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Clinical Proteomics

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https://read.qxmd.com/read/30774579/characterization-of-the-plasma-proteome-of-nonhuman-primates-during-ebola-virus-disease-or-melioidosis-a-host-response-comparison
#1
Michael D Ward, Ernst E Brueggemann, Tara Kenny, Raven E Reitstetter, Christopher R Mahone, Sylvia Trevino, Kelly Wetzel, Ginger C Donnelly, Cary Retterer, Robert B Norgren, Rekha G Panchal, Travis K Warren, Sina Bavari, Lisa H Cazares
Background: In-depth examination of the plasma proteomic response to infection with a wide variety of pathogens can assist in the development of new diagnostic paradigms, while providing insight into the interdependent pathogenic processes which encompass a host's immunological and physiological responses. Ebola virus (EBOV) causes a highly lethal infection termed Ebola virus disease (EVD) in primates and humans. The Gram negative non-spore forming bacillus Burkholderia pseudomallei ( Bp ) causes melioidosis in primates and humans, characterized by severe pneumonia with high mortality...
2019: Clinical Proteomics
https://read.qxmd.com/read/30774578/quantitative-proteomic-characterization-of-lung-tissue-in-idiopathic-pulmonary-fibrosis
#2
Yaqiong Tian, Hui Li, Yujuan Gao, Chuanmei Liu, Ting Qiu, Hongyan Wu, Mengshu Cao, Yingwei Zhang, Hui Ding, Jingyu Chen, Hourong Cai
Background: Idiopathic pulmonary fibrosis (IPF) is a progressive, eventually fatal disease. IPF is characterized by excessive accumulation of the extracellular matrix (ECM) in the alveolar parenchyma and progressive lung scarring. The pathogenesis of IPF and whether the ECM involved in the process remain unknown. Methods: To identify potential treatment target and ECM associated proteins that may be involved in the development of IPF, we employed isobaric tag for relative and absolute quantitation (iTRAQ) combined liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach to examine protein expression in lung tissues from IPF patients...
2019: Clinical Proteomics
https://read.qxmd.com/read/30733650/proteomic-analysis-of-plasma-exosomes-to-differentiate-malignant-from-benign-pulmonary-nodules
#3
Muyu Kuang, Xiaoting Tao, Yizhou Peng, Wenjing Zhang, Yafang Pan, Lei Cheng, Chongze Yuan, Yue Zhao, Hengyu Mao, Lingdun Zhuge, Zhenhua Zhou, Haiquan Chen, Yihua Sun
Background: It is difficult to distinguish benign pulmonary nodules (PNs) from malignant PNs by conventional examination. Therefore, novel biomarkers that can identify the nature of PNs are needed. Exosomes have recently been identified as an attractive alternative approach since tumor-specific molecules can be found in exosomes isolated from biological fluids. Methods: Plasma exosomes were extracted via the exoEasy reagent method. The major proteins from plasma exosomes in patients with PNs were identified via labelfree analysis and screened for differentially expressed proteins...
2019: Clinical Proteomics
https://read.qxmd.com/read/30718987/ulcerative-colitis-functional-analysis-of-the-in-depth-proteome
#4
Armin Schniers, Rasmus Goll, Yvonne Pasing, Sveinung Wergeland Sørbye, Jon Florholmen, Terkel Hansen
Background: Ulcerative colitis (UC) is one major form of inflammatory bowel disease. The cause and the pathophysiology of the disease are not fully understood and we therefor aim in this study to identify important pathophysiological features in UC from proteomics data. Methods: Colon mucosa biopsies from inflamed tissue of untreated UC patients at diagnosis and from healthy controls were obtained during colonoscopy. Quantitative protein data was acquired by bottom-up proteomics and furthermore processed with MaxQuant...
2019: Clinical Proteomics
https://read.qxmd.com/read/30679934/combination-of-laser-microdissection-2d-dige-and-maldi-tof-ms-to-identify-protein-biomarkers-to-predict-colorectal-cancer-spread
#5
Chandra Kirana, Lifeng Peng, Rose Miller, John P Keating, Corinne Glenn, Hongjun Shi, T William Jordan, Guy J Maddern, Richard S Stubbs
Biomarkers are urgently required to support current histological staging to provide additional accuracy in stratifying colorectal cancer (CRC) patients according to risk of spread to properly assign adjuvant chemotherapy after surgery. Chemotherapy is given to patients with stage III to reduce the risk of recurrence but is controversial in stage II patients. Up to 25% of stage II patients will relapse within 5 years after tumor removal and when this occurs cure is seldom possible. The aim of this study was to identify protein biomarkers to stratify risk of spread of CRC patients...
