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Cancers Oct 2023The accurate diagnosis of small-cell lung cancer (SCLC) is crucial, as treatment strategies differ from those of other lung cancers. This systematic review aims to... (Review)
Review
The accurate diagnosis of small-cell lung cancer (SCLC) is crucial, as treatment strategies differ from those of other lung cancers. This systematic review aims to identify proteins differentially expressed in SCLC compared to normal lung tissue, evaluating their potential utility in diagnosing and prognosing the disease. Additionally, the study identifies proteins differentially expressed between SCLC and large cell neuroendocrine carcinoma (LCNEC), aiming to discover biomarkers distinguishing between these two subtypes of neuroendocrine lung cancers. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, a comprehensive search was conducted across PubMed/MEDLINE, Scopus, Embase, and Web of Science databases. Studies reporting proteomics information and confirming SCLC and/or LCNEC through histopathological and/or cytopathological examination were included, while review articles, non-original articles, and studies based on animal samples or cell lines were excluded. The initial search yielded 1705 articles, and after deduplication and screening, 16 articles were deemed eligible. These studies revealed 117 unique proteins significantly differentially expressed in SCLC compared to normal lung tissue, along with 37 unique proteins differentially expressed between SCLC and LCNEC. In conclusion, this review highlights the potential of proteomics technology in identifying novel biomarkers for diagnosing SCLC, predicting its prognosis, and distinguishing it from LCNEC.
PubMed: 37894372
DOI: 10.3390/cancers15205005 -
Frontiers in Immunology 2022Multiple sclerosis (MS) is an inflammatory demyelinating and degenerative disease of the central nervous system (CNS). Although inflammatory responses are efficiently...
Multiple sclerosis (MS) is an inflammatory demyelinating and degenerative disease of the central nervous system (CNS). Although inflammatory responses are efficiently treated, therapies for progression are scarce and suboptimal, and biomarkers to predict the disease course are insufficient. Cure or preventive measures for MS require knowledge of core pathological events at the site of the tissue damage. Novelties in systems biology have emerged and paved the way for a more fine-grained understanding of key pathological pathways within the CNS, but they have also raised questions still without answers. Here, we systemically review the power of tissue and single-cell/nucleus CNS omics and discuss major gaps of integration into the clinical practice. Systemic search identified 49 transcriptome and 11 proteome studies of the CNS from 1997 till October 2021. Pioneering molecular discoveries indicate that MS affects the whole brain and all resident cell types. Despite inconsistency of results, studies imply increase in transcripts/proteins of semaphorins, heat shock proteins, myelin proteins, apolipoproteins and HLAs. Different lesions are characterized by distinct astrocytic and microglial polarization, altered oligodendrogenesis, and changes in specific neuronal subtypes. In all white matter lesion types, are highly expressed, and STAT6- and TGFβ-signaling are increased. In the grey matter lesions, TNF-signaling seems to drive cell death, and especially -expressing neurons may be susceptible to neurodegeneration. The vast heterogeneity at both cellular and lesional levels may underlie the clinical heterogeneity of MS, and it may be more complex than the current disease phenotyping in the clinical practice. Systems biology has not solved the mystery of MS, but it has discovered multiple molecules and networks potentially contributing to the pathogenesis. However, these results are mostly descriptive; focused functional studies of the molecular changes may open up for a better interpretation. Guidelines for acceptable quality or awareness of results from low quality data, and standardized computational and biological pipelines may help to overcome limited tissue availability and the "snap shot" problem of omics. These may help in identifying core pathological events and point in directions for focus in clinical prevention.
Topics: Brain; Humans; Multiple Sclerosis; Proteome; Transcriptome; White Matter
PubMed: 35309325
DOI: 10.3389/fimmu.2022.761225 -
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 Genetics 2023In the last years, liquid biopsy gained increasing clinical relevance for detecting and monitoring several cancer types, being minimally invasive, highly informative and... (Review)
Review
In the last years, liquid biopsy gained increasing clinical relevance for detecting and monitoring several cancer types, being minimally invasive, highly informative and replicable over time. This revolutionary approach can be complementary and may, in the future, replace tissue biopsy, which is still considered the gold standard for cancer diagnosis. "Classical" tissue biopsy is invasive, often cannot provide sufficient bioptic material for advanced screening, and can provide isolated information about disease evolution and heterogeneity. Recent literature highlighted how liquid biopsy is informative of proteomic, genomic, epigenetic, and metabolic alterations. These biomarkers can be detected and investigated using single-omic and, recently, in combination through multi-omic approaches. This review will provide an overview of the most suitable techniques to thoroughly characterize tumor biomarkers and their potential clinical applications, highlighting the importance of an integrated multi-omic, multi-analyte approach. Personalized medical investigations will soon allow patients to receive predictable prognostic evaluations, early disease diagnosis, and subsequent treatments.
