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Clinical Proteomics

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https://www.readbyqxmd.com/read/29449793/clinical-proteomic-analysis-of-scrub-typhus-infection
#1
Edmond Changkyun Park, Sang-Yeop Lee, Sung Ho Yun, Chi-Won Choi, Hayoung Lee, Hyun Seok Song, Sangmi Jun, Gun-Hwa Kim, Chang-Seop Lee, Seung Il Kim
Background: Scrub typhus is an acute and febrile infectious disease caused by the Gram-negative α-proteobacterium Orientia tsutsugamushi from the family Rickettsiaceae that is widely distributed in Northern, Southern and Eastern Asia. In the present study, we analysed the serum proteome of scrub typhus patients to investigate specific clinical protein patterns in an attempt to explain pathophysiology and discover potential biomarkers of infection. Methods: Serum samples were collected from three patients (before and after treatment with antibiotics) and three healthy subjects...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29445323/urine-proteomics-of-primary-membranous-nephropathy-using-nanoscale-liquid-chromatography-tandem-mass-spectrometry-analysis
#2
Lu Pang, Qianqian Li, Yan Li, Yi Liu, Nan Duan, Haixia Li
Background: Primary membranous nephropathy (PMN) is an important cause of nephrotic syndrome in adults. Urine proteome may provide important clues of pathophysiological mechanisms in PMN. In the current study, we analyzed and compared the proteome of urine from patients with PMN and normal controls. Methods: We performed two technical replicates (TMT1 and TMT2) to analyze and compare the urine proteome from patients with PMN and normal controls by tandem mass tag (TMT) technology coupled with nanoscale liquid chromatography tandem mass spectrometry analysis (LC-MS/MS)...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29416445/the-cancer-proteomic-landscape-and-the-hupo-cancer-proteome-project
#3
Connie R Jimenez, Hui Zhang, Christopher R Kinsinger, Edouard C Nice
The Human Cancer Proteome Project (Cancer-HPP) is an international initiative organized by HUPO whose key objective is to decipher the human cancer proteome through a coordinated effort by cancer proteome researchers around the world. The ultimate goal is to map the entire human cancer proteome to disclose tumor biology and drive improved diagnostics, treatment and management of cancer. Here we report the progress in the cancer proteomics field to date, and discuss future proteomic developments that will be needed to optimally delineate cancer phenotypes and advance the molecular characterization of this significant disease that is one of the leading causes of death worldwide...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29344009/evaluation-of-nipple-aspirate-fluid-as-a-diagnostic-tool-for-early-detection-of-breast-cancer
#4
REVIEW
Sadr-Ul Shaheed, Catherine Tait, Kyriacos Kyriacou, Richard Linforth, Mohamed Salhab, Chris Sutton
There has been tremendous progress in detection of breast cancer in postmenopausal women, resulting in two-thirds of women surviving more than 20 years after treatment. However, breast cancer remains the leading cause of cancer-related deaths in premenopausal women. Breast cancer is increasing in younger women due to changes in life-style as well as those at high risk as carriers of mutations in high-penetrance genes. Premenopausal women with breast cancer are more likely to be diagnosed with aggressive tumours and therefore have a lower survival rate...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29321722/distinct-virulent-network-between-healthcare-and-community-associated-staphylococcus-aureus-based-on-proteomic-analysis
#5
Lei He, Hongwei Meng, Qian Liu, Mo Hu, Yanan Wang, Xiaoying Chen, Xiaoyun Liu, Min Li
Background: Staphylococcus aureus (S. aureus or SA) is a leading cause of healthcare-associated (HA-) and community-associated (CA) infection. HA-SA isolates usually cause nosocomial pneumonia, bloodstream infections, catheter-related urinary tract infections, etc. On the other hand, CA-SA isolates usually cause highly fatal diseases, such as SSTIs as well as post influenza necrotic hemorrhagic pneumonia. The differences of the infection types are partially due to the unique characteristics between HA-SA and CA-SA isolates...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29321721/antigen-85b-peptidomic-analysis-allows-species-specific-mycobacterial-identification
#6
