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Clinical Proteomics

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https://www.readbyqxmd.com/read/29048850/-stable-isotope-labeling-and-parallel-reaction-monitoring-based-proteomic-quantification-for-biomarker-screening-and-validation-of-hepatocellular-carcinoma
#1
Sulan Wang, Huaping Gao, Jing Zhang, Xiang Ye
Liver cancer is the fifth most common cancer with extremely low five year survival rate. Early diagnosis is of great importance for cancer therapy. In this work, stable isotope labeling-based relative quantitative proteomics and parallel reaction monitoring-based target proteomics were combined for cancer biomarker screening and validation. By using this strategy, 70 significantly changed proteins in hepatocellular carcinoma tissues were obtained, among which seven proteins were further validated. The validated proteins contain the clinically used hepatocellular carcinoma (HCC) biomarker alpha-fetoprotein (AFP) and the reported biomarker candidates Heat shock protein HSP 90-beta (HSP90), fatty acid-binding protein, epidermal (FABP5) and alcohol dehydrogenase 4 (ADH4), which demonstrated the robustness of the strategy...
September 8, 2017: Se Pu, Chinese Journal of Chromatography
https://www.readbyqxmd.com/read/29046488/principles-and-applications-of-rabbit-models-for-atherosclerosis-research
#2
Jianglin Fan, Yajie Chen, Haizhao Yan, Manabu Niimi, Yanli Wang, Jingyan Liang
Rabbits are one of the most used experimental animals for biomedical research, particularly as a bioreactor for the production of antibodies. However, many unique features of the rabbit have also made it as an excellent species for examining a number of aspects of human diseases such as atherosclerosis. Rabbits are phylogenetically closer to humans than rodents, in addition to their relatively proper size, tame disposition, and ease of use and maintenance in the laboratory facility. Due to their short life spans, short gestation periods, high numbers of progeny, low cost (compared with other large animals) and availability of genomics and proteomics, rabbits usually serve to bridge the gap between smaller rodents (mice and rats) and larger animals, such as dogs, pigs and monkeys, and play an important role in many translational research activities such as pre-clinical testing of drugs and diagnostic methods for patients...
October 19, 2017: Journal of Atherosclerosis and Thrombosis
https://www.readbyqxmd.com/read/29046389/the-antibody-repertoire-of-colorectal-cancer
#3
Seong Won Cha, Stefano Bonissone, Seungjin Na, Pavel A Pevzner, Vineet Bafna
Immunotherapy is becoming increasingly important in the fight against cancers, utilizing and manipulating the body's immune response to treat tumors. Understanding the immune repertoire - the collection of immunological proteins - of treated and untreated cells is possible at the genomic, but technically difficult at the protein level. Standard protein databases do not include the highly divergent sequences of somatic rearranged immunoglobulin genes, and may lead to missed identifications in a mass spectrometry search...
October 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29042634/a-novel-quantification-driven-proteomic-strategy-identifies-an-endogenous-peptide-of-pleiotrophin-as-a-new-biomarker-of-alzheimer-s-disease
#4
Tobias Skillbäck, Niklas Mattsson, Karl Hansson, Ekaterina Mirgorodskaya, Rahil Dahlén, Wiesje van der Flier, Philip Scheltens, Floor Duits, Oskar Hansson, Charlotte Teunissen, Kaj Blennow, Henrik Zetterberg, Johan Gobom
We present a new, quantification-driven proteomic approach to identifying biomarkers. In contrast to the identification-driven approach, limited in scope to peptides that are identified by database searching in the first step, all MS data are considered to select biomarker candidates. The endopeptidome of cerebrospinal fluid from 40 Alzheimer's disease (AD) patients, 40 subjects with mild cognitive impairment, and 40 controls with subjective cognitive decline was analyzed using multiplex isobaric labeling. Spectral clustering was used to match MS/MS spectra...
