scholarly journals Searching for New Biomarkers of Renal Diseases through Proteomics

2012 ◽  
Vol 58 (2) ◽  
pp. 353-365 ◽  
Author(s):  
Ana Konvalinka ◽  
James W Scholey ◽  
Eleftherios P Diamandis
Keyword(s):  
Mass Spectrometry ◽  
Prognostic Markers ◽  
Renal Diseases ◽  
Sample Collection ◽  
Technological Advances ◽  
Regulatory Bodies ◽  
New Biomarkers ◽  
Study Designs ◽  
Treatment Responsiveness ◽  
Proteomic Methods

Abstract BACKGROUND Technological advances have resulted in a renaissance of proteomic studies directed at finding markers of disease progression, diagnosis, or responsiveness to therapy. Renal diseases are ideally suited for such research, given that urine is an easily accessible biofluid and its protein content is derived mainly from the kidney. Current renal prognostic markers have limited value, and renal biopsy remains the sole method for establishing a diagnosis. Mass spectrometry instruments, which can detect thousands of proteins at nanomolar (or even femtomolar) concentrations, may be expected to allow the discovery of improved markers of progression, diagnosis, or treatment responsiveness. CONTENT In this review we describe the strengths and limitations of proteomic methods and the drawbacks of existing biomarkers, and provide an overview of opportunities in the field. We also highlight several proteomic studies of biomarkers of renal diseases selected from the plethora of studies performed. SUMMARY It is clear that the field of proteomics has not yet fulfilled its promise. However, ongoing efforts to standardize sample collection and preparation, improve study designs, perform multicenter validations, and create joint industry–regulatory bodies offer promise for the recognition of novel molecules that could change clinical nephrology forever.

scholarly journals Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data

2019 ◽  
Author(s):  
Vera Ignjatovic ◽  
Philipp E Geyer ◽  
Krishnan K Palaniappan ◽  
Jessica E Chaaban ◽  
Gilbert S Omenn ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Human Plasma ◽  
Protein Composition ◽  
Bioinformatic Analysis ◽  
Individual Variability ◽  
Research Progress ◽  
Sample Collection ◽  
Technological Advances ◽  
Plasma Proteomics ◽  
Key Aspects

AbstractThe proteomic analyses of human blood and blood-derived products (e.g. plasma) offers an attractive avenue to translate research progress from the laboratory into the clinic. However, due to its unique protein composition, performing proteomics assays with plasma is challenging. Plasma proteomics has regained interest due to recent technological advances, but challenges imposed by both complications inherent to studying human biology (e.g. inter-individual variability), analysis of biospecimen (e.g. sample variability), as well as technological limitations remain. As part of the Human Proteome Project (HPP), the Human Plasma Proteome Project (HPPP) brings together key aspects of the plasma proteomics pipeline. Here, we provide considerations and recommendations concerning study design, plasma collection, quality metrics, plasma processing workflows, mass spectrometry (MS) data acquisition, data processing and bioinformatic analysis. With exciting opportunities in studying human health and disease though this plasma proteomics pipeline, a more informed analysis of human plasma will accelerate interest whilst enhancing possibilities for the incorporation of proteomics-scaled assays into clinical practice.Abstract Figure

scholarly journals RNA-Centric Approaches to Profile the RNA–Protein Interaction Landscape on Selected RNAs

2021 ◽  
Vol 7 (1) ◽  
pp. 11 ◽  
Author(s):  
André P. Gerber
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Regulatory Networks ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Complexes ◽  
Cell Protein ◽  
Transcriptional Regulatory Networks ◽  
Technological Advances

RNA–protein interactions frame post-transcriptional regulatory networks and modulate transcription and epigenetics. While the technological advances in RNA sequencing have significantly expanded the repertoire of RNAs, recently developed biochemical approaches combined with sensitive mass-spectrometry have revealed hundreds of previously unrecognized and potentially novel RNA-binding proteins. Nevertheless, a major challenge remains to understand how the thousands of RNA molecules and their interacting proteins assemble and control the fate of each individual RNA in a cell. Here, I review recent methodological advances to approach this problem through systematic identification of proteins that interact with particular RNAs in living cells. Thereby, a specific focus is given to in vivo approaches that involve crosslinking of RNA–protein interactions through ultraviolet irradiation or treatment of cells with chemicals, followed by capture of the RNA under study with antisense-oligonucleotides and identification of bound proteins with mass-spectrometry. Several recent studies defining interactomes of long non-coding RNAs, viral RNAs, as well as mRNAs are highlighted, and short reference is given to recent in-cell protein labeling techniques. These recent experimental improvements could open the door for broader applications and to study the remodeling of RNA–protein complexes upon different environmental cues and in disease.

scholarly journals Clinical Perspective on Proteomic and Glycomic Biomarkers for Diagnosis, Prognosis, and Prediction of Pancreatic Cancer

