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International Journal of Molecular... Sep 2023Periodontitis is one of the primary causes of tooth loss, and is also related to various systemic diseases. Early detection of this condition is crucial when it comes to... (Meta-Analysis)
Meta-Analysis Review
Periodontitis is one of the primary causes of tooth loss, and is also related to various systemic diseases. Early detection of this condition is crucial when it comes to preventing further oral damage and the associated health complications. This study offers a systematic review of the literature published up to April 2023, and aims to clearly explain the role of proteomics in identifying salivary biomarkers for periodontitis. Comprehensive searches were conducted on PubMed and Web of Science to shortlist pertinent studies. The inclusion criterion was those that reported on mass spectrometry-driven proteomic analyses of saliva samples from periodontitis cohorts, while those on gingivitis or other oral diseases were excluded. An assessment for risk of bias was carried out using the Newcastle-Ottawa Scale and Quality Assessment of Diagnostic Accuracy Studies or the NIH quality assessment tool, and a meta-analysis was performed for replicable candidate biomarkers, i.e., consistently reported candidate biomarkers (in specific saliva samples, and periodontitis subgroups, reported in ≥2 independent cohorts/reports) were identified. A Gene Ontology enrichment analysis was conducted using the Database for Annotation, Visualization, and Integrated Discovery bioinformatics resources, which consistently expressed candidate biomarkers, to explore the predominant pathway wherein salivary biomarkers consistently manifested. Of the 15 studies included, 13 were case-control studies targeting diagnostic biomarkers for periodontitis participants (periodontally healthy/diseased, = 342/432), while two focused on biomarkers responsive to periodontal treatment ( = 26 participants). The case-control studies were considered to have a low risk of bias, while the periodontitis treatment studies were deemed fair. Summary estimate and confidence/credible interval, etc. determination for the identified putative salivary biomarkers could not be ascertained due to the low number of studies in each case. The results from the included case-control studies identified nine consistently expressed candidate biomarkers (from nine studies with 230/297 periodontally healthy/diseased participants): (i) those that were upregulated: alpha-amylase, serum albumin, complement C3, neutrophil defensin, profilin-1, and S100-P; and (ii) those that were downregulated: carbonic anhydrase 6, immunoglobulin J chain, and lactoferrin. All putative biomarkers exhibited consistent regulation patterns. The implications of the current putative marker proteins identified were reviewed, with a focus on their potential roles in periodontitis diagnosis and pathogenesis, and as putative therapeutic targets. Although in its early stages, mass spectrometry-based salivary periodontal disease biomarker proteomics detection appeared promising. More mass spectrometry-based proteomics studies, with or without the aid of already available clinical biochemical approaches, are warranted to aid the discovery, identification, and validation of periodontal health/disease indicator molecule(s). Protocol registration number: CRD42023447722; supported by RD-02-202410 and GRF17119917.
Topics: Humans; Proteomics; Periodontitis; Mass Spectrometry; Biomarkers; Proteins; Periodontal Diseases; Saliva
PubMed: 37834046
DOI: 10.3390/ijms241914599 -
Expert Reviews in Molecular Medicine Apr 2022Preterm birth (PTB) is one of the leading causes of deaths in infants under the age of five. Known risk factors of PTB include genetic factors, lifestyle choices or... (Review)
Review
Preterm birth (PTB) is one of the leading causes of deaths in infants under the age of five. Known risk factors of PTB include genetic factors, lifestyle choices or infection. Identification of omic biomarkers associated with PTB could aid clinical management of women at high risk of early labour and thereby reduce neonatal morbidity. This systematic literature review aimed to identify and summarise maternal omic and multi-omic (genomics, transcriptomics, proteomics and metabolites) biomarker studies of PTB. Original research articles were retrieved from three databases: PubMed, Web of Science and Science Direct, using specified search terms for each omic discipline. PTB studies investigating genomics, transcriptomics, proteomics or metabolomics biomarkers prior to onset of labour were included. Data were collected and reviewed independently. Pathway analyses were completed on the biomarkers from non-targeted omic studies using Reactome pathway analysis tool. A total of 149 omic studies were identified; most of the literature investigated proteomic biomarkers. Pathway analysis identified several cellular processes associated with the omic biomarkers reported in the literature. Study heterogeneity was observed across the research articles, including the use of different gestation cut-offs to define PTB. Infection/inflammatory biomarkers were identified across majority of papers using a range of targeted and non-targeted approaches.