2019: Clinical Proteomics
https://read.qxmd.com/read/30675135/validation-of-a-novel-model-for-the-early-detection-of-hepatocellular-carcinoma
#6
Philip M Hemken, Lori J Sokoll, Xiaoqing Yang, Jianliang Dai, Debra Elliott, Susan H Gawel, Michael Lucht, Ziding Feng, Jorge A Marrero, Sudhir Srivastava, Daniel W Chan, Gerard J Davis
Background: The biomarkers alpha-fetoprotein (AFP) and protein induced by vitamin K absence/antagonist-II (PIVKA-II) may be useful for detecting early-stage hepatocellular carcinoma (HCC). We evaluated the performance of AFP and PIVKA-II levels, alone and in combination with clinical factors, for the early detection of HCC. Methods: In a case-control study, serum AFP and PIVKA-II were measured using the ARCHITECT immunoassay analyzer system in a cohort of 119 patients with HCC, 215 patients with non-malignant liver disease, and 34 healthy subjects...
2019: Clinical Proteomics
https://read.qxmd.com/read/30622446/high-accuracy-differentiating-autoimmune-pancreatitis-from-pancreatic-ductal-adenocarcinoma-by-immunoglobulin-g-glycosylation
#7
Hsi-Chang Shih, Ming-Chu Chang, Chein-Hung Chen, I-Lin Tsai, San-Yuan Wang, Ya-Po Kuo, Chung-Hsuan Chen, Yu-Ting Chang
Background: Misdiagnosis of autoimmune pancreatitis (AIP) as pancreatic cancer (PDAC) or vice versa can cause dismal patents' outcomes. Changes in IgG glycosylation are associated with cancers and autoimmune diseases. This study investigated the IgG glycosylation profiles as diagnostic and prognostic biomarkers in PDAC and AIP. Methods: Serum IgG-glycosylation profiles from 86 AIP patients, 115 PDAC patients, and 57 controls were analyzed using liquid chromatography-electrospray ionization mass spectrometry...
2019: Clinical Proteomics
https://read.qxmd.com/read/30618510/identification-of-cytauxzoon-felis-antigens-via-protein-microarray-and-assessment-of-expression-library-immunization-against-cytauxzoonosis
#8
Megan E Schreeg, Henry S Marr, Jaime L Tarigo, Meredith K Sherrill, Hilton K Outi, Elizabeth H Scholl, David M Bird, Adam Vigil, Chris Hung, Rie Nakajima, Li Liang, Angela Trieu, Denise L Doolan, Jennifer E Thomas, Michael G Levy, Mason V Reichard, Philip L Felgner, Leah A Cohn, Adam J Birkenheuer
Background: Cytauxzoonosis is a disease of felids in North America caused by the tick-transmitted apicomplexan parasite Cytauxzoon felis . Cytauxzoonosis is particularly virulent for domestic cats, but no vaccine currently exists. The parasite cannot be cultivated in vitro, presenting a significant limitation for vaccine development. Methods: Recent sequencing of the C. felis genome has identified over 4300 putative protein-encoding genes. From this pool we constructed a protein microarray containing 673 putative C...
2018: Clinical Proteomics
https://read.qxmd.com/read/30607141/fast-quantitative-urinary-proteomic-profiling-workflow-for-biomarker-discovery-in-kidney-cancer
#9
Lin Lin, Quan Yu, Jiaxin Zheng, Zonglong Cai, Ruijun Tian
Background: Urine has evolved as a promising body fluids in clinical proteomics because it can be easily and noninvasively obtained and can reflect physiological and pathological status of the human body. Many efforts have been made to characterize more urinary proteins in recent years, but few have focused on the analysis throughput and detection reproducibility. Increasing the urine proteomic profiling throughput and reproducibility is urgently needed for discovering potential biomarker in large cohorts...
2018: Clinical Proteomics
https://read.qxmd.com/read/30602943/proteomics-identification-of-radiation-induced-changes-of-membrane-proteins-in-the-rat-model-of-arteriovenous-malformation-in-pursuit-of-targets-for-brain-avm-molecular-therapy
#10
Margaret Simonian, Dyna Shirasaki, Vivienne S Lee, David Bervini, Michael Grace, Rachel R Ogorzalek Loo, Joseph A Loo, Mark P Molloy, Marcus A Stoodley
Background: Rapid identification of novel targets and advancement of a vascular targeting strategy requires a comprehensive assessment of AVM endothelial membrane protein changes in response to irradiation. The aim of this study is to provide additional potential target protein molecules for evaluation in animal trials to promote intravascular thrombosis in AVM vessels post radiosurgery. Methods: We employed in vivo biotinylation methodology that we developed, to label membrane proteins in the rat model of AVM post radiosurgery...
