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Clinical Proteomics

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https://www.readbyqxmd.com/read/28097685/cartilage-oligomeric-matrix-protein-comp-neo-epitope-in-the-synovial-fluid-of-horses-with-acute-lameness-a-new-biomarker-for-the-early-stages-of-osteoarthritis
#1
E Skiöldebrand, S Ekman, L MattssonHultén, E Svala, K Björkman, A Lindahl, A Lundqvist, P Önnerfjord, C Sihlbom, U Rüetschi
BACKGROUND: Clinical tools to diagnose the early changes of osteoarthritis (OA) that occur in the articular cartilage are lacking. OBJECTIVES: We sought to identify and quantify a novel cartilage oligomeric matrix protein (COMP) neo-epitope in the synovial fluid from the joints of healthy horses and those with different stages of OA. STUDY DESIGN: In vitro quantitative proteomics and assay development with application in synovial fluids samples obtained from biobanks of well-characterised horses...
January 17, 2017: Equine Veterinary Journal
https://www.readbyqxmd.com/read/28092471/genomics-pipelines-and-data-integration-challenges-and-opportunities-in-the-research-setting
#2
Jeremy Davis-Turak, Sean M Courtney, E Starr Hazard, W Bailey Glen, Willian da Silveira, Timothy Wesselman, Larry P Harbin, Bethany J Wolf, Dongjun Chung, Gary Hardiman
The emergence and mass utilization of high-throughput (HT) technologies, including sequencing technologies (genomics) and mass spectrometry (proteomics, metabolomics, lipids), has allowed geneticists, biologists, and biostatisticians to bridge the gap between genotype and phenotype on a massive scale. These new technologies have brought rapid advances in our understanding of cell biology, evolutionary history, microbial environments, and are increasingly providing new insights and applications towards clinical care and personalized medicine...
January 16, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28091625/mplex-a-method-for-simultaneous-pathogen-inactivation-and-extraction-of-samples-for-multi-omics-profiling
#3
Kristin E Burnum-Johnson, Jennifer E Kyle, Amie J Eisfeld, Cameron P Casey, Kelly G Stratton, Juan F Gonzalez, Fabien Habyarimana, Nicholas M Negretti, Amy C Sims, Sadhana Chauhan, Larissa B Thackray, Peter J Halfmann, Kevin B Walters, Young-Mo Kim, Erika M Zink, Carrie D Nicora, Karl K Weitz, Bobbie-Jo M Webb-Robertson, Ernesto S Nakayasu, Brian Ahmer, Michael E Konkel, Vladimir Motin, Ralph S Baric, Michael S Diamond, Yoshihiro Kawaoka, Katrina M Waters, Richard D Smith, Thomas O Metz
The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can take place only subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements...
January 16, 2017: Analyst
https://www.readbyqxmd.com/read/28087425/variations-of-metabolites-and-proteome-in-lonicera-japonica-thunb-buds-and-flowers-under-uv-radiation
#4
Wei Zhu, Wen Zheng, Xingjiang Hu, Xiaobao Xu, Lin Zhang, Jingkui Tian
Lonicera japonica Thunb., also known as Jin Yin Hua and Japanese honeysuckle, is used as a herbal medicine in Asian countries. Its flowers have been used in folk medicine in the clinic and in making food or healthy beverages for over 1500years in China. To investigate the molecular processes involved in L. japonica development from buds to flowers exposed to UV radiation, a comparative proteomics analysis was performed. Fifty-four proteins were identified as differentially expressed, including 42 that had increased expression and 12 that had decreased expression...
January 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28087010/breaking-the-ice-urine-proteomics-of-medullary-sponge-kidney-disease
#5
Somchai Chutipongtanate
Urinary proteomics is a promising tool for biomarker investigation, particularly in complex kidney diseases. Fabris and colleagues report that urinary laminin subunit alpha-2 is a potential diagnostic marker of medullary sponge kidney (MSK) disease by using a label-free quantitative proteomics platform and a clinically compatible enzyme-linked immunosorbent assay. The neglected issue of stone pathogenesis was also evidenced. This commentary discusses several considerations in biomarker validation, and how urinary proteomics breaks new ground in MSK research...
