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Expert Review of Proteomics

Sandra Murphy, Margit Zweyer, Rustam R Mundegar, Dieter Swandulla, Kay Ohlendieck
The clinical evaluation of neuromuscular symptoms often includes the assessment of altered blood proteins or changed enzyme activities. However, the blood concentration of many muscle-derived serum markers is not specific for different neuromuscular disorders and also shows alterations in the course of these diseases. Thus, the establishment of more reliable biomarker signatures for improved muscle diagnostics is required. Areas covered: To address the lack of muscle disease-specific marker molecules, mass spectrometry-based proteomics was applied to the systematic identification and biochemical characterization of new serum biomarker candidates...
January 17, 2018: Expert Review of Proteomics
Grégory Dubourg, Hervé Chaudet, Jean-Christophe Lagier, Didier Raoult
Describing the human hut gut microbiota is one the most exciting challenges of the 21st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions...
January 16, 2018: Expert Review of Proteomics
Ping Jin, Jiang Lan, Kui Wang, Mark S Baker, Canhua Huang, Edouard C Nice
As we move from a discovery to a translational phase in proteomics, with a focus on developing validated clinical assays to assist personalized medicine, there is a growing need for strong bidirectional interactions with the clinical pathology community. Thus, while on one hand the proteomics community will provide candidate biomarkers to assist in diagnosis, prognosis, surveillance, identification of individualized patient medication and development and validation of new assays for diagnostic use, on the other the pathology community will assist with specific tissue identification and selection (e...
January 8, 2018: Expert Review of Proteomics
Arun V Everest-Dass, Edward S X Moh, Christopher Ashwood, Abdulrahman M M Shathili, Nicolle H Packer
Protein glycosylation is recognized as an important post-translational modification, with specific substructures having significant effects on protein folding, conformation, distribution, stability and activity. However, due to the structural complexity of glycans, elucidating glycan structure-function relationships is demanding. The fine detail of glycan structures attached to proteins (including sequence, branching, linkage and anomericity) is still best analysed after the glycans are released from the purified or mixture of glycoproteins (glycomics)...
December 29, 2017: Expert Review of Proteomics
Merry L Lindsey, Mira Jung, Michael E Hall, Kristine Y DeLeon-Pennell
The cardiac extracellular matrix (ECM) provides anatomical, biochemical, and physiological support to the left ventricle. ECM proteins are difficult to detect using unbiased proteomic approaches due to solubility issues and a relatively low abundance compared to cytoplasmic and mitochondrial proteins present in highly prevalent cardiomyocytes. Areas covered: Proteomic capabilities have dramatically improved over the past 20 years, due to enhanced sample preparation protocols and increased capabilities in mass spectrometry (MS), database searching, and bioinformatics analysis...
December 29, 2017: Expert Review of Proteomics
Alex Van Belkum, David Broadwell, Douglas Lovern, Lauren Petersen, George Weinstock, W Michael Dunne
No abstract text is available yet for this article.
December 28, 2017: Expert Review of Proteomics
Daniela Braconi, Giulia Bernardini, Lia Millucci, Annalisa Santucci
In the post-genomic era, the opportunity to combine and integrate cutting-edge analytical platforms and data processing systems allowed the birth of foodomics, "a discipline that studies the Food and Nutrition domains through the application of advanced omics technologies to improve consumer's well-being, health, and confidence". Since then, this discipline has rapidly evolved and researchers are now facing the daunting tasks to meet consumers' needs in terms of food traceability, sustainability, quality, safety and integrity...
December 22, 2017: Expert Review of Proteomics
Claudius Mueller, Amanda Haymond, Justin B Davis, Alexa Williams, Virginia Espina
Breast cancer subtypes are currently defined by a combination of morphologic, genomic, and proteomic characteristics. These subtypes provide a molecular portrait of the tumor, that aids diagnosis, prognosis, and treatment escalation/de-escalation options. Gene expression signatures describing intrinsic breast cancer subtypes for predicting risk of recurrence have been rapidly adopted in the clinic. Despite the use of subtype classifications, many patients develop drug resistance, breast cancer recurrence, or therapy failure...
December 22, 2017: Expert Review of Proteomics
Hisashi Narimatsu, Takashi Sato
Serum proteins are generally glycosylated and solubilized, and are thus present as glycoproteins. The glycan structure of glycoproteins reflects cell differentiation status; glycan structures generated by diseased cells are distinguishable from those produced by healthy cells. Proteins may therefore serve as markers of tissues that secrete them. Several strategies for the identification of novel serum biomarkers using a combination of glycoscience-based technologies have been recently proposed. The selection of lectins for use as probes for identification of altered glycan structures represents a critical step...
December 21, 2017: Expert Review of Proteomics
Heng Wee Tan, Yan-Ming Xu, Dan-Dan Wu, Andy T Y Lau
The human respiratory system is highly prone to diseases and complications. Many lung diseases, including lung cancer (LC), tuberculosis (TB), and chronic obstructive pulmonary disease (COPD) have been among the most common causes of death worldwide. Cystic fibrosis (CF), the most common genetic disease in Caucasians, has adverse impacts on the lungs. Bronchial proteomics plays a significant role in understanding the underlying mechanisms and pathogenicity of lung diseases and provides insights for biomarker and therapeutic target discoveries...
December 20, 2017: Expert Review of Proteomics
Xiaobo Yu, Brianne Petritis, Hu Duan, Danke Xu, Joshua LaBaer
Cell-free protein microarrays represent a special form of protein microarray which display proteins made fresh at the time of the experiment, avoiding storage and denaturation. They have been used increasingly in basic and translational research over the past decade to study protein-protein interactions, the pathogen-host relationship, post-translational modifications, and antibody biomarkers of different human diseases. Their role in the first blood-based diagnostic test for early stage breast cancer highlights their value in managing human health...