2018: Clinical Proteomics
https://read.qxmd.com/read/30598658/the-plasma-peptides-of-ovarian-cancer
#11
Jaimie Dufresne, Pete Bowden, Thanusi Thavarajah, Angelique Florentinus-Mefailoski, Zhuo Zhen Chen, Monika Tucholska, Tenzin Norzin, Margaret Truc Ho, Morla Phan, Nargiz Mohamed, Amir Ravandi, Eric Stanton, Arthur S Slutsky, Claudia C Dos Santos, Alexander Romaschin, John C Marshall, Christina Addison, Shawn Malone, Daren Heyland, Philip Scheltens, Joep Killestein, Charlotte E Teunissen, Eleftherios P Diamandis, K W Michael Siu, John G Marshall
Background: It may be possible to discover new diagnostic or therapeutic peptides or proteins from blood plasma by using liquid chromatography and tandem mass spectrometry to identify, quantify and compare the peptides cleaved ex vivo from different clinical populations. The endogenous tryptic peptides of ovarian cancer plasma were compared to breast cancer and female cancer normal controls, other diseases with their matched or normal controls, plus ice cold plasma to control for pre-analytical variation...
2018: Clinical Proteomics
https://read.qxmd.com/read/30598657/proteomic-analysis-of-serum-proteins-from-hiv-aids-patients-with-talaromyces-marneffei-infection-by-tmt-labeling-based-quantitative-proteomics
#12
Yahong Chen, Aiqiong Huang, Wen Ao, Zhengwu Wang, Jinjin Yuan, Qing Song, Dahai Wei, Hanhui Ye
Background: Talaromyces marneffei (TM) is an emerging pathogenic fungus that can cause a fatal systemic mycosis in patients infected with human immunodeficiency virus (HIV). Although global awareness regarding HIV/TM coinfection is increasing little is known about the mechanism that mediates the rapid progression to HIV/AIDS disease in coinfected individuals. The aim of this study was to analyze the serum proteome of HIV/TM coinfected patients and to identify the associated protein biomarkers for TM in patients with HIV/AIDS...
2018: Clinical Proteomics
https://read.qxmd.com/read/30519149/the-plasma-peptidome
#13
Jaimie Dufresne, Pete Bowden, Thanusi Thavarajah, Angelique Florentinus-Mefailoski, Zhuo Zhen Chen, Monika Tucholska, Tenzin Norzin, Margaret Truc Ho, Morla Phan, Nargiz Mohamed, Amir Ravandi, Eric Stanton, Arthur S Slutsky, Claudia C Dos Santos, Alexander Romaschin, John C Marshall, Christina Addison, Shawn Malone, Daren Heyland, Philip Scheltens, Joep Killestein, Charlotte Teunissen, Eleftherios P Diamandis, K W M Siu, John G Marshall
Background: It may be possible to discover new diagnostic or therapeutic peptides or proteins from blood plasma using LC-ESI-MS/MS to identify, with a linear quadrupole ion trap to identify, quantify and compare the statistical distributions of peptides cleaved ex vivo from plasma samples from different clinical populations. Methods: A systematic method for the organic fractionation of plasma peptides was applied to identify and quantify the endogenous tryptic peptides from human plasma from multiple institutions by C18 HPLC followed nano electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) with a linear quadrupole ion trap...
2018: Clinical Proteomics
https://read.qxmd.com/read/30519148/a-two-step-strategy-for-identification-of-plasma-protein-biomarkers-for-endometrial-and-ovarian-cancer
#14
Stefan Enroth, Malin Berggrund, Maria Lycke, Martin Lundberg, Erika Assarsson, Matts Olovsson, Karin Stålberg, Karin Sundfeldt, Ulf Gyllensten
Background: Over 500,000 women worldwide are diagnosed with ovarian or endometrial cancer each year. We have used a two-step strategy to identify plasma proteins that could be used to improve the diagnosis of women with an indication of gynecologic tumor and in population screening. Methods: In the discovery step we screened 441 proteins in plasma using the proximity extension assay (PEA) and five Olink Multiplex assays (CVD II, CVD III, INF I, ONC II, NEU I) in women with ovarian cancer (n = 106), endometrial cancer (n = 74), benign ovarian tumors (n = 150) and healthy population controls (n = 399)...
2018: Clinical Proteomics
https://read.qxmd.com/read/30479584/correction-to-quantitative-phosphoproteomic-analysis-reveals-reciprocal-activation-of-receptor-tyrosine-kinases-between-cancer-epithelial-cells-and-stromal-fibroblasts
#15
Xinyan Wu, Muhammad Saddiq Zahari, Santosh Renuse, Nandini A Sahasrabuddhe, Raghothama Chaerkady, Mi-Sik Kim, Mary Jo Fackler, Martha Stampfer, Edward Gabrielson, Saraswati Sukumar, Akhilesh Pandey
[This corrects the article DOI: 10.1186/s12014-018-9197-x.].
