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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 -
A systematic review of the proteomic profile of in vivo acquired enamel pellicle on permanent teeth.Journal of Dentistry Oct 2021To provide a comprehensive review on the proteomic profile of in vivo acquired enamel pellicle (AEP) formed on permanent teeth. (Review)
Review
OBJECTIVES
To provide a comprehensive review on the proteomic profile of in vivo acquired enamel pellicle (AEP) formed on permanent teeth.
DATA/SOURCES
PubMed, EMBASE (Ovid) and Web of Science databases were searched for eligible studies (up to December 2020). Studies reporting mass spectrometry-based proteomic analysis of in vivo AEP were included. Risk of bias assessment was performed. Qualitative and quantitative proteomic data were extracted, integrated, then followed by bioinformatic analysis.
STUDY SELECTION
Eleven studies were included, involving 122 systemically and dentally healthy adults from four different research groups. Pooled AEP samples from study participants were the normal practice for all included studies. A total of 257/93/108/870 non-redundant proteins were detectable from the in vivo ≤ 5 min/10-min/60-min/2-h AEP samples, respectively. Fifteen "core in vivo 2-h AEP proteins", generally associated with immune and/or inflammatory responses, were consistently identifiable from all four research groups. Eight included studies conducted relative quantitative proteomic analysis, while no statistical analysis could be undertaken due to the inherent limitation of the relative quantification in the proteomics analyses of these studies.
CONCLUSIONS
A systematic review on adult in vivo AEP proteomic profile was undertaken. The results provide a comprehensive appreciation of the AEP proteome in healthy individuals from in vivo sampling. Further studies are warranted to clarify the biological role of AEP on oral health, particularly at an individual level.
CLINICAL SIGNIFICANCE
A comprehensive appreciation of the proteomic profile of in vivo AEP in healthy individuals is essential to further understand its functions in oral health and disease. The information generated also provides insights for future studies.
Topics: Adult; Dental Pellicle; Humans; Mass Spectrometry; Proteome; Proteomics
PubMed: 34487803
DOI: 10.1016/j.jdent.2021.103799 -
Briefings in Bioinformatics Jan 2022The emergence of single cell RNA sequencing has facilitated the studied of genomes, transcriptomes and proteomes. As available single-cell RNA-seq datasets are released...
The emergence of single cell RNA sequencing has facilitated the studied of genomes, transcriptomes and proteomes. As available single-cell RNA-seq datasets are released continuously, one of the major challenges facing traditional RNA analysis tools is the high-dimensional, high-sparsity, high-noise and large-scale characteristics of single-cell RNA-seq data. Deep learning technologies match the characteristics of single-cell RNA-seq data perfectly and offer unprecedented promise. Here, we give a systematic review for most popular single-cell RNA-seq analysis methods and tools based on deep learning models, involving the procedures of data preprocessing (quality control, normalization, data correction, dimensionality reduction and data visualization) and clustering task for downstream analysis. We further evaluate the deep model-based analysis methods of data correction and clustering quantitatively on 11 gold standard datasets. Moreover, we discuss the data preferences of these methods and their limitations, and give some suggestions and guidance for users to select appropriate methods and tools.
Topics: Cluster Analysis; Deep Learning; Gene Expression Profiling; Sequence Analysis, RNA; Single-Cell Analysis
PubMed: 34472590
DOI: 10.1093/bib/bbab345 -
Expert Review of Proteomics Aug 2021Knee osteoarthritis (OA) is a joint disease, affecting multiple tissues in the joint. Early detection and intervention may delay OA development and avoid total knee...
INTRODUCTION
Knee osteoarthritis (OA) is a joint disease, affecting multiple tissues in the joint. Early detection and intervention may delay OA development and avoid total knee arthroplasty. Specific biomarker profiles for early detection and guiding clinical decision-making of OA have not yet been identified. One technique that can contribute to the finding of this 'OA biomarker' is mass spectrometry (MS), which offers the possibility to analyze different molecules in tissues or fluids. Several proteomic, lipidomic, metabolomic and other - omic approaches aim to identify these molecular profiles; however, variation in methods and techniques complicate the finding of promising candidate biomarkers.
AREAS COVERED
In this systematic review, we aim to provide an overview of molecules in knee OA patients. Possible biomarkers in several tissue types of OA and non-OA patients, as well as current limitations and possible future suggestions will be discussed.
