-
Investigative Ophthalmology & Visual... May 2021Glaucoma remains a poorly understood disease, and identifying biomarkers for early diagnosis is critical to reducing the risk of glaucoma-related visual impairment and...
PURPOSE
Glaucoma remains a poorly understood disease, and identifying biomarkers for early diagnosis is critical to reducing the risk of glaucoma-related visual impairment and blindness. The aim of this review is to provide current metabolic profiles for glaucoma through a summary and analysis of reported metabolites associated with glaucoma.
METHODS
We searched PubMed and Web of Science for metabolomics studies of humans on glaucoma published before November 11, 2020. Studies were included if they assessed the biomarkers of any types of glaucoma and performed mass spectrometry-based or nuclear magnetic resonance-based metabolomics approach. Pathway enrichment analysis and topology analysis were performed to generate a global view of metabolic signatures related to glaucoma using the MetaboAnalyst 3.0.
RESULTS
In total, 18 articles were included in this review, among which 13 studies were focused on open-angle glaucoma (OAG). Seventeen metabolites related to OAG were repeatedly identified, including seven amino acids (arginine, glycine, alanine, lysine, methionine, phenylalanine, tyrosine), two phosphatidylcholine (PC aa C34:2, PC aa C36:4), three complements (acetylcarnitine, propionylcarnitine, butyrylcarnitine), carnitine, glutamine, hypoxanthine, spermine, and spermidine. The pathway analysis implied a major role of amino metabolism in OAG pathophysiology and revealed the metabolic characteristics between different biological samples.
CONCLUSIONS
In this review, we summarize existing metabolomic studies related to glaucoma biomarker identification and point out a series of metabolic disorders in OAG patients, providing information on the molecular mechanism changes in glaucoma. Additional studies are needed to validate existing findings, and future research will need to explore the potential overlap between different biological fluids.
Topics: Biomarkers; Glaucoma, Open-Angle; Humans; Metabolome; Metabolomics
PubMed: 33956051
DOI: 10.1167/iovs.62.6.9 -
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 -
Biomarkers : Biochemical Indicators of... Aug 2014Systemic sclerosis (SSc) is an autoimmune disease with incompletely known physiopathology. There is a great challenge to predict its course and therapeutic response... (Review)
Review
CONTEXT
Systemic sclerosis (SSc) is an autoimmune disease with incompletely known physiopathology. There is a great challenge to predict its course and therapeutic response using biomarkers.
OBJECTIVE
To critically review proteomic biomarkers discovered from biological specimens from systemic sclerosis patients using mass spectrometry technologies.
METHODS
Medline and Embase databases were searched in February 2014.
RESULTS
Out of the 199 records retrieved, a total of 20 records were included, identifying 116 candidate proteomic biomarkers.
CONCLUSION
Research in SSc proteomic biomarkers should focus on biomarker validation, as there are valuable mass-spectrometry proteomics studies in the literature.
Topics: Biomarkers; Humans; Mass Spectrometry; Proteome; Proteomics; Reproducibility of Results; Scleroderma, Systemic; Sensitivity and Specificity
PubMed: 24831309
DOI: 10.3109/1354750X.2014.920046 -
Journal of Cellular and Molecular... May 2017Advances in mass spectrometry technologies have created new opportunities for discovering novel protein biomarkers in systemic lupus erythematosus (SLE). We performed a... (Meta-Analysis)
Meta-Analysis Review
Advances in mass spectrometry technologies have created new opportunities for discovering novel protein biomarkers in systemic lupus erythematosus (SLE). We performed a systematic review of published reports on proteomic biomarkers identified in SLE patients using mass spectrometry-based proteomics and highlight their potential disease association and clinical utility. Two electronic databases, MEDLINE and EMBASE, were systematically searched up to July 2015. The methodological quality of studies included in the review was performed according to Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. Twenty-five studies were included in the review, identifying 241 SLE candidate proteomic biomarkers related to various aspects of the disease including disease diagnosis and activity or pinpointing specific organ involvement. Furthermore, 13 of the 25 studies validated their results for a selected number of biomarkers in an independent cohort, resulting in the validation of 28 candidate biomarkers. It is noteworthy that 11 candidate biomarkers were identified in more than one study. A significant number of potential proteomic biomarkers that are related to a number of aspects of SLE have been identified using mass spectrometry proteomic approaches. However, further studies are required to assess the utility of these biomarkers in routine clinical practice.