2018: Clinical Proteomics
https://read.qxmd.com/read/30479583/differential-analysis-of-quantitative-proteome-and-acetyl-proteome-profiling-between-premenopausal-and-postmenopausal-ovarian-tissues
#16
Jinling Yi, Huatianshu Hu, Peipei Shi, Song Shi, Junda Zhao, Linna Xu, Weining Yang, Bin Li, Jin Zhu, Shien Zou
Background: Natural menopause is always accompanied by specific signs and symptoms, suggesting physiological changes in this peoriod. However, no systematic study has assessed the changes at molecular level in the ovaries during the menopausal transition so far. This study integrated quantitative proteome and acetyl-proteome to comprehensively uncover the changes of ovarian protein and protein-acetylation profiles in this transitional period. The findings would provide novel insights into the biology of menopause and help relieve and treat the associated signs and symptoms, further improving the women's health care...
2018: Clinical Proteomics
https://read.qxmd.com/read/30410428/using-matrix-assisted-laser-desorption-ionisation-mass-spectrometry-maldi-ms-profiling-in-order-to-predict-clinical-outcomes-of-patients-with-heart-failure
#17
Thong Huy Cao, Donald J L Jones, Paulene A Quinn, Daniel Chu Siong Chan, Narayan Hafid, Helen M Parry, Mohapradeep Mohan, Jatinderpal K Sandhu, Stefan D Anker, John G Cleland, Kenneth Dickstein, Gerasimos Filippatos, Hans L Hillege, Marco Metra, Piotr Ponikowski, Nilesh J Samani, Dirk J Van Veldhuisen, Faiez Zannad, Aeilko H Zwinderman, Adriaan A Voors, Chim C Lang, Leong L Ng
Background: Current risk prediction models in heart failure (HF) including clinical characteristics and biomarkers only have moderate predictive value. The aim of this study was to use matrix assisted laser desorption ionisation mass spectrometry (MALDI-MS) profiling to determine if a combination of peptides identified with MALDI-MS will better predict clinical outcomes of patients with HF. Methods: A cohort of 100 patients with HF were recruited in the biomarker discovery phase (50 patients who died or had a HF hospital admission vs...
2018: Clinical Proteomics
https://read.qxmd.com/read/30386187/proteomic-profiling-of-liver-tissue-from-the-mdx-4cv-mouse-model-of-duchenne-muscular-dystrophy
#18
Sandra Murphy, Margit Zweyer, Michael Henry, Paula Meleady, Rustam R Mundegar, Dieter Swandulla, Kay Ohlendieck
Background: Duchenne muscular dystrophy is a highly complex multi-system disease caused by primary abnormalities in the membrane cytoskeletal protein dystrophin. Besides progressive skeletal muscle degeneration, this neuromuscular disorder is also associated with pathophysiological perturbations in many other organs including the liver. To determine potential proteome-wide alterations in liver tissue, we have used a comparative and mass spectrometry-based approach to study the dystrophic mdx - 4cv mouse model of dystrophinopathy...
2018: Clinical Proteomics
https://read.qxmd.com/read/30323719/quality-assessment-and-interference-detection-in-targeted-mass-spectrometry-data-using-machine-learning
#19
Shadi Toghi Eshghi, Paul Auger, W Rodney Mathews
Advances in the field of targeted proteomics and mass spectrometry have significantly improved assay sensitivity and multiplexing capacity. The high-throughput nature of targeted proteomics experiments has increased the rate of data production, which requires development of novel analytical tools to keep up with data processing demand. Currently, development and validation of targeted mass spectrometry assays require manual inspection of chromatographic peaks from large datasets to ensure quality, a process that is time consuming, prone to inter- and intra-operator variability and limits the efficiency of data interpretation from targeted proteomics analyses...
2018: Clinical Proteomics
https://read.qxmd.com/read/30258344/investigation-of-post-translational-modifications-in-type-2-diabetes
#20
REVIEW
Bhaswati Chatterjee, Suman S Thakur
The investigation of post-translational modifications (PTMs) plays an important role for the study of type 2 diabetes. The importance of PTMs has been realized with the advancement of analytical techniques. The challenging detection and analysis of post-translational modifications is eased by different enrichment methods and by high throughput mass spectrometry based proteomics studies. This technology along with different quantitation methods provide accurate knowledge about the changes happening in disease conditions as well as in normal conditions...
2018: Clinical Proteomics
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