2021 ◽  
Vol 22 (5) ◽  
pp. 2655
Author(s):  
Randa G. Hanna-Sawires ◽  
Jorinde H. Schiphuis ◽  
Manfred Wuhrer ◽  
Hans F. A. Vasen ◽  
Monique E. van Leerdam ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Surgical Techniques ◽  
Protein Glycosylation ◽  
Ductal Adenocarcinoma ◽  
Careful Study ◽  
Prognosis And Prediction ◽  
Prognostic Stratification ◽  
Neo Adjuvant Chemotherapy ◽  
New Biomarkers ◽  
Study Designs

Pancreatic ductal adenocarcinoma (PDAC) is known as a highly aggressive malignant disease. Prognosis for patients is notoriously poor, despite improvements in surgical techniques and new (neo)adjuvant chemotherapy regimens. Early detection of PDAC may increase the overall survival. It is furthermore foreseen that precision medicine will provide improved prognostic stratification and prediction of therapeutic response. In this review, omics-based discovery efforts are presented that aim for novel diagnostic and prognostic biomarkers of PDAC. For this purpose, we systematically evaluated the literature published between 1999 and 2020 with a focus on protein- and protein-glycosylation biomarkers in pancreatic cancer patients. Besides genomic and transcriptomic approaches, mass spectrometry (MS)-based proteomics and glycomics of blood- and tissue-derived samples from PDAC patients have yielded new candidates with biomarker potential. However, for reasons discussed in this review, the validation and clinical translation of these candidate markers has not been successful. Consequently, there has been a change of mindset from initial efforts to identify new unimarkers into the current hypothesis that a combination of biomarkers better suits a diagnostic or prognostic panel. With continuing development of current research methods and available techniques combined with careful study designs, new biomarkers could contribute to improved detection, prognosis, and prediction of pancreatic cancer.

scholarly journals Proteomic insights into synaptic signaling in the brain: the past, present and future

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yalan Xu ◽  
Xiuyue Song ◽  
Dong Wang ◽  
Yin Wang ◽  
Peifeng Li ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Complexes ◽  
Synaptic Signaling ◽  
Brain Functions ◽  
The Past ◽  
Data Independent Acquisition ◽  
Technological Advances ◽  
Neural Communication ◽  
Chemical Synapses ◽  
The Brain

AbstractChemical synapses in the brain connect neurons to form neural circuits, providing the structural and functional bases for neural communication. Disrupted synaptic signaling is closely related to a variety of neurological and psychiatric disorders. In the past two decades, proteomics has blossomed as a versatile tool in biological and biomedical research, rendering a wealth of information toward decoding the molecular machinery of life. There is enormous interest in employing proteomic approaches for the study of synapses, and substantial progress has been made. Here, we review the findings of proteomic studies of chemical synapses in the brain, with special attention paid to the key players in synaptic signaling, i.e., the synaptic protein complexes and their post-translational modifications. Looking toward the future, we discuss the technological advances in proteomics such as data-independent acquisition mass spectrometry (DIA-MS), cross-linking in combination with mass spectrometry (CXMS), and proximity proteomics, along with their potential to untangle the mystery of how the brain functions at the molecular level. Last but not least, we introduce the newly developed synaptomic methods. These methods and their successful applications marked the beginnings of the synaptomics era.

scholarly journals SARS-CoV-2 and the role of fomite transmission: a systematic review

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 233
Author(s):  
Igho J. Onakpoya ◽  
Carl J. Heneghan ◽  
Elizabeth A. Spencer ◽  
Jon Brassey ◽  
Annette Plüddemann ◽  
...  
Keyword(s):  
Systematic Review ◽  
Sample Collection ◽  
Quality Of Reporting ◽  
Cycle Threshold ◽  
Healthcare Settings ◽  
Viral Culture ◽  
Mechanistic Pathway ◽  
General Wards ◽  
Study Designs

Background: SARS-CoV-2 RNA has been detected in fomites which suggests the virus could be transmitted via inanimate objects. However, there is uncertainty about the mechanistic pathway for such transmissions. Our objective was to identify, appraise and summarise the evidence from primary studies and systematic reviews assessing the role of fomites in transmission.  Methods: This review is part of an Open Evidence Review on Transmission Dynamics of SARS-CoV-2. We conduct ongoing searches using WHO Covid-19 Database, LitCovid, medRxiv, and Google Scholar; assess study quality based on five criteria and report important findings on an ongoing basis. Results: We found 64 studies: 63 primary studies and one systematic review (n=35). The settings for primary studies were predominantly in hospitals (69.8%) including general wards, ICU and SARS-CoV-2 isolation wards. There were variations in the study designs including timing of sample collection, hygiene procedures, ventilation settings and cycle threshold. The overall quality of reporting was low to moderate. The frequency of positive SARS-CoV-2 tests across 51 studies (using RT-PCR) ranged from 0.5% to 75%. Cycle threshold values ranged from 20.8 to 44.1. Viral concentrations were reported in 17 studies; however, discrepancies in the methods for estimation prevented comparison. Eleven studies (17.5%) attempted viral culture, but none found a cytopathic effect. Results of the systematic review showed that healthcare settings were most frequently tested (25/35, 71.4%), but laboratories reported the highest frequency of contaminated surfaces (20.5%, 17/83).  Conclusions: The majority of studies report identification of SARS-CoV-2 RNA on inanimate surfaces; however, there is a lack of evidence demonstrating the recovery of viable virus. Lack of positive viral cultures suggests that the risk of transmission of SARS-CoV-2 through fomites is low. Heterogeneity in study designs and methodology prevents comparisons of findings across studies. Standardized guidelines for conducting and reporting research on fomite transmission is warranted.