EXPERT OPINION
According to this review, we do not believe one specific biomarker will function as predictive molecule for OA. Likely, a group of molecules will give insight in OA development and possible therapeutic targets. For clinical implementation of MS-analysis in clinical decision-making, standardized procedures, large cohort studies and sharing protocols and data is necessary.
Topics: Adipose Tissue; Biomarkers; Humans; Knee Joint; Mass Spectrometry; Osteoarthritis, Knee; Proteomics
PubMed: 34228576
DOI: 10.1080/14789450.2021.1952868 -
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 -
Clinical Nutrition ESPEN Apr 2021The gut microbiome is an essential factor for the health of the host. Several factors may alter the gut's microbiota composition, including genetic factors, lifestyle,...
BACKGROUND & AIMS
The gut microbiome is an essential factor for the health of the host. Several factors may alter the gut's microbiota composition, including genetic factors, lifestyle, aging, and dietary intervention. This process can be an essential element in the prevention and treatment of diseases associated with microbiome dysfunction through appropriate dietary interventions. Based on this context, a systematic review was carried out in order to assess the effect of dietary intervention on the profile of the gut microbiota throughout different stages of life.
METHODS
The systematic review was conducted following the Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA), with the eligibility criteria following the principle of PICOS. The literature search was carried out in 2019 throughout PubMed/MEDLINE, Scopus, and Science Direct. Thus, 1237 studies were selected, and 40 articles were included by criteria.
RESULTS
According to the level of evidence of Centre for Evidence-Based Medicine (OCEBM), 21 studies reached the level of evidence B1, 15 articles were classified with B2, and four articles with B3. No dietary intervention was applied at all stages of life, nor with similar proportions of intervention. No dietary intervention was applied at all stages of life, nor with similar proportions of intervention. On the other hand, dietary interventions alter the intestinal microbiota in different pathological realities.
CONCLUSIONS
Different dietary interventions change the microbiome composition at all stages of life in healthy and pathological individuals. However, more clinical studies are needed to identify the specifics of each stage in response to interventions.
Topics: Diet; Gastrointestinal Microbiome; Humans; Life Style
PubMed: 33745615
DOI: 10.1016/j.clnesp.2021.01.024 -
Food Science & Nutrition Jan 2021This systematic review aimed at investigating longitudinal changes in human milk bioactive protein concentrations in Chinese population. Both English and Chinese... (Review)
Review
This systematic review aimed at investigating longitudinal changes in human milk bioactive protein concentrations in Chinese population. Both English and Chinese databases were searched. The data were pooled into six defined lactation stages. Weighted means of protein concentrations in each stage and the statistical significance of means of different lactation stages were calculated. The data of 11 bioactive proteins were retrieved. Concentrations of sIgA, IgM, and IgG decreased sharply during the first 14 days of lactation. The levels of α-lactalbumin, lactoferrin, and β-casein also decreased throughout lactation. Conversely, lysozyme levels increased over lactation. The changing patterns of the serum albumin, osteopontin, and bile salt-stimulated lipase (BSSL) were not conclusive. This study represents the most comprehensive summary of bioactive proteins in Chinese human milk. In the future, mass spectrometry-based analysis of human milk proteomics may be used to investigate the longitudinal changes of many more bioactive proteins.
PubMed: 33473267
DOI: 10.1002/fsn3.2061 -
Life Sciences Apr 2021Age-associated memory loss is highly prevalent in the elder population. The inception of neurodegenerative diseases acts as a causative factor for the onset of memory...
Age-associated memory loss is highly prevalent in the elder population. The inception of neurodegenerative diseases acts as a causative factor for the onset of memory loss in aged individuals. The pathophysiological mechanisms of memory loss associated with the onset of neurodegenerative diseases and normal aging processes share certain similarities as well as differences. The normal age-associated memory loss is attributed to the impairment of calcium metabolism, dysregulated cholesterol metabolism, the prevalence of oxidative stress, inappropriate functioning of hormones as well as genetic factors. Vital information regarding the key biological processes and the druggable targets involved in the onset of memory loss in the elder population has been provided in this article. The genomic and proteomic profiles of key druggable targets retrieved from the experimental evidence, co-expression studies and databases are also presented in this article. The genomic and proteomic information of druggable targets will aid in the identification of therapeutic agents which could effectively regulate the key biological processes involved in the age-associated memory loss.