PubMed: 35379367
DOI: 10.1017/erm.2022.13 -
Frontiers in Immunology 2021Although proteomics has been employed in the study of several models of liver injury, proteomic methods have only recently been applied not only to biomarker discovery...
BACKGROUND
Although proteomics has been employed in the study of several models of liver injury, proteomic methods have only recently been applied not only to biomarker discovery and validation but also to improve understanding of the molecular mechanisms involved in transplantation.
METHODS
The study was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology and the guidelines for performing systematic literature reviews in bioinformatics (BiSLR). The PubMed, ScienceDirect, and Scopus databases were searched for publications through April 2020. Proteomics studies designed to understand liver transplant outcomes, including ischemia-reperfusion injury (IRI), rejection, or operational tolerance in human or rat samples that applied methodologies for differential expression analysis were considered.
RESULTS
The analysis included 22 studies after application of the inclusion and exclusion criteria. Among the 497 proteins annotated, 68 were shared between species and 10 were shared between sample sources. Among the types of studies analyzed, IRI and rejection shared a higher number of proteins. The most enriched pathway for liver biopsy samples, IRI, and rejection was metabolism, compared to cytokine-cytokine receptor interactions for tolerance.
CONCLUSIONS
Proteomics is a promising technique to detect large numbers of proteins. However, our study shows that several technical issues such as the identification of proteoforms or the dynamic range of protein concentration in clinical samples hinder the successful identification of biomarkers in liver transplantation. In addition, there is a need to minimize the experimental variability between studies, increase the sample size and remove high-abundance plasma proteins.
Topics: Animals; Biomarkers; Computational Biology; Humans; Liver Transplantation; Proteomics
PubMed: 34381445
DOI: 10.3389/fimmu.2021.672829 -
Cancers Nov 2017In order to find low abundant proteins secretome and tumor tissue proteome data have been explored in the last few years for the diagnosis of colorectal cancer (CRC).... (Review)
Review
In order to find low abundant proteins secretome and tumor tissue proteome data have been explored in the last few years for the diagnosis of colorectal cancer (CRC). In this review we aim to summarize the results of studies evaluating markers derived from the secretome and tumor proteome for blood based detection of colorectal cancer. Observing the preferred reporting items for systematic reviews and meta-analysis (PRISMA) guidelines PubMed and Web of Science databases were searched systematically for relevant studies published up to 18 July 2017. After screening for predefined eligibility criteria a total of 47 studies were identified. Information on diagnostic performance indicators, methodological procedures and validation was extracted. Functions of proteins were identified from the UniProt database and the the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool was used to assess study quality. Forty seven studies meeting inclusion criteria were identified. Overall, 83 different proteins were identified, with carcinoembryonic Antigen (CEA) being by far the most commonly reported (reported in 24 studies). Evaluation of the markers or marker combinations in blood samples from CRC cases and controls yielded apparently very promising diagnostic performances, with area under the curve >0.9 in several cases, but lack of internal or external validation, overoptimism due to overfitting and spectrum bias due to evaluation in clinical setting rather than screening settings are major concerns. Secretome and tumor proteome-based biomarkers when validated in blood yield promising candidates. However, for discovered protein markers to be clinically applicable as screening tool they have to be specific for early stages and need to be validated externally in larger studies with participants recruited in true screening setting.