Wei Zhang, Qingbo Shu, Zhen Zhao, Jia Fan, Christopher J Lyon, Adrian M Zelazny, Ye Hu
Background: Nontuberculous mycobacteria (NTM)-mediated infections are a growing cause of worldwide morbidity, but lack of rapid diagnostics for specific NTM species can delay the initiation of appropriate treatment regimens. We thus examined whether mass spectrometry analysis of an abundantly secreted mycobacterial antigen could identify specific NTM species. Methods: We analyzed predicted tryptic peptides of the major mycobacterial antigen Ag85B for their capacity to distinguish Mycobacterium tuberculosis and three NTM species responsible for the majority of pulmonary infections caused by slow-growing mycobacterial species...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29234243/random-and-independent-sampling-of-endogenous-tryptic-peptides-from-normal-human-edta-plasma-by-liquid-chromatography-micro-electrospray-ionization-and-tandem-mass-spectrometry
#7
Jaimie Dufresne, Angelique Florentinus-Mefailoski, Juliet Ajambo, Ammara Ferwa, Peter Bowden, John Marshall
Background: Normal human EDTA plasma samples were collected on ice, processed ice cold, and stored in a freezer at - 80 °C prior to experiments. Plasma test samples from the - 80 °C freezer were thawed on ice or intentionally warmed to room temperature. Methods: Protein content was measured by CBBR binding and the release of alcohol soluble amines by the Cd ninhydrin assay. Plasma peptides released over time were collected over C18 for random and independent sampling by liquid chromatography micro electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) and correlated with X!TANDEM...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29225558/vulvar-squamous-cell-carcinoma-aggressiveness-is-associated-with-differential-expression-of-collagen-and-stat1
#8
Emily R Holthoff, Stephanie D Byrum, Samuel G Mackintosh, Thomas Kelly, Alan J Tackett, Charles M Quick, Steven R Post
Background: Vulvar squamous cell carcinoma (vSCC) is a rare but debilitating disease. One vSCC variant comprises tumor cells that grow and expand as a cohesive sheet of cells that "pushes" and compresses the associated lymphoplasmacytic (LPC) stroma. Another vSCC variant features tumor cells that grow in loose association with one another and infiltrate the associated fibromyxoid (FMX) stroma consisting mainly of extracellular matrix. Clinically, infiltrative vSCC with FMX stroma (Inf/FMX) is significantly associated with lymph node metastases and recurrence...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29213220/the-proteins-cleaved-by-endogenous-tryptic-proteases-in-normal-edta-plasma-by-c18-collection-of-peptides-for-liquid-chromatography-micro-electrospray-ionization-and-tandem-mass-spectrometry
#9
Jaimie Dufresne, Angelique Florentinus-Mefailoski, Juliet Ajambo, Ammara Ferwa, Peter Bowden, John Marshall
The tryptic peptides from ice cold versus room temperature plasma were identified by C18 liquid chromatography and micro electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). Samples collected on ice showed low levels of endogenous tryptic peptides compared to the same samples incubated at room temperature. Plasma on ice contained peptides from albumin, complement, and apolipoproteins and others that were observed by the X!TANDEM and SEQUEST algorithms. In contrast to ice cold samples, after incubation at room temperature, greater numbers of tryptic peptides from well characterized plasma proteins, and from cellular proteins were observed...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29209155/optimization-of-quantitative-proteomic-analysis-of-clots-generated-from-plasma-of-patients-with-venous-thromboembolism
#10
Aneta Stachowicz, Jakub Siudut, Maciej Suski, Rafał Olszanecki, Ryszard Korbut, Anetta Undas, Jacek R Wiśniewski
Background: It is well known that fibrin network binds a large variety of proteins, including inhibitors and activators of fibrinolysis, which may affect clot properties, such as stability and susceptibility to fibrinolysis. Specific plasma clot composition differs between individuals and may change in disease states. However, the plasma clot proteome has not yet been in-depth analyzed, mainly due to technical difficulty related to the presence of a highly abundant protein-fibrinogen and fibrin that forms a plasma clot...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29176938/a-proteomic-approach-to-understanding-the-pathogenesis-of-idiopathic-macular-hole-formation
