoms remain essentially unexplored, especially those of the poorly known genus .
Topics: Animals; Colombia; Snake Venoms; Elapidae; Toxins, Biological; Coral Snakes; Elapid Venoms
PubMed: 37999521
DOI: 10.3390/toxins15110658 -
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 -
Cancers Dec 2023Urogenital cancers, which include prostate, bladder, and kidney malignancies, exert a substantial impact on global cancer-related morbidity and mortality. Proteomic... (Review)
Review
Urogenital cancers, which include prostate, bladder, and kidney malignancies, exert a substantial impact on global cancer-related morbidity and mortality. Proteomic biomarkers, emerging as valuable tools, aim to enhance early detection, prognostic accuracy, and the development of personalized therapeutic strategies. This study undertook a comprehensive systematic review and meta-analysis of the existing literature investigating the role and potential of proteomic biomarkers in plasma, tissue, and urine samples in urogenital cancers. Our extensive search across several databases identified 1879 differentially expressed proteins from 37 studies, signifying their potential as unique biomarkers for these cancers. A meta-analysis of the significantly differentially expressed proteins was executed, accentuating the findings through visually intuitive volcano plots. A functional enrichment analysis unveiled their significant involvement in diverse biological processes, including signal transduction, immune response, cell communication, and cell growth. A pathway analysis highlighted the participation of key pathways such as the nectin adhesion pathway, TRAIL signaling pathway, and integrin signaling pathways. These findings not only pave the way for future investigations into early detection and targeted therapeutic approaches but also underscore the fundamental role of proteomics in advancing our understanding of the molecular mechanisms underpinning urogenital cancer pathogenesis. Ultimately, these findings hold remarkable potential to significantly enhance patient care and improve clinical outcomes.
PubMed: 38201450
DOI: 10.3390/cancers16010022 -
Caspian Journal of Internal Medicine 2020Some studies have investigated the effects of iron on breast carcinogenesis and reported different findings about the association between Fe and breast cancer risk. This... (Review)
Review
BACKGROUND
Some studies have investigated the effects of iron on breast carcinogenesis and reported different findings about the association between Fe and breast cancer risk. This study was conducted to estimate this effect using meta-analysis method.
METHODS
A total of 20 articles published between 1984 and 2017 worldwide were selected through searching PubMed, Scopus, Embase, Web of Science, and Cochrane Library. Keywords such Breast Cancer, Neoplasm, Trace elements, Iron, Breast tissue concentration, Plasma concentration, Scalp hair concentration, toenail concentration and their combination were used in the search.
RESULTS
The total number of participants was 4,110 individuals comprising 1,624 patients with breast cancer and 2,486 healthy subjects. Fe concentration was measured in the various subgroups in both case and control groups. There were significant correlations between Fe concentration and breast cancer in breast tissue subgroup (SMD: 0.67 [95% CI: 0.17 to 1.17; P=0.009]). Whereas, there was no meaningful difference in Fe status between women with and without breast cancer related to scalp hair and plasma subgroups; (SMD: -3.74 [95% CI: -7.58 to 0.10; P=0.056] and (SMD:-1.14[95% CI: -2.30 to 0.03; P=0.055], respectively.
CONCLUSION
The present meta-analysis indicated a positive and straight association between iron concentrations and risk of breast cancer but because of high heterogeneity we recommend more accurate future studies.
PubMed: 32042380
DOI: 10.22088/cjim.11.1.1 -
Fertility Research and Practice Mar 2021Infertile women's mental health problems, including depression, are key fertility health issues that affect infertile women more severely than infertile men. Depression... (Review)
Review
BACKGROUND
Infertile women's mental health problems, including depression, are key fertility health issues that affect infertile women more severely than infertile men. Depression may threaten the health of individuals and reduce the quality of their lives. Considering the role and impact of depression on responses to infertility treatments, a systematic review and meta-analysis were conducted to investigate the prevalence of depression symptoms among infertile women.
METHODS
International databases (PubMed, Cochrane Library, Web of Sciences, Scopus, Embase, and PsycINFO), national databases (SID and Magiran), and Google Scholar were searched by two independent reviewers for articles published from 2000 to April 5, 2020. The search procedure was performed in both Persian and English using keywords such as "depression," "disorders," "infertility," "prevalence," and "epidemiology." The articles were evaluated in terms of their titles, abstracts, and full texts. The reviewers evaluated the quality of the articles using the Newcastle-Ottawa Scale, after which they analyzed the findings using STATA version 14. The I and Egger's tests were performed to examine heterogeneity and publication bias, respectively.
RESULTS
Thirty-two articles were subjected to the meta-analysis, and a random effects model was used in the examination given the heterogeneity of the articles. The samples in the reviewed studies encompassed a total of 9679 infertile women. The lowest and highest pooled prevalence rates were 21.01% (95% confidence interval [CI]: 15.61-34.42), as determined using the Hospital Anxiety and Depression Scale, and 52.21% (95% CI: 43.51-60.91), as ascertained using the Beck Depression Inventory, respectively. The pooled prevalence values of depression among infertile women were 44.32% (95% CI: 35.65-52.99) in low- and middle-income countries and 28.03% (95% CI: 19.61-36.44) in high-income countries.
CONCLUSION
The prevalence of depression among infertile women was higher than that among the general population of a given country. Especially in low- and middle-income countries, appropriate measures, planning, and policy that target the negative effects of depression on infertile women's lives should be established to reduce related problems.
PubMed: 33663615
DOI: 10.1186/s40738-021-00098-3 -
Proteomes Nov 2017We performed a systematic review and meta-analysis of proteomics literature that reports human skeletal muscle responses in the context of either pathological decline... (Review)
Review
A Systematic Review and Meta-Analysis of Proteomics Literature on the Response of Human Skeletal Muscle to Obesity/Type 2 Diabetes Mellitus (T2DM) Versus Exercise Training.
We performed a systematic review and meta-analysis of proteomics literature that reports human skeletal muscle responses in the context of either pathological decline associated with obesity/T2DM and physiological adaptations to exercise training. Literature was collected from PubMed and DOAJ databases following PRISMA guidelines using the search terms 'proteom*', and 'skeletal muscle' combined with either 'obesity, insulin resistance, diabetes, impaired glucose tolerance' or 'exercise, training'. Eleven studies were included in the systematic review, and meta-analysis was performed on a sub-set (four studies) of the reviewed literature that reported the necessary primary data. The majority of proteins ( = 73) more abundant in the muscle of obese/T2DM individuals were unique to this group and not reported to be responsive to exercise training. The main response of skeletal muscle to exercise training was a greater abundance of proteins of the mitochondrial electron transport chain, tricarboxylic acid cycle and mitochondrial respiratory chain complex I assembly. In total, five proteins were less abundant in muscle of obese/T2DM individuals and were also reported to be more abundant in the muscle of endurance-trained individuals, suggesting one of the major mechanisms of exercise-induced protection against the deleterious effects of obesity/T2DM occurs at complex I of the electron transport chain.
PubMed: 29137117
DOI: 10.3390/proteomes5040030 -
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