PubMed: 29144439
DOI: 10.3390/cancers9110156 -
Journal of Microbiological Methods Dec 2022Consumers demand more fresh, safe, and high-quality food. As this is partiallycorrelated to the microbial profile, several microbiological examination tools are... (Review)
Review
Consumers demand more fresh, safe, and high-quality food. As this is partiallycorrelated to the microbial profile, several microbiological examination tools are available. Incontrast to meat, no microbiological normalized methods to assess the microbiological quality of fresh marine fish have been agreed on. As a result, studies on the detection and diversity of spoilage associated organisms (SAOs) in fish often apply various detection, isolation, and identification techniques. This complicates the comparison and interpretation of data reported, and often results in different or inconclusive results. Therefore, the present review aimed to present a critical overview of the isolation/cultivation and detection techniques currently applied in fish microbiology. After a comprehensive search in the PubMed, Web of Science and Scopus databases, a total of 111 studies fulfilled the review selection criteria. Results revealed that when relying on culture media for the isolation of SAOs in fish, it is essential to include a salt-containing medium next to plate count agar that is currently used as the reference medium for the enumeration of bacteria on fish. In terms of identification, MALDI-TOF MS and 16S rRNA gene sequencing are currently the most promising tools, though other housekeeping genes should be targeted as well, and, the biggest challenge at this point is still the lack of comprehensive proteomic and sequence databases for SAOs. A full replacement of cultivation by next generation sequencing is difficult to recommend due to the absence of a standardized experimental methodology, especially for fish, and the relatively high sequencing costs. Additionally, a discrepancy between culture-dependent and independent methods in revealing the bacterial diversity, and abundancy, from marine fish was demonstrated by several authors. It is therefore recommended to consider both approaches as complements of one another, rather than substitutes, and to include them simultaneously to yield more complete results regarding the SAOs in fresh marine fish. As such, a thorough understanding of the biology of spoilage organisms and process will be obtained to prolong the shelf-life and deliver a high-quality product.
Topics: Animals; Bacteria; Fishes; Food Microbiology; Meat; Proteomics; RNA, Ribosomal, 16S
PubMed: 36243229
DOI: 10.1016/j.mimet.2022.106599 -
Cancer Medicine Jul 2022Salivary diagnostics and their utility as a nonaggressive approach for breast cancer diagnosis have been extensively studied in recent years. This meta-analysis assesses... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Salivary diagnostics and their utility as a nonaggressive approach for breast cancer diagnosis have been extensively studied in recent years. This meta-analysis assesses the diagnostic value of salivary biomarkers in differentiating between patients with breast cancer and controls.
METHODS
We conducted a meta-analysis and systematic review of studies related to salivary diagnostics published in PubMed, EMBASE, Scopus, Ovid, Science Direct, Web of Science (WOS), and Google Scholar. The articles were chosen utilizing inclusion and exclusion criteria, as well as assessing their quality. Specificity and sensitivity, along with negative and positive likelihood ratios (NLR and PLR) and diagnostic odds ratio (DOR), were calculated based on random- or fixed-effects model. Area under the curve (AUC) and summary receiver-operating characteristic (SROC) were plotted and evaluated, and Fagan's Nomogram was evaluated for clinical utility.
RESULTS
Our systematic review and meta-analysis included 14 papers containing 121 study units with 8639 adult subjects (4149 breast cancer patients and 4490 controls without cancer). The pooled specificity and sensitivity were 0.727 (95% CI: 0.713-0.740) and 0.717 (95% CI: 0.703-0.730), respectively. The pooled NLR and PLR were 0.396 (95% CI: 0.364-0.432) and 2.597 (95% CI: 2.389-2.824), respectively. The pooled DOR was 7.837 (95% CI: 6.624-9.277), with the AUC equal to 0.801. The Fagan's nomogram showed post-test probabilities of 28% and 72% for negative and positive outcomes, respectively. We also conducted subgroup analyses to determine specificity, sensitivity, DOR, PLR, and NLR based on the mean age of patients (≤52 or >52 years old), saliva type (stimulated and unstimulated saliva), biomarker measurement method (mass spectrometry [MS] and non-MS measurement methods), sample size (≤55 or >55), biomarker type (proteomics, metabolomics, transcriptomics and proteomics, and reagent-free biophotonic), and nations.