October 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29042303/changes-in-serum-proteins-in-dogs-with-ehrlichia-canis-infection
#5
Damián Escribano, Hüseyin Cihan, Silvia Martínez-Subiela, Pinar Levent, Meric Kocaturk, Nilüfer Aytug, Jose Joaquin Cerón, Asta Tvarijonaviciute, Zeki Yilmaz
The aim of this study was the identification of proteins differentially represented in the serum proteome of seropositive dogs with (Group 1) and without (Group 2) clinical-pathologic signs consistent with ehrlichiosis compared to healthy dogs. Serum samples were collected from 20 dogs of various breeds with naturally occurring ehrlichiosis (10 dogs belonged to Group 1 and 10 to Group 2) and 10 healthy dogs. Two-dimensional electrophoresis (2DE) of pooled serum for each of tge group of dogs were run in triplicate...
October 14, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29041828/urine-protein-biomarkers-for-detection-of-cardiovascular-disease-and-their-use-for-the-clinic
#6
Sarah Röthlisberger, Johanna Pedroza-Diaz
Cardiovascular disease (CVD) is the leading noncommunicable disease and main cause of death worldwide. Traditionally, blood has been the sample of choice for biomarker discovery, however, urine has roused great interest in recent years as a source of biomarkers. Sample collection is simple, non-invasive, and there is the possibility of implementing minimal cost tests in primary care settings. Areas covered: In this review, we systematically searched PubMed for proteomic studies of CVD, with the criteria that urine was included as a biological sample...
October 18, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29039718/current-status-of-proteomics-of-soft-tissue-sarcomas
#7
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 17, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29039124/recent-progress-in-mass-spectrometry-proteomics-for-biomedical-research
#8
REVIEW
Xu Li, Wenqi Wang, Junjie Chen
Proteins are the key players in many cellular processes. Their composition, trafficking, and interactions underlie the dynamic processes of life. Furthermore, diseases are frequently accompanied by malfunction of proteins at multiple levels. Understanding how biological processes are regulated at the protein level is critically important to understanding the molecular basis for diseases and often shed light on disease prevention, diagnosis, and treatment. With rapid advances in mass spectrometry (MS) instruments and experimental methodologies, MS-based proteomics has become a reliable and essential tool for elucidating biological processes at the protein level...
October 13, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/29037750/environmental-toxicology-and-omics-a-question-of-sex
#9
Xuefang Liang, April Feswick, Denina Simmons, Christopher J Martyniuk
Molecular initiating events and downstream transcriptional/proteomic responses provide valuable information for adverse outcome pathways, which can be used predict the effects of chemicals on physiological systems. There has been a paucity of research that addresses sex-specific expression profiling in toxicology and due to cost, time, and logistical considerations, sex as a variable has not been widely considered. In response to this deficiency, federal agencies in the United States, Canada, and Europe have highlighted the importance of including sex as a variable in scientific investigations...
October 13, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29036683/cr2cancer-a-database-for-chromatin-regulators-in-human-cancer
#10
Beibei Ru, Jianlong Sun, Yin Tong, Ching Ngar Wong, Aditi Chandra, Acacia Tsz So Tang, Larry Ka Yue Chow, Wai Lam Wun, Zarina Levitskaya, Jiangwen Zhang
Chromatin regulators (CRs) can dynamically modulate chromatin architecture to epigenetically regulate gene expression in response to intrinsic and extrinsic signalling cues. Somatic alterations or misexpression of CRs might reprogram the epigenomic landscape of chromatin, which in turn lead to a wide range of common diseases, notably cancer. Here, we present CR2Cancer, a comprehensive annotation and visualization database for CRs in human cancer constructed by high throughput data analysis and literature mining...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036198/the-homeodomain-interacting-protein-kinase-hpk-1-preserves-protein-homeostasis-and-longevity-through-master-regulatory-control-of-the-hsf-1-chaperone-network-and-torc1-restricted-autophagy-in-caenorhabditis-elegans
#11
Ritika Das, Justine A Melo, Manjunatha Thondamal, Elizabeth A Morton, Adam B Cornwell, Beresford Crick, Joung Heon Kim, Elliot W Swartz, Todd Lamitina, Peter M Douglas, Andrew V Samuelson
An extensive proteostatic network comprised of molecular chaperones and protein clearance mechanisms functions collectively to preserve the integrity and resiliency of the proteome. The efficacy of this network deteriorates during aging, coinciding with many clinical manifestations, including protein aggregation diseases of the nervous system. A decline in proteostasis can be delayed through the activation of cytoprotective transcriptional responses, which are sensitive to environmental stress and internal metabolic and physiological cues...