PubMed: 37077538
DOI: 10.3389/fgene.2023.1152470 -
Iranian Journal of Otorhinolaryngology Jul 2022After more than a year of the COVID-19 pandemic, audio-vestibular problems have been reported as consequences. Several limited case report studies with different...
INTRODUCTION
After more than a year of the COVID-19 pandemic, audio-vestibular problems have been reported as consequences. Several limited case report studies with different methodologies were published. This study aimed to describe the impact of COVID-19 on the auditory-vestibular system and communication problems in subjects with hearing impairment.
MATERIALS AND METHODS
The current systematic review was performed based on the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guideline. PubMed, Web of Science, and Google Scholar were searched to find relevant articles using combined keywords.
RESULTS
Out of 26 final studies, 20 studies dealt with the effects of COVID-19 on the auditory and vestibular system, and six articles examined the COVID-19 effects on hearing-impaired people and patients. In these studies, dizziness (17.8%), tinnitus (8.1%), and vertigo (2.8%) were common symptoms. Most studies were case reports (42.30%), and in terms of quality, nine studies (34.61%) were in the suitable quality group.
CONCLUSIONS
COVID-19 might cause auditory-vestibular system problems by directly affecting the structures or functions of the inner ear or by weakening the immune system. The need for taking preventive measures during the COVID-19 pandemic has caused communication and social challenges, particularly for people with hearing loss.
PubMed: 36035653
DOI: 10.22038/IJORL.2022.60404.3079 -
Frontiers in Immunology 2024Anaphylaxis manifests as a severe immediate-type hypersensitivity reaction initiated through the immunological activation of target B-cells by allergens, leading to the... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Anaphylaxis manifests as a severe immediate-type hypersensitivity reaction initiated through the immunological activation of target B-cells by allergens, leading to the release of mediators. However, the well-known underlying pathological mechanisms do not fully explain the whole variety of clinical and immunological presentations. We performed a systemic review of proteomic and metabolomic studies and analyzed the extracted data to improve our understanding and identify potential new biomarkers of anaphylaxis.
METHODS
Proteomic and metabolomic studies in both human subjects and experimental models were extracted and selected through a systematic search conducted on databases such as PubMed, Scopus, and Web of Science, up to May 2023.
RESULTS
Of 137 retrieved publications, we considered 12 for further analysis, including seven on proteome analysis and five on metabolome analysis. A meta-analysis of the four human studies identified 118 proteins with varying expression levels in at least two studies. Beside established pathways of mast cells and basophil activation, functional analysis of proteomic data revealed a significant enrichment of biological processes related to neutrophil activation and platelet degranulation and metabolic pathways of arachidonic acid and icosatetraenoic acid. The pathway analysis highlighted also the involvement of neutrophil degranulation, and platelet activation. Metabolome analysis across different models showed 13 common metabolites, including arachidonic acid, tryptophan and lysoPC(18:0) lysophosphatidylcholines.
CONCLUSION
Our review highlights the underestimated role of neutrophils and platelets in the pathological mechanisms of anaphylactic reactions. These findings, derived from a limited number of publications, necessitate confirmation through human studies with larger sample sizes and could contribute to the development of new biomarkers for anaphylaxis.
SYSTEMATIC REVIEW REGISTRATION
https://www.crd.york.ac.uk/PROSPERO/, identifier CRD42024506246.
Topics: Humans; Anaphylaxis; Arachidonic Acid; Proteomics; Allergens; Biomarkers
PubMed: 38384462
DOI: 10.3389/fimmu.2024.1328212 -
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 -
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 -
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