CONCLUSION
Saliva, as a noninvasive biomarker, has the potential to accurately differentiate breast cancer patients from healthy controls.
Topics: Adult; Biomarkers; Breast Neoplasms; Female; Humans; Middle Aged; Odds Ratio; ROC Curve; Sensitivity and Specificity
PubMed: 35315584
DOI: 10.1002/cam4.4640 -
Frontiers in Oral Health 2023Some salivary proteins seem to be differently abundant among caries-free (CF) and caries-affected (CA) individuals, but previous results are contradictory precluding... (Review)
Review
OBJECTIVE
Some salivary proteins seem to be differently abundant among caries-free (CF) and caries-affected (CA) individuals, but previous results are contradictory precluding that definitive conclusion be drawn. A pooled analysis of the available evidence may provide more robust data on identifying oral cavity protein patterns among CF and CA individuals. This systematic review and meta-analysis (PROSPERO CRD42021269079) aimed to compare the oral cavity protein abundance among caries-free and caries-affected individuals.
METHODS
This study was conducted following PRISMA guidelines. PubMed, Embase, and Web of Science databases were systematically assessed (up to February 2023) to retrieve clinical studies written in English, German, or in Latin-based languages that compared the oral cavity protein abundance among CF and CA individuals. Data extraction and methodological quality assessment (NIH guidelines) were independently performed by two investigators. Qualitative synthesis was performed from all included studies and meta-analysis was performed using a random-effects model with inverse variance for studies that reported the concentration of proteins or enzymatic activity. Standardized mean difference (SMD) with respective 95% confidence interval (CI) were calculated for each outcome.
RESULTS
A total of 90 studies (two cohort and 88 cross-sectional designs) of more than 6,000 participants were selected for data extraction, being the quality of evidence graded as "fair" for most of them. The oral cavity of CF individuals presented lower total protein concentration [SMD = 0.37 (95% CI: 0.07-0.68; 18 studies)], lower total antioxidant capacity [SMD = 1.29 (95% CI: 0.74-1.85); 17 studies], and lower carbonic anhydrase activity [SMD = 0.83 (95% CI: 0.58-1.09); three studies], whereas CA individuals presented lower carbonic anhydrase concentration [SMD = -0.66 (95% CI: -1.00 to -0.32); three studies], urease [SMD = -0.95 (IC 95%: -1.72 to -0.17); four studies], and arginine deiminase system [SMD = -2.07 (95% CI: -3.53 to -0.62); three studies] activities. Antimicrobial peptides, secretory immunoglobulin-A concentrations and alpha-amylase activity were similar among individuals.
CONCLUSION
Differences on oral cavity protein abundance were observed among CF and CA individuals. These data indicate some protein patterns for the oral health and dental caries conditions. Even when statistically significant, some of the results were not very consistent. Cohort studies need to be conducted to validate these results.
PubMed: 37780687
DOI: 10.3389/froh.2023.1265817 -
The Journal of Parasitology Jan 2022Cystic echinococcosis is a zoonotic disease caused by the larval stage of Echinococcus granulosus. This affliction is an endemic worldwide condition that represents a...