October 16, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29036190/clusternomics-integrative-context-dependent-clustering-for-heterogeneous-datasets
#12
Evelina Gabasova, John Reid, Lorenz Wernisch
Integrative clustering is used to identify groups of samples by jointly analysing multiple datasets describing the same set of biological samples, such as gene expression, copy number, methylation etc. Most existing algorithms for integrative clustering assume that there is a shared consistent set of clusters across all datasets, and most of the data samples follow this structure. However in practice, the structure across heterogeneous datasets can be more varied, with clusters being joined in some datasets and separated in others...
October 16, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29036182/proteome-analysis-of-bronchoalveolar-lavage-from-calves-infected-with-bovine-respiratory-syncytial-virus-insights-in-pathogenesis-and-perspectives-for-new-treatments
#13
Sara Hägglund, Krister Blodörn, Katarina Näslund, Karin Vargmar, Sara Bergström Lind, Jia Mi, Mariluz Araínga, Sabine Riffault, Geraldine Taylor, John Pringle, Jean François Valarcher
Human and bovine respiratory syncytial viruses (HRSV/BRSV) are major causes of severe lower respiratory tract infections in children and calves, respectively. Shared epidemiological, clinical, pathological and genetic characteristics of these viruses make comparative research highly relevant. To characterise the host response against BRSV infection, bronchoalveolar lavage supernatant (BAL) from i) non-vaccinated, BRSV-infected ii) vaccinated, BRSV-infected and iii) non-infected calves was analysed by tandem mass spectrometry...
2017: PloS One
https://www.readbyqxmd.com/read/29035320/personomics-the-missing-link-in-the-evolution-from-precision-medicine-to-personalized-medicine
#14
Roy C Ziegelstein
Clinical practice guidelines have been developed for many common conditions based on data from randomized controlled trials. When medicine is informed solely by clinical practice guidelines, however, the patient is not treated as an individual, but rather a member of a group. Precision medicine, as defined herein, characterizes unique biological characteristics of the individual or of specimens obtained from an individual to tailor diagnostics and therapeutics to a specific patient. These unique biological characteristics are defined by the tools of precision medicine: genomics, proteomics, metabolomics, epigenomics, pharmacogenomics, and other "-omics...
October 16, 2017: Journal of Personalized Medicine
https://www.readbyqxmd.com/read/29033026/economic-impact-of-rapid-diagnostic-methods-in-clinical-microbiology-price-of-the-test-or-overall-clinical-impact
#15
Rafael Cantón, Elia Gómez G de la Pedrosa
The need to reduce the time it takes to establish a microbiological diagnosis and the emergence of new molecular microbiology and proteomic technologies has fuelled the development of rapid and point-of-care techniques, as well as the so-called point-of-care laboratories. These laboratories are responsible for conducting both techniques partially to response to the outsourcing of the conventional hospital laboratories. Their introduction has not always been accompanied with economic studies that address their cost-effectiveness, cost-benefit and cost-utility, but rather tend to be limited to the unit price of the test...
October 13, 2017: Enfermedades Infecciosas y Microbiología Clínica
https://www.readbyqxmd.com/read/29032615/regulation-of-the-prometastatic-neuregulin-mmp13-axis-by-src-family-kinases-therapeutic-implications
#16
Ana Orive-Ramos, Samuel Seoane, Alberto Ocaña, Atanasio Pandiella, Juan Carlos Montero
Metastatic dissemination of tumor cells is responsible for the fatal outcome of breast cancer. Therefore, understanding the mechanisms involved in dissemination is essential for the development of new therapeutic strategies to prevent metastasis. One mechanism involved in metastatic dissemination of breast cancer cells is dependent on control of the production of matrix metalloproteinases by the neuregulins (NRGs). The NRGs are polypeptide factors that act by binding to the ErbB/HER subfamily of receptor tyrosine kinases...