Topics: Biomarkers; Humans; Lupus Erythematosus, Systemic; Mass Spectrometry; Proteomics
PubMed: 27878954
DOI: 10.1111/jcmm.13031 -
Diabetologia Dec 2014Gestational diabetes mellitus is associated with adverse maternal and fetal outcomes during, as well as subsequent to, pregnancy, including increased risk of type 2... (Review)
Review
AIMS/HYPOTHESIS
Gestational diabetes mellitus is associated with adverse maternal and fetal outcomes during, as well as subsequent to, pregnancy, including increased risk of type 2 diabetes and cardiovascular disease. Because of the importance of early risk stratification in preventing these complications, improved first-trimester biomarker determination for diagnosing gestational diabetes would enhance our ability to optimise both maternal and fetal health. Metabolomic profiling, the systematic study of small molecule products of biochemical pathways, has shown promise in the identification of key metabolites associated with the pathogenesis of several metabolic diseases, including gestational diabetes. This article provides a systematic review of the current state of research on biomarkers and gestational diabetes and discusses the clinical relevance of metabolomics in the prediction, diagnosis and management of gestational diabetes.
METHODS
We conducted a systematic search of MEDLINE (PubMed) up to the end of February 2014 using the key term combinations of 'metabolomics,' 'metabonomics,' 'nuclear magnetic spectroscopy,' 'mass spectrometry,' 'metabolic profiling' and 'amino acid profile' combined (AND) with 'gestational diabetes'. Additional articles were identified through searching the reference lists from included studies. Quality assessment of included articles was conducted through the use of QUADOMICS.
RESULTS
This systematic review included 17 articles. The biomarkers most consistently associated with gestational diabetes were asymmetric dimethylarginine and NEFAs. After QUADOMICS analysis, 13 of the 17 included studies were classified as 'high quality'.
CONCLUSIONS/INTERPRETATION
Existing metabolomic studies of gestational diabetes present inconsistent findings regarding metabolite profile characteristics. Further studies are needed in larger, more racially/ethnically diverse populations.
Topics: Biomarkers; Diabetes, Gestational; Female; Humans; Metabolomics; Pregnancy
PubMed: 25193282
DOI: 10.1007/s00125-014-3371-0 -
Metabolism: Clinical and Experimental Jan 2022The global COVID-19 pandemic has led to extensive development in many fields, including the diagnosis of COVID-19 infection by mass spectrometry. The aim of this... (Meta-Analysis)
Meta-Analysis
BACKGROUND
The global COVID-19 pandemic has led to extensive development in many fields, including the diagnosis of COVID-19 infection by mass spectrometry. The aim of this systematic review and meta-analysis was to assess the accuracy of mass spectrometry diagnostic tests developed so far, across a wide range of biological matrices, and additionally to assess risks of bias and applicability in studies published to date.
METHOD
23 retrospective observational cohort studies were included in the systematic review using the PRISMA-DTA framework, with a total of 2858 COVID-19 positive participants and 2544 controls. Risks of bias and applicability were assessed via a QUADAS-2 questionnaire. A meta-analysis was also performed focusing on sensitivity, specificity, diagnostic accuracy and Youden's Index, in addition to assessing heterogeneity.
FINDINGS
Sensitivity averaged 0.87 in the studies reviewed herein (interquartile range 0.81-0.96) and specificity 0.88 (interquartile range 0.82-0.98), with an area under the receiver operating characteristic summary curve of 0.93. By subgroup, the best diagnostic results were achieved by viral proteomic analyses of nasopharyngeal swabs and metabolomic analyses of plasma and serum. The performance of other sampling matrices (breath, sebum, saliva) was less good, indicating that these protocols are currently insufficiently mature for clinical application.
CONCLUSIONS
This systematic review and meta-analysis demonstrates the potential for mass spectrometry and 'omics in achieving accurate test results for COVID-19 diagnosis, but also highlights the need for further work to optimize and harmonize practice across laboratories before these methods can be translated to clinical applications.
Topics: COVID-19; COVID-19 Testing; Humans; Mass Spectrometry; Sensitivity and Specificity
PubMed: 34715115
DOI: 10.1016/j.metabol.2021.154922 -
Pathogens (Basel, Switzerland) Sep 2023Early detection of Mycoplasmal mastitis is greatly hampered by late seroconversion, slow growth of Mycoplasma organisms, intermittent shedding, and the high cost of... (Review)
Review
Early detection of Mycoplasmal mastitis is greatly hampered by late seroconversion, slow growth of Mycoplasma organisms, intermittent shedding, and the high cost of diagnostic tests. To improve future diagnostic development, examining the available techniques is necessary. Accordingly, the present study systematically reviewed diagnostic studies published between January 2000 and April 2023 utilizing the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) protocol. The protocol registration was performed according to the Open Science Framework (osf.io/ug79h), and the electronic search was conducted in the World Catalog, Mendeley, ProQuest, ScienceDirect, Semantic Scholar, PubMed, Google Scholar, Prime Scholar, and PubMed Central databases using a Boolean operator and inclusion and exclusion criteria. Of the 1194 pieces of literature retrieved, 67 studies were included. Four broad categories of up to 16 diagnostic approaches were reported: microbial culture, serological, DNA-based, and mass spectrometry. Overall, DNA-based techniques were the most published (48.0%), with recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP) as the most promising user-friendly, equipment-free techniques. On the other hand, mass spectrometry was reported as the least utilized (2.9%) given the high equipment cost. Though costly and laboratory-allied, DNA-based techniques, particularly PCRs, were reported as the most rapid and specific approach.