#11
Pingbo Zhang, Min Zhu, Yuming Zhao, Jiang Qian, Craig Dufresne, Randi Turner, Richard D Semba, Sharon D Solomon
Idiopathic macular holes (IMH) are full-thickness defects of retinal tissue that cause severe vision loss due to disruption of the anatomic fovea. Abnormal vitreous traction is involved in the formation of macular holes. Both glial cells and hyalocytes contribute to epiretinal membrane formation in IMH. In order to gain further insight into the pathophysiology of IMH, we conducted a discovery phase investigation of the vitreous proteome in four patients with macular holes and six controls using one-dimensional gel fractionation and liquid chromatography-tandem mass spectrometry analyses on an Orbitrap Elite mass spectrometer...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29176937/proteomic-profiling-identifies-markers-for-inflammation-related-tumor-fibroblast-interaction
#12
Daniel Drev, Andrea Bileck, Zeynep N Erdem, Thomas Mohr, Gerald Timelthaler, Andrea Beer, Christopher Gerner, Brigitte Marian
Background: Cancer associated fibroblasts are activated in the tumor microenvironment and contribute to tumor progression, angiogenesis, extracellular matrix remodeling, and inflammation. Methods: To identify proteins characteristic for fibroblasts in colorectal cancer we used liquid chromatography-tandem mass spectrometry to derive protein abundance from whole-tissue homogenates of human colorectal cancer/normal mucosa pairs. Alterations of protein levels were determined by two-sided t test with greater than threefold difference and an FDR of < 0...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29142508/proteomic-characterisation-of-bovine-and-avian-purified-protein-derivatives-and-identification-of-specific-antigens-for-serodiagnosis-of-bovine-tuberculosis
#13
José Antonio Infantes-Lorenzo, Inmaculada Moreno, María de Los Ángeles Risalde, Álvaro Roy, Margarita Villar, Beatriz Romero, Nieves Ibarrola, José de la Fuente, Eugenia Puentes, Lucía de Juan, Christian Gortázar, Javier Bezos, Lucas Domínguez, Mercedes Domínguez
Background: Bovine purified protein derivative (bPPD) and avian purified protein derivative (aPPD) are widely used for bovine tuberculosis diagnosis. However, little is known about their qualitative and quantitative characteristics, which makes their standardisation difficult. In addition, bPPD can give false-positive tuberculosis results because of sequence homology between Mycobacterium bovis (M. bovis) and M. avium proteins. Thus, the objective of this study was to carry out a proteomic characterisation of bPPD, aPPD and an immunopurified subcomplex from bPPD called P22 in order to identify proteins contributing to cross-reactivity among these three products in tuberculosis diagnosis...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29093647/freeze-dried-plasma-proteins-are-stable-at-room-temperature-for-at-least-1-year
#14
Jaimie Dufresne, Trung Hoang, Juliet Ajambo, Angelique Florentinus-Mefailoski, Peter Bowden, John Marshall
Thirty human EDTA plasma samples from male and female subjects ranging in age from 24 to 74 years were collected on ice, processed ice cold and stored frozen at -80 °C, in liquid nitrogen (LN2), or freeze dried and stored at room temperature in a desiccator (FDRT) or freeze dried and stored at -20 °C for 1 year (FD-20). In a separate experiment, EDTA plasma samples were collected onto ice, processed ice cold and maintained on ice ± protease inhibitors versus incubated at room temperature for up to 96 h...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29051715/a-multiplex-platform-for-the-identification-of-ovarian-cancer-biomarkers
#15
Kristin L M Boylan, Kate Geschwind, Joseph S Koopmeiners, Melissa A Geller, Timothy K Starr, Amy P N Skubitz
BACKGROUND: Currently, there are no FDA approved screening tools for detecting early stage ovarian cancer in the general population. Development of a biomarker-based assay for early detection would significantly improve the survival of ovarian cancer patients. METHODS: We used a multiplex approach to identify protein biomarkers for detecting early stage ovarian cancer. This new technology (Proseek(®) Multiplex Oncology Plates) can simultaneously measure the expression of 92 proteins in serum based on a proximity extension assay...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29026368/serum-protein-pattern-associated-with-organ-damage-and-lupus-nephritis-in-systemic-lupus-erythematosus-revealed-by-pea-immunoassay