February 2017: Kidney International
https://www.readbyqxmd.com/read/28079714/radiomic-phenotyping-in-brain-cancer-to-unravel-hidden-information-in-medical-images
#6
Srishti Abrol, Aikaterini Kotrotsou, Ahmed Salem, Pascal O Zinn, Rivka R Colen
Radiomics is a new area of research in the field of imaging with tremendous potential to unravel the hidden information in digital images. The scope of radiology has grown exponentially over the last two decades; since the advent of radiomics, many quantitative imaging features can now be extracted from medical images through high-throughput computing, and these can be converted into mineable data that can help in linking imaging phenotypes with clinical data, genomics, proteomics, and other "omics" information...
January 11, 2017: Topics in Magnetic Resonance Imaging: TMRI
https://www.readbyqxmd.com/read/28077444/protein-interactions-during-the-flavivirus-and-hepacivirus-life-cycle
#7
Gisa Gerold, Janina Bruening, Bettina Weigel, Thomas Pietschmann
Protein-protein interactions govern biological functions in cells, in the extracellular milieu and at the border between cells and extracellular space. Viruses are small intracellular parasites and thus rely on protein interactions to produce progeny inside host cells and to spread from cell to cell. Usage of host proteins by viruses can have severe consequences e.g. apoptosis, metabolic disequilibria or altered cell proliferation and mobility. Understanding protein interactions during virus infection can thus educate us on viral infection and pathogenesis mechanisms...
January 11, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28075340/bioactive-nutrients-and-nutrigenomics-in-age-related-diseases
#8
REVIEW
Tania Rescigno, Luigina Micolucci, Mario F Tecce, Anna Capasso
The increased life expectancy and the expansion of the elderly population are stimulating research into aging. Aging may be viewed as a multifactorial process that results from the interaction of genetic and environmental factors, which include lifestyle. Human molecular processes are influenced by physiological pathways as well as exogenous factors, which include the diet. Dietary components have substantive effects on metabolic health; for instance, bioactive molecules capable of selectively modulating specific metabolic pathways affect the development/progression of cardiovascular and neoplastic disease...
January 8, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28071820/response-profiling-using-shotgun-proteomics-enables-global-metallodrug-mechanisms-of-action-to-be-established
#9
Dominique Kreutz, Andrea Bileck, Kerstin Plessl, Denise Wolrab, Michael Groessl, Bernhard K Keppler, Samuel M Meier, Christopher Gerner
Response profiling using shotgun proteomics for establishing global metallodrug mechanisms of action in two colon carcinoma cell lines, HCT116 and SW480, has been applied and evaluated with the clinically approved arsenic trioxide. Surprisingly, the complete established mechanism of action of arsenic trioxide was observed by protein regulations in SW480, but not HCT116 cells. Comparing the basal protein expression in the two cell lines revealed an 80 % convergence of protein identification, but with significant expression differences, which in turn seem to affect the extent of protein regulation...
November 7, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28070115/proposal-for-a-prospective-registry-for-moyamoya-disease-in-japan
#10
Ken Kazumata, Masaki Ito, Haruto Uchino, Hiroshi Nishihara, Kiyohiro Houkin
The number of clinical research papers published worldwide on moyamoya disease (MMD) has increased recently. However, the majority of the literature comprises retrospective single-center studies collecting data on small numbers of patients. Several multi-center studies are ongoing in Japan; however, the current data are insufficient for comprehensively outlining the various characteristics of MMD. To enhance our knowledge on epidemiologic, vascular, and genetic aspects of MMD, a prospective multicenter registry will be established in Japan that will help to streamline clinical research as well as improve clinical treatments and long-term outcomes...