October 15, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/29032385/exercise-training-response-heterogeneity-physiological-and-molecular-insights
#17
REVIEW
Lauren M Sparks
The overall beneficial effects of exercise are well studied, but why some people do not respond favourably to exercise is less understood. The National Institutes of Health Common Fund has recently launched the large-scale discovery project 'Molecular Transducers of Physical Activity in Humans' to examine the physiological and molecular (i.e. genetic, epigenetic, lipidomic, metabolomic, proteomic, etc.) responses to exercise training. A nationwide, multicentre clinical trial such as this one also provides a unique opportunity to robustly investigate the non-response to exercise in thousands of individuals that have undergone supervised aerobic- and resistance-based exercise training interventions...
October 14, 2017: Diabetologia
https://www.readbyqxmd.com/read/29032348/systems-proteomics-approaches-to-study-bacterial-pathogens-application-to-mycobacterium-tuberculosis
#18
REVIEW
Amir Banaei-Esfahani, Charlotte Nicod, Ruedi Aebersold, Ben C Collins
Significant developments and improvements in basic and clinical research notwithstanding, infectious diseases still claim at least 13 million lives annually. Classical research approaches have deciphered many molecular mechanisms underlying infection. Today it is increasingly recognized that multiple molecular mechanisms cooperate to constitute a complex system that is used by a given pathogen to interfere with the biochemical processes of the host. Therefore, systems-level approaches now complement the standard molecular biology techniques to investigate pathogens and their interactions with the human host...
October 12, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29032071/comparing-intestinal-versus-diffuse-gastric-cancer-using-a-peff-oriented-proteomic-pipeline
#19
Helisa Helena Wippel, Marlon Dias Mariano Santos, Milan Avila Clasen, Louise Ulrich Kurt, Fabio Cesar Sousa Nogueira, Carlos Eduardo Carvalho, Thaís Messias McCormick, Guilherme Pinto Bravo Neto, Lysangela Ronalte Alves, Maria da Gloria da Costa Carvalho, Paulo Costa Carvalho, Juliana de Saldanha da Gama Fischer
Gastric cancer is the fifth most common malignant neoplasia and the third leading cause of cancer death worldwide. Mac-Cormick et al. recently showed the importance of considering the anatomical region of the tumor in proteomic gastric cancer studies; more differences were found between distinct anatomical regions than when comparing healthy versus diseased tissue. Thus, failing to consider the anatomical region could lead to differential proteins that are not disease specific. With this as motivation, we compared the proteomic profiles of intestinal and diffuse adenocarcinoma from the same anatomical region, the corpus...
October 11, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29030347/extracellular-matrix-proteomics-reveals-interplay-of-aggrecan-and-aggrecanases-in-vascular-remodeling-of-stented-coronary-arteries
#20
Gonca Suna, Wojciech Wojakowski, Marc Lynch, Javier Barallobre-Barreiro, Xiaoke Yin, Ursula Mayr, Ferheen Baig, Ruifang Lu, Marika Fava, Robert Hayward, Chris Molenaar, Stephen J White, Tomasz Roleder, Krzysztof Milewski, Pawel Gasior, Piotr P Buszman, Pawel E Buszman, Marjan Jahangiri, Cathy Shanahan, Jonathan M Hill, Manuel Mayr
Background -Extracellular matrix (ECM) remodeling contributes to in-stent restenosis and thrombosis. Despite its important clinical implications little is known about ECM changes post-stent implantation. Methods -Bare-metal (BMS) and drug-eluting stents (DES) were implanted in pig coronary arteries with an overstretch under optical coherence tomography guidance. Stented segments were harvested 1, 3, 7, 14 and 28 days post-stenting for proteomics analysis of the media and neointima. Results -A total of 151 ECM and ECM-associated proteins were identified by mass spectrometry...
October 13, 2017: Circulation
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