Topics: Aging; Biological Phenomena; Calcium; Cholesterol; Genome; Genomics; Hormones; Humans; Memory Disorders; Neurodegenerative Diseases; Oxidative Stress; Proteomics
PubMed: 33460668
DOI: 10.1016/j.lfs.2021.119079 -
European Urology Jun 2021Genomic stratification can impact prostate cancer (PC) care through diagnostic, prognostic, and predictive biomarkers that aid in clinical decision-making. The temporal...
CONTEXT
Genomic stratification can impact prostate cancer (PC) care through diagnostic, prognostic, and predictive biomarkers that aid in clinical decision-making. The temporal and spatial genomic heterogeneity of PC together with the challenges of acquiring metastatic tissue biopsies hinder implementation of tissue-based molecular profiling in routine clinical practice. Blood-based liquid biopsies are an attractive, minimally invasive alternative.
OBJECTIVE
To review the clinical value of blood-based liquid biopsy assays in PC and identify potential applications to accelerate the development of precision medicine.
EVIDENCE ACQUISITION
A systematic review of PubMed/MEDLINE was performed to identify relevant literature on blood-based circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and extracellular vesicles (EVs) in PC.
EVIDENCE SYNTHESIS
Liquid biopsy has emerged as a practical tool to profile tumor dynamics over time, elucidating features that evolve (genome, epigenome, transcriptome, and proteome) with tumor progression. Liquid biopsy tests encompass analysis of DNA, RNA, and proteins that can be detected in CTCs, ctDNA, or EVs. Blood-based liquid biopsies have demonstrated promise in the context of localized tumors (diagnostic signatures, risk stratification, and disease monitoring) and advanced disease (response/resistance biomarkers and prognostic markers).
CONCLUSIONS
Liquid biopsies have value as a source of prognostic, predictive, and response biomarkers in PC. Most clinical applications have been developed in the advanced metastatic setting, where CTC and ctDNA yields are significantly higher. However, standardization of assays and analytical/clinical validation is necessary prior to clinical implementation.
PATIENT SUMMARY
Traces of tumors can be isolated from blood samples from patients with prostate cancer either as whole cells or as DNA fragments. These traces provide information on tumor features. These minimally invasive tests can guide diagnosis and treatment selection.
Topics: Biomarkers, Tumor; Circulating Tumor DNA; Clinical Decision-Making; Humans; Liquid Biopsy; Male; Neoplastic Cells, Circulating; Prostatic Neoplasms
PubMed: 33422353
DOI: 10.1016/j.eururo.2020.12.037 -
Journal of Neurochemistry May 2021HIV-associated neurocognitive disorders (HAND) are common features of the effect of human immunodeficiency virus (HIV)-1 within the central nervous system (CNS). The...
HIV-associated neurocognitive disorders (HAND) are common features of the effect of human immunodeficiency virus (HIV)-1 within the central nervous system (CNS). The underlying neuropathophysiology of HAND is incompletely known. Furthermore, there are no markers to effectively predict or stratify the risk of HAND. Recent advancements in the fields of proteomics and metabolomics have shown promise in addressing these concerns, however, it is not clear if these approaches may provide new insight into pathways and markers related to HAND. We therefore conducted a systematic review of studies using proteomic and/or metabolomic approaches in the aim of identifying pathways or markers associated with neurocognitive impairment in people living with HIV (PLWH). Thirteen studies were eligible, including 11 proteomic and 2 metabolomic investigations of HIV-positive clinical samples (cerebrospinal fluid (CSF), brain tissue, and serum). Across varying profiling techniques and sample types, the majority of studies found an association of markers with neurocognitive function in PLWH. These included metabolic marker myo-inositol and proteomic markers superoxide dismutase, gelsolin, afamin, sphingomyelin, and ceramide. Certain markers were found to be dysregulated across various sample types. Afamin and gelsolin overlapped in studies of blood and CSF and sphingomyelin and ceramide overlapped in studies of CSF and brain tissue. The association of these markers with neurocognitive functioning may indicate the activity of certain pathways, potentially those related to the underlying neuropathophysiology of HAND.
Topics: AIDS Dementia Complex; Biomarkers; Cognition Disorders; Humans; Metabolomics; Proteomics
PubMed: 33421125
DOI: 10.1111/jnc.15295