January 6, 2017: Neurologia Medico-chirurgica
https://www.readbyqxmd.com/read/28069558/from-genome-to-proteome-looking-beyond-dna-and-rna-in-chronic-lymphocytic-leukemia
#11
Lauren A Thurgood, Karen M Lower, Bryone J Kuss, Tim K Chataway
Chronic lymphocytic leukemia (CLL) remains the most common leukemia in the Western world. Whilst its disease course is extremely heterogeneous (ranging from indolent to aggressive), current methods are unable to accurately predict the clinical journey of each patient. There is clearly a pressing need for both improved prognostication and treatment options for patients with this disease.Whilst molecular studies have analyzed both genetic mutations and gene expression profiles of these malignant B-cells, and as a result have shed light on the pathogenesis of CLL, proteomic studies have been largely overlooked to date...
January 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28067027/high-density-lipoproteins-in-high-resolution-will-proteomics-solve-the-paradox-for-cardiovascular-risk
#12
Ferheen Baig, Abhishek Joshi, Manuel Mayr
While lipid abnormalities continue to account for over 60% of the population attributable for myocardial infarction, the well-known inverse correlation between plasma high-density lipoprotein cholesterol and cardiovascular risk has failed to deliver clinically useful therapeutic interventions. Thus, there is an unmet need to better understand the functionality of different high-density lipoprotein particles. Targeted high resolution lipoproteomics provides an innovative approach to studying the kinetics of high-density lipoprotein particles...
January 9, 2017: Proteomics
https://www.readbyqxmd.com/read/28065164/plasma-proteome-and-metabolome-characterization-of-an-experimental-human-thyrotoxicosis-model
#13
Maik Pietzner, Beatrice Engelmann, Tim Kacprowski, Janine Golchert, Anna-Luise Dirk, Elke Hammer, K Alexander Iwen, Matthias Nauck, Henri Wallaschofski, Dagmar Führer, Thomas F Münte, Nele Friedrich, Uwe Völker, Georg Homuth, Georg Brabant
BACKGROUND: Determinations of thyrotropin (TSH) and free thyroxine (FT4) represent the gold standard in evaluation of thyroid function. To screen for novel peripheral biomarkers of thyroid function and to characterize FT4-associated physiological signatures in human plasma we used an untargeted OMICS approach in a thyrotoxicosis model. METHODS: A sample of 16 healthy young men were treated with levothyroxine for 8 weeks and plasma was sampled before the intake was started as well as at two points during treatment and after its completion, respectively...
January 9, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28064424/gender-related-hippocampal-proteomics-study-from-young-rats-after-chronic-unpredicted-mild-stress-exposure
#14
Lin-Na Ning, Teng Zhang, Jiang Chu, Na Qu, Li Lin, Ying-Yan Fang, Yan Shi, Peng Zeng, Er-Li Cai, Xiao-Ming Wang, Qun Wang, You-Ming Lu, Xin-Wen Zhou, Qi Zhang, Qing Tian
Clinical data have shown women are more susceptible to depression. This study was performed to identify differentially regulated proteins from hippocampus in chronic unpredicted mild stress (CUMS)-exposed male and female young rats. After 7 weeks of CUMS, depressed male (M-D) and female rats (F-D) and unstressed male (M-C) and female controls (F-C) were studied. By proteomics analysis, 74 differential proteins in F-C/M-C, 79 in F-D/M-D, 77 in F-D/F-C, and 32 in M-D/M-C were found. Further, the synapse-related proteins, cytoskeleton protein tau, and stress-related kinases in hippocampus were assayed by Western blotting...
January 7, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28064163/predicting-albuminuria-response-to-spironolactone-treatment-with-urinary-proteomics-in-patients-with-type-2-diabetes-and-hypertension
#15
Morten Lindhardt, Frederik Persson, Christina Oxlund, Ib A Jacobsen, Petra Zürbig, Harald Mischak, Peter Rossing, Hiddo J L Heerspink
BACKGROUND: The mineralocorticoid receptor antagonist spironolactone significantly reduces albuminuria in patients with diabetes. Prior studies have shown large between-patient variability in albuminuria treatment response. We previously developed and validated a urinary proteomic classifier that predicts onset and progression of chronic kidney disease. Here, we tested whether the proteomic classifier based on 273 urinary peptides (CKD273) predicts albuminuria response to spironolactone treatment...