#16
Anna Petrackova, Andrea Smrzova, Petr Gajdos, Marketa Schubertova, Petra Schneiderova, Pavel Kromer, Vaclav Snasel, Martina Skacelova, Frantisek Mrazek, Josef Zadrazil, Pavel Horak, Eva Kriegova
BACKGROUND: Systemic lupus erythematosus (SLE) is a remarkably heterogeneous autoimmune disease. Despite tremendous efforts, our knowledge of serum protein patterns in severe SLE phenotypes is still limited. We investigated the serum protein pattern of SLE, with special emphasis on irreversible organ damage and active lupus nephritis (LN) as assessed by renal Systemic Lupus Erythematosus Disease Activity Index. METHODS: We used proximity extension immunoassay (PEA, Proseek Multiplex, Olink) to assess the serum levels of ninety-two inflammation-related proteins in Czech patients with SLE (n = 75) and age-matched healthy control subjects (n = 23)...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28814946/protein-signatures-of-molecular-pathways-in-non-small-cell-lung-carcinoma-nsclc-comparison-of-glycoproteomics-and-global-proteomics
#17
Shuang Yang, Lijun Chen, Daniel W Chan, Qing Kay Li, Hui Zhang
BACKGROUND: Non-small cell lung carcinoma (NSCLC) remains the leading cause of cancer deaths in the United States. More than half of NSCLC patients have clinical presentations with locally advanced or metastatic disease at the time of diagnosis. The large-scale genomic analysis of NSCLC has demonstrated that molecular alterations are substantially different between adenocarcinoma (ADC) and squamous cell carcinoma (SqCC). However, a comprehensive analysis of proteins and glycoproteins in different subtypes of NSCLC using advanced proteomic approaches has not yet been conducted...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28814945/glomerular-abundance-of-complement-proteins-characterized-by-proteomic-analysis-of-laser-captured-microdissected-glomeruli-associates-with-progressive-disease-in-iga-nephropathy
#18
Teodora Ioana Flavia Paunas, Kenneth Finne, Sabine Leh, Hans-Peter Marti, Tom Eirik Mollnes, Frode Berven, Bjørn Egil Vikse
BACKGROUND: The clinical course of IgA nephropathy (IgAN) is variable and complement activation may predict prognosis. The present study investigated whether glomerular abundance of complement proteins associates with progression to end-stage renal disease (ESRD) in patients for whom prognosis could not be predicted based on clinical variables. METHODS: Based on data from the Norwegian Kidney Biopsy Registry and the Norwegian Renal Registry, three groups were included: IgAN patients with (n = 9) or without (n = 16) progression to ESRD during 10 years, and controls (n = 15) with a normal kidney biopsy...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28785178/down-regulation-of-metabolic-proteins-in-hepatocellular-carcinoma-with-portal-vein-thrombosis
#19
Wei-Chen Lee, Hong-Shiue Chou, Ting-Jung Wu, Chen-Fang Lee, Pao-Yueh Hsu, Hsiu-Ying Hsu, Tsung-Han Wu, Kun-Ming Chan
BACKGROUND: Hepatocellular carcinoma is an aggressive malignancy with poor prognosis and easy to recur even the tumor is totally removed by surgery. Portal vascular invasion is one of the major factors contributing to tumor recurrence and poor prognosis. However, why hepatocellular carcinoma is easy to grow into vessels is unclear. METHODS: Surgical specimens from seven hepatocellular carcinoma patients with portal vein thrombosis and seven patients without vascular invasion were utilized to analyze protein expression by proteomic technique...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28769740/discovery-and-validation-of-a-colorectal-cancer-classifier-in-a-new-blood-test-with-improved-performance-for-high-risk-subjects
#20
Lisa J Croner, Roslyn Dillon, Athit Kao, Stefanie N Kairs, Ryan Benz, Ib J Christensen, Hans J Nielsen, John E Blume, Bruce Wilcox
BACKGROUND: The aim was to improve upon an existing blood-based colorectal cancer (CRC) test directed to high-risk symptomatic patients, by developing a new CRC classifier to be used with a new test embodiment. The new test uses a robust assay format-electrochemiluminescence immunoassays-to quantify protein concentrations. The aim was achieved by building and validating a CRC classifier using concentration measures from a large sample set representing a true intent-to-test (ITT) symptomatic population...
2017: Clinical Proteomics
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