Cystic echinococcosis is a zoonotic disease caused by the larval stage of Echinococcus granulosus. This affliction is an endemic worldwide condition that represents a neglected parasitic disease with important socioeconomic repercussions. Proteomic characterization of larval and adult stages of E. granulosus, as well as the association between expression profiles and host interactions, is relevant for a better understanding of parasite biology, and eventually for drug design and vaccine development. This study aimed to develop a synthesis of the evidence available related to proteomics of E. granulosus. A systematic review was carried out to collect data concerning the proteomics of E. granulosus, without language or host restriction, published between 1980 and 2019. A systematic search was carried out in the Trip Database, BIREME-BVS, SciELO, Web of Science, PubMed, EMBASE, SCOPUS, EBSCO host, and LILACS, using MeSH terms, free words, and Boolean connectors, and adapting strategies to each source of information. Additionally, a manual cross-reference search was performed. Variables studied were the year of publication, geographic origin of the study, number of samples, hosts, parasitic organs, proteomic techniques, and parasite proteins verified. Nine-hundred and thirty-six related articles were identified: 17 fulfilled selection criteria, including slightly more than 188 samples. Most articles were published between 2014 and 2019 (64.7%) and were from Brazil and China (35.3% each). In reference to confirmed hosts in the primary articles, cattle (41.2%) and humans (23.5%) were the most frequently reported. Concerning proteomic techniques applied in the primary articles, LC-MS/MS was the most used (41.1%), and 890 proteins were reported by the primary articles. As the results of our search suggest, the information related to E. granulosus proteomics is scarce, heterogeneous, and scattered throughout several articles that include a diversity of tissues, samples, intermediate hosts, and proteomic techniques. Consequently, the level of evidence generated by our search is type 4.
Topics: Animals; Echinococcosis; Echinococcus granulosus; Helminth Proteins; Proteomics
PubMed: 35119469
DOI: 10.1645/20-86 -
International Journal of Reproductive... Jul 2019One of the causes of maternal and fetal mortality and morbidity is pregnancy-induced hypertension, the most common form of which is preeclampsia that causes many... (Review)
Review
BACKGROUND
One of the causes of maternal and fetal mortality and morbidity is pregnancy-induced hypertension, the most common form of which is preeclampsia that causes many complications for mother and fetus.
OBJECTIVE
The aim of this systematic review and meta-analysis was to determine the relationship between body mass index (BMI) and preeclampsia in Iran.
MATERIALS AND METHODS
Using valid keywords in the SID database, PubMed, Scopus, data obtained from all the articles, which were reviewed in Iran between 2000 and 2016, were combined using the meta-analysis method (random-effects model) and analyzed using STATA version 11.1.
RESULTS
A total number of 5,946 samples were enrolled in 16 studies with the mean BMI values of 25.13, 27.42, and 26.33 kg /m in the healthy, mild, and severe preeclamptic groups, respectively.
CONCLUSION
The results of this study revealed that there is a significant relationship between BMI and the risk of preeclampsia, so it can be said that BMI may be one of the ways to diagnose preeclampsia.
PubMed: 31508571
DOI: 10.18502/ijrm.v17i7.4857 -
Journal of Cancer Research and... 2020Development of human genetic and proteomic research has increased the interest in alternative head-and-neck cancer (HNC) detection methods. The aim of this article, the... (Meta-Analysis)
Meta-Analysis
Development of human genetic and proteomic research has increased the interest in alternative head-and-neck cancer (HNC) detection methods. The aim of this article, the second of two-part series, was to review the scientific literature about novel HNC genetic and proteomic biomarkers. A comprehensive review of the current literature was conducted according to the Preferred Reporting Item for Systematic Review and Meta-analyses guidelines by accessing the NCBI PubMed database. Authors conducted the search of articles in English language published from 2004 to 2015. A total of 50 relevant studies were included in the review. Thirty of them concerned proteomic and twenty genetic alterations in HNC. The present systematic review discovered 242 genes and 44 proteins associated with HNC. Due to inconsistent and sparse results, novel biomarkers cannot be firmly established. Prognostic capacity of genetic markers was not evaluated. Proteins (14-3-3γ, extracellular matrix metalloproteinase inducer, and PA28γ) were described as most valuable for prognostic observation of HNC. A strict methodological protocol for molecular studies must be established.
Topics: Biomarkers, Tumor; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Head and Neck Neoplasms; Humans; Mutation; Prognosis; Proteomics
PubMed: 32719245
DOI: 10.4103/jcrt.JCRT_145_17