PubMed: 37764986
DOI: 10.3390/pathogens12091178 -
Biotechnology Journal Jan 2018The sustained emergence of new declared bacterial species makes typing a continuous challenge for microbiologists. Molecular biology techniques have a very significant... (Review)
Review
The sustained emergence of new declared bacterial species makes typing a continuous challenge for microbiologists. Molecular biology techniques have a very significant role in the context of bacterial typing, but they are often very laborious, time consuming, and eventually fail when dealing with very closely related species. Spectroscopic-based techniques appear in some situations as a viable alternative to molecular methods with advantages in terms of analysis time and cost. Infrared and mass spectrometry are among the most exploited techniques in this context: particularly, infrared spectroscopy emerged as a very promising method with multiple reported successful applications. This article presents a systematic review on infrared spectroscopy applications for bacterial typing, highlighting fundamental aspects of infrared spectroscopy, a detailed literature review (covering different taxonomic levels and bacterial species), advantages, and limitations of the technique over molecular biology methods and a comparison with other competing spectroscopic techniques such as MALDI-TOF MS, Raman, and intrinsic fluorescence. Infrared spectroscopy possesses a high potential for bacterial typing at distinct taxonomic levels and worthy of further developments and systematization. The development of databases appears fundamental toward the establishment of infrared spectroscopy as a viable method for bacterial typing.
Topics: Bacteria; Bacterial Typing Techniques; Humans; Phylogeny; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Spectrophotometry, Infrared
PubMed: 29090857
DOI: 10.1002/biot.201700449 -
Biomolecules & Therapeutics Nov 2021Researchers have endeavored to identify the etiology of inflammatory bowel diseases, including Crohn's disease and ulcerative colitis. Though the pathogenesis of... (Review)
Review
Researchers have endeavored to identify the etiology of inflammatory bowel diseases, including Crohn's disease and ulcerative colitis. Though the pathogenesis of inflammatory bowel diseases remains unknown, dysregulation of the immune system in the host gastrointestinal tract is believed to be the major causative factor. Omics is a powerful methodological tool that can reveal biochemical information stored in clinical samples. Lipidomics is a subset of omics that explores the lipid classes associated with inflammation. One objective of the present systematic review was to facilitate the identification of biochemical targets for use in future lipidomic studies on inflammatory bowel diseases. The use of high-resolution mass spectrometry to observe alterations in global lipidomics might help elucidate the immunoregulatory mechanisms involved in inflammatory bowel diseases and discover novel biomarkers for them. Assessment of the characteristics of previous clinical trials on inflammatory bowel diseases could help researchers design and establish patient selection and analytical method criteria for future studies on these conditions. In this study, we curated literature exclusively from four databases and extracted lipidomics-related data from literature, considering criteria. This paper suggests that the lipidomics approach toward research in inflammatory bowel diseases can clarify their pathogenesis and identify clinically valuable biomarkers to predict and monitor their progression.
PubMed: 34565718
DOI: 10.4062/biomolther.2021.125 -
Clinical Endocrinology Apr 2023To explore the associations between endogenous testosterone blood concentrations and muscle mass, strength and performance in community dwelling women. DESIGN,...
OBJECTIVE
To explore the associations between endogenous testosterone blood concentrations and muscle mass, strength and performance in community dwelling women. DESIGN, PATIENTS AND MEASUREMENTS: Online databases, including Ovid MEDLINE, EMBASE and Web of Science, were searched for observational studies, with at least 100 female participants, reporting associations between endogenous testosterone blood concentrations and muscle mass, strength and performance. The findings were synthesized in a narrative review. Heterogeneity in study design and analysis precluded a meta-analysis.
RESULTS
Of the 36 articles retrieved for full-text review, 10 met the inclusion criteria. Eight studies were cross-sectional, 1 longitudinal and 1 provided both cross-sectional and longitudinal data. Testosterone was measured by liquid chromatography-tandem mass spectrometry in two studies and by immunoassay in 8. An association between total testosterone and muscle mass, strength or performance in women was not found. The studies of calculated free or bioavailable testosterone and lean muscle mass reported a positive association, but no association was reported for muscle strength or performance. Each included study was limited by a high risk of bias in at least one assessed domain.
CONCLUSIONS
This review does not support an association between testosterone and muscle mass, strength or performance in women. This, together with the reported associations between free or bioavailable testosterone and muscle mass should be interpreted cautiously due to the predominant use of immunoassay and the inaccuracy of calculated variables. Additionally, biological significance of nonprotein bound testosterone has not been established. Further studies examining the relationship between precisely measured testosterone and muscle mass and function in women are required.
Topics: Observational Studies as Topic; Testosterone; Muscle Strength; Muscles; Postmenopause; Premenopause; Body Composition; Humans; Female
PubMed: 36585396
DOI: 10.1111/cen.14874