scholarly journals Comparative Analysis of Mass-Spectrometry-Based Proteomic Methods for Protein Target Discovery Using a One-Pot Approach

2019 ◽  
Vol 31 (2) ◽  
pp. 217-226 ◽  
Author(s):  
Aurora Cabrera ◽  
Nancy Wiebelhaus ◽  
Baiyi Quan ◽  
Renze Ma ◽  
He Meng ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Comparative Analysis ◽  
One Pot ◽  
Target Discovery ◽  
Protein Target ◽  
Proteomic Methods

Computational methods for NMR and MS for structure elucidation II: database resources and advanced methods

2019 ◽  
Vol 4 (11) ◽  
Author(s):  
Marilia Valli ◽  
Helena Mannochio Russo ◽  
Alan Cesar Pilon ◽  
Meri Emili Ferreira Pinto ◽  
Nathalia B. Dias ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Computational Methods ◽  
Structure Elucidation ◽  
Computational Tools ◽  
Technological Advances ◽  
Similarity Networks ◽  
Product Chemistry

Abstract Technological advances have contributed to the evolution of the natural product chemistry and drug discovery programs. Recently, computational methods for nuclear magnetic resonance (NMR) and mass spectrometry (MS) have speeded up and facilitated the process of structural elucidation even in high complex biological samples. In this chapter, the current computational tools related to NMR and MS databases and spectral similarity networks, as well as their applications on dereplication and determination of biological biomarkers, are addressed.

Recent Technological Advances in the Mass Spectrometry-based Nanomedicine Studies: An Insight from Nanoproteomics

2019 ◽  
Vol 25 (13) ◽  
pp. 1536-1553 ◽  
Author(s):  
Jing Tang ◽  
Yunxia Wang ◽  
Yi Li ◽  
Yang Zhang ◽  
Runyuan Zhang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Information Sources ◽  
Protein Quantification ◽  
Protein Profiling ◽  
Label Free ◽  
Dynamic Information ◽  
Data Repositories ◽  
Research Directions ◽  
Technological Advances ◽  
Recent Trends

Nanoscience becomes one of the most cutting-edge research directions in recent years since it is gradually matured from basic to applied science. Nanoparticles (NPs) and nanomaterials (NMs) play important roles in various aspects of biomedicine science, and their influences on the environment have caused a whole range of uncertainties which require extensive attention. Due to the quantitative and dynamic information provided for human proteome, mass spectrometry (MS)-based quantitative proteomic technique has been a powerful tool for nanomedicine study. In this article, recent trends of progress and development in the nanomedicine of proteomics were discussed from quantification techniques and publicly available resources or tools. First, a variety of popular protein quantification techniques including labeling and label-free strategies applied to nanomedicine studies are overviewed and systematically discussed. Then, numerous protein profiling tools for data processing and postbiological statistical analysis and publicly available data repositories for providing enrichment MS raw data information sources are also discussed.

scholarly journals Circulating Tumor Cells in Pancreatic Cancer: Current Perspectives

Cancers ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1659 ◽  
Author(s):  
Verena Martini ◽  
Sylvia Timme-Bronsert ◽  
Stefan Fichtner-Feigl ◽  
Jens Hoeppner ◽  
Birte Kulemann
Keyword(s):  
Pancreatic Cancer ◽  
Tumor Cells ◽  
Circulating Tumor Cells ◽  
Prognostic Markers ◽  
Cancer Prognosis ◽  
Detection Methods ◽  
Ductal Adenocarcinoma ◽  
Detection Tool ◽  
The Usa ◽  
New Biomarkers

Pancreatic cancer is the fourth leading cause of cancer-related death in the USA and Europe; early symptoms and screenings are lacking, and it is usually diagnosed late with a poor prognosis. Circulating tumor cells (CTCs) have been promising new biomarkers in solid tumors. In the last twenty years (1999–2019), 140 articles have contained the key words “Circulating tumor cells, pancreatic cancer, prognosis and diagnosis.” Articles were evaluated for the use of CTCs as prognostic markers and their correlation to survival in pancreatic ductal adenocarcinoma (PDAC). In the final selected 17 articles, the CTC detection rate varied greatly between different enrichment methodologies and ranged from 11% to 92%; the majority of studies used the antigen-dependent CellSearch© system for CTC detection. Fifteen of the reviewed studies showed a correlation between CTC presence and a worse overall survival. The heterogeneity of CTC-detection methods and the lack of uniform results hinder a comparison of the evaluated studies. However, CTCs can be detected in pancreatic cancer and harbor a hope to serve as an early detection tool. Larger studies are needed to corroborate CTCs as valid biomarkers in pancreatic cancer.

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