December 7, 2017: Expert Review of Proteomics
Arjun Chakraborty, Minnie Sarwal
The standard of care for monitoring renal transplant patients include transplant biopsy and serum creatinine measurements. These are invasive procedures and are late and nonspecific markers of injury. Proteomics and proteins can provide biomarkers for monitoring pathology and become a useful tool in detection and treatment of conditions that occur after transplant. Areas covered: A survey of 273 studies in the biomarker detection field which included proteomics relating to renal pathology and normal controls was done...
November 14, 2017: Expert Review of Proteomics
Young-Ki Paik, Gilbert S Omenn, William S Hancock, Lydie Lane, Christopher M Overall
The mission of the Chromosome-Centric Human Proteome Project (C-HPP), is to map and annotate the entire predicted human protein set (~20,000 proteins) encoded by each chromosome. The initial steps of the project are focused on 'missing proteins (MPs)', which lacked documented evidence for existence at protein level. In addition to remaining 2,579 MPs, we also target those annotated proteins having unknown functions, uPE1 proteins, alternative splice isoforms and post-translational modifications. We also consider how to investigate various protein functions involved in cis-regulatory phenomena, amplicons lncRNAs and smORFs...
November 10, 2017: Expert Review of Proteomics
Baohai Shao, Jay W Heinecke
Many lines of evidence indicate that low levels of HDL cholesterol increase the risk of cardiovascular disease (CVD). However, recent clinical studies of statin-treated subjects with established atherosclerosis cast doubt on the hypothesis that elevating HDL cholesterol levels reduces CVD risk. Areas covered: It is critical to identify new HDL metrics that capture HDL's proposed cardioprotective effects. One promising approach is quantitative MS/MS-based HDL proteomics. This article focuses on recent studies of the feasibility and challenges of using this strategy in translational studies...
November 8, 2017: Expert Review of Proteomics
Barbara W Sódar, Árpád Kovács, Tamás Visnovitz, Éva Pállinger, Károly Vékey, Gabriella Pocsfalvi, Lilla Turiák, Edit I Buzás
Extracellular vesicles are emerging sources of biomarkers for modern preventive and precision medicine. Extracellular vesicles in body fluids offer a unique opportunity for integrative biomarker approaches due to their complex biocargo that includes proteins, lipids, nucleic acids and metabolites. Mass spectrometry-based proteomics data suggest that a significant portion of human proteins are sorted into extracellular vesicles and amenable for biomarker discovery schemes. Areas covered: this review focuses on key aspects of isolation, quality control and subsequent analysis of blood plasma- and conditioned medium-derived extracellular vesicle proteins, and summarizes the current state-of-the-art in the field...
October 26, 2017: Expert Review of Proteomics
Tadashi Kondo
Proteomics has been used in soft tissue sarcoma (STS) research in the attempts to improve the understanding of the disease background and develop novel clinical applications. Using various proteomics modalities, aberrant regulations of numerous intriguing proteins were identified in STSs, and the possible utilities of identified proteins as biomarkers or therapeutic targets have been explored. STS is an exceptionally diverse group of malignant diseases with highly complex molecular backgrounds and, therefore, an overview of the achievements and prospects of STS proteomics could enhance our knowledge of the possibilities and limitations of cancer proteomics...
October 25, 2017: Expert Review of Proteomics
Abdo Alnabulsi, Graeme I Murray
Colorectal cancer (CRC) is a common type of cancer with a relatively poor survival rate. The survival rate of patients could be improved if CRC is detected early. Biomarkers associated with early stages of tumor development might provide useful tools for the early diagnosis of colorectal cancer. Area covered: Online searches using PubMed and Google Scholar were performed using keywords and with a focus on recent proteomic studies. The aim of this review is to highlight the need for biomarkers to improve the detection rate of early CRC and provide an overview of proteomic technologies used for biomarker discovery and validation...
October 24, 2017: Expert Review of Proteomics
Masaru Katoh
No abstract text is available yet for this article.
October 23, 2017: Expert Review of Proteomics
Paula Intasqui, Ricardo P Bertolla, Marcus Vinicius Sadi
Although prostate cancer constitutes one of the most important, death-related diseases in the male population, there is still a need for identification of sensitive biomarkers that could precociously detect the disease and differentiate aggressive from indolent cancers, in order to decrease overtreatment. Proteomics research has improved understanding on mechanisms underlying tumorigenesis, cancer cells migration and invasion potential, and castration resistance. This review has focused on proteomic studies of prostate cancer published in the recent years, with a special emphasis on determination of biomarkers for cancer progression and diagnosis...
January 2018: Expert Review of Proteomics
Elena Martinez-Garcia, Carlos Lopez-Gil, Irene Campoy, Julia Vallve, Eva Coll, Silvia Cabrera, Santiago Ramon Y Cajal, Xavier Matias-Guiu, Jan Van Oostrum, Jaume Reventos, Antonio Gil-Moreno, Eva Colas
Endometrial cancer (EC) is the fourth most common cancer in women in developed countries. The identification of sensitive and specific biomarkers to improve early detection of EC is crucial for an appropriate management of this disease, in which 30% of patients are diagnosed only at advanced stages, which is associated with high levels of morbidity and mortality. Despite major efforts and investments made to identify EC biomarkers, no protein has yet reached the stage of clinical application. Areas covered: This review gathers the numerous candidate biomarkers for EC diagnosis proposed in proteomic studies published from 1978 to 2017...
January 2018: Expert Review of Proteomics
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