January 7, 2017: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/28061542/an-efficient-method-for-native-protein-purification-in-the-selected-range-from-prostate-cancer-tissue-digests
#16
Rumana Ahmad, Carrie D Nicora, Anil K Shukla, Richard D Smith, Wei-Jun Qian, Alvin Y Liu
BACKGROUND: Prostate cancer (CP) cells differ from their normal counterpart in gene expression. Genes encoding secreted or extracellular proteins with increased expression in CP may serve as potential biomarkers. For their detection and quantification, assays based on monoclonal antibodies are best suited for development in the clinical setting. One approach to obtain antibodies is to use recombinant proteins as immunogen. However, the synthesis of recombinant protein for each identified candidate is time-consuming and expensive...
December 2016: Chinese Clinical Oncology
https://www.readbyqxmd.com/read/28061466/prostate-cancer-proteomics-current-trends-and-future-perspectives-for-biomarker-discovery
#17
Cristiana Pistol Tanase, Elena Codrici, Ionela Daniela Popescu, Simona Mihai, Ana-Maria Enciu, Laura Georgiana Necula, Adrian Preda, Gener Ismail, Radu Albulescu
The clinical and fundamental research in prostate cancer - the most common urological cancer in men - is currently entering the proteomic and genomic era. The focus has switched from one single marker (PSA) to panels of biomarkers (including proteins involved in ribosomal function and heat shock proteins). Novel genetic markers (such as Transmembrane protease serine 2 (TMPRSS2)-ERG fusion gene mRNA) or prostate cancer gene 3 (PCA3) had already entered the clinical practice, raising the question whether subsequent protein changes impact the evolution of the disease and the response to treatment...
January 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28057717/pathology-driven-comprehensive-proteomic-profiling-of-the-prostate-cancer-tumour-microenvironment
#18
Lisa Staunton, Claire Tonry, Rosina Lis, Virginia Espina, Lance Liotta, Rosanna Inziatari, Michaela Bowden, Aurelie Fabre, John O'Leary, Stephen P Finn, Massimo Loda, Stephen R Pennington
: Prostate cancer (PCa) is the second most common cancer in men worldwide. Gleason grading is an important predictor of PCa outcomes and is influential in determining patient treatment options. Clinical decisions based on a Gleason score of 7 are difficult as the prognosis for individuals diagnosed with Gleason 4+3 cancer is much worse than for those diagnosed with Gleason 3+4 cancer. Laser capture microdissection (LCM) is a highly precise method to isolate specific cell populations or discrete microregions from tissues...
January 5, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28057495/iron-and-restless-legs-syndrome-treatment-genetics-and-pathophysiology
#19
James R Connor, Stephanie M Patton, Konrad Oexle, Richard Allen
In this article, we review the original findings from MRI and autopsy studies that demonstrated brain iron status is insufficient in individuals with restless legs syndrome (RLS). The concept of deficient brain iron status is supported by proteomic studies from cerebrospinal fluid (CSF) and from the clinical findings where intervention with iron, either dietary or intravenous, can improve RLS symptoms. Therefore, we include a section on peripheral iron status and how peripheral status may influence both the RLS symptoms and treatment strategy...
November 10, 2016: Sleep Medicine
https://www.readbyqxmd.com/read/28056859/molecular-chess-hallmarks-of-anti-cancer-drug-resistance
#20
REVIEW
Ian A Cree, Peter Charlton
BACKGROUND: The development of resistance is a problem shared by both classical chemotherapy and targeted therapy. Patients may respond well at first, but relapse is inevitable for many cancer patients, despite many improvements in drugs and their use over the last 40 years. REVIEW: Resistance to anti-cancer drugs can be acquired by several mechanisms within neoplastic cells, defined as (1) alteration of drug targets, (2) expression of drug pumps, (3) expression of detoxification mechanisms, (4) reduced susceptibility to apoptosis, (5) increased ability to repair DNA damage, and (6) altered proliferation...
January 5, 2017: BMC Cancer
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