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Clinical Proteomics

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https://www.readbyqxmd.com/read/29983670/cd44-glycoprotein-in-cancer-a-molecular-conundrum-hampering-clinical-applications
#1
Rita Azevedo, Cristiana Gaiteiro, Andreia Peixoto, Marta Relvas-Santos, Luís Lima, Lúcio Lara Santos, José Alexandre Ferreira
CD44 is a heavily glycosylated membrane receptor playing a key role in cell adhesion, signal transduction and cytoskeleton remodelling. It is also one of the most studied glycoproteins in cancer, frequently explored for stem cell identification, and associated with chemoresistance and metastasis. However, CD44 is a general designation for a large family of splicing variants exhibiting different degrees of glycosylation and, potentially, functionally distinct roles. Moreover, structural diversity associated with ambiguous nomenclature has delayed clinical developments...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29946230/quantitative-phosphoproteomic-analysis-reveals-reciprocal-activation-of-receptor-tyrosine-kinases-between-cancer-epithelial-cells-and-stromal-fibroblasts
#2
Xinyan Wu, Muhammad Saddiq Zahari, Santosh Renuse, Nandini A Sahasrabuddhe, Raghothama Chaerkady, Min-Sik Kim, Mary Jo Fackler, Martha Stampfer, Edward Gabrielson, Saraswati Sukumar, Akhilesh Pandey
Background: Cancer-associated fibroblasts (CAFs) are one of the most important components of tumor stroma and play a key role in modulating tumor growth. However, a mechanistic understanding of how CAFs communicate with tumor cells to promote their proliferation and invasion is far from complete. A major reason for this is that most current techniques and model systems do not capture the complexity of signal transduction that occurs between CAFs and tumor cells. Methods: In this study, we employed a stable isotope labeling with amino acids in cell culture (SILAC) strategy to label invasive breast cancer cells, MDA-MB-231, and breast cancer patient-derived CAF this has already been defined above cells...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29760600/comprehensive-proteome-analysis-of-nasal-lavage-samples-after-controlled-exposure-to-welding-nanoparticles-shows-an-induced-acute-phase-and-a-nuclear-receptor-lxr-rxr-activation-that-influence-the-status-of-the-extracellular-matrix
#3
Neserin Ali, Stefan Ljunggren, Helen M Karlsson, Aneta Wierzbicka, Joakim Pagels, Christina Isaxon, Anders Gudmundsson, Jenny Rissler, Jörn Nielsen, Christian H Lindh, Monica Kåredal
Background: Epidemiological studies have shown that many welders experience respiratory symptoms. During the welding process a large number of airborne nanosized particles are generated, which might be inhaled and deposited in the respiratory tract. Knowledge of the underlying mechanisms behind observed symptoms is still partly lacking, although inflammation is suggested to play a central role. The aim of this study was to investigate the effects of welding fume particle exposure on the proteome expression level in welders suffering from respiratory symptoms, and changes in protein mediators in nasal lavage samples were analyzed...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29719495/comparative-analysis-of-human-sperm-glycocalyx-from-different-freezability-ejaculates-by-lectin-microarray-and-identification-of-aba-as-sperm-freezability-biomarker
#4
Ai-Jie Xin, Yan-Cheng Wu, Hui Lu, Li Cheng, Yi-Hua Gu, Hua Diao, Guo-Wu Chen, Bin Wu, Zheng Li, Sheng-Ce Tao, Xiao-Xi Sun, Hui-Juan Shi
Background: Semen cryopreservation has been widely applied in assisted reproductive technologies and sperm bank, but it causes considerable impairments on sperm quality. It is necessary to find an evaluation indicator for determining the sperm-freezing tolerance. Methods: The glycocalyx of good freezability ejaculates was compared with poor freezability ejaculates by lectin microarray. The significant different lectins were validated by flow cytometry (FACS). To analyze the relationship between the potential biomarker and the tolerance of sperm to cryopreservation, 60 samples with different recovery rates were collected and detected the lectin-binding intensity by FACS...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29719494/identification-of-serum-proteins-ahsg-fga-and-apoa-i-as-diagnostic-biomarkers-for-gastric-cancer
#5
Feiyu Shi, Hong Wu, Kai Qu, Qi Sun, Fanni Li, Chengxin Shi, Yaguang Li, Xiaofan Xiong, Qian Qin, Tianyu Yu, Xin Jin, Liang Cheng, Qingxia Wei, Yingchao Li, Junjun She
Background: The development of clinically accessible biomarkers is critical for the early diagnosis of gastric cancer (GC) in patients. High-throughput proteomics techniques could not only effectively generate a serum peptide profile but also provide a new approach to identify potentially diagnostic and prognostic biomarkers for cancer patients. Methods: In this study, we aim to identify potentially discriminating serum biomarkers for GC. In the discovery cohort, we screened potential biomarkers using magnetic-bead-based purification and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in 64 samples from 32 GC patients that were taken both pre- and post-operatively and 30 healthy volunteers that served as controls...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29713252/quantitative-proteomic-analysis-of-pancreatic-cyst-fluid-proteins-associated-with-malignancy-in-intraductal-papillary-mucinous-neoplasms
#6
Misol Do, Dohyun Han, Joseph Injae Wang, Hyunsoo Kim, Wooil Kwon, Youngmin Han, Jin-Young Jang, Youngsoo Kim
Background: The application of advanced imaging technologies for identifying pancreatic cysts has become widespread. However, accurately differentiating between low-grade dysplasia (LGD), high-grade dysplasia (HGD), and invasive intraductal papillary mucinous neoplasms (IPMNs) remains a diagnostic challenge with current biomarkers, necessitating the development of novel biomarkers that can distinguish IPMN malignancy. Methods: Cyst fluid samples were collected from nine IPMN patients (3 LGD, 3 HGD, and 3 invasive IPMN) during their pancreatectomies...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29681787/the-response-to-neoadjuvant-chemoradiotherapy-with-5-fluorouracil-in-locally-advanced-rectal-cancer-patients-a-predictive-proteomic-signature
#7
Anaïs Chauvin, Chang-Shu Wang, Sameh Geha, Perrine Garde-Granger, Alex-Ane Mathieu, Vincent Lacasse, François-Michel Boisvert
Background: Colorectal cancer is the third most common and the fourth most lethal cancer in the world. In the majority of cases, patients are diagnosed at an advanced stage or even metastatic, thus explaining the high mortality. The standard treatment for patients with locally advanced non-metastatic rectal cancer is neoadjuvant radio-chemotherapy (NRCT) with 5-fluorouracil (5-FU) followed by surgery, but the resistance rate to this treatment remains high with approximately 30% of non-responders...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29657559/activation-peptide-of-the-coagulation-factor-xiii-ap-f13a1-as-a-new-biomarker-for-the-screening-of-colorectal-cancer
#8
Julien Peltier, Jean-Pierre Roperch, Stéphane Audebert, Jean-Paul Borg, Luc Camoin
Background: Colorectal cancer (CRC) remains a major cause of cancer fatalities in developed countries. The risk of death is correlated to the stage of CRC during the primary diagnosis. Early diagnosis is closely associated with enhanced survival rate. We therefore investigated the AP-F13A1 as a potential protein marker of CRC. Methods: The protein expression of FXIII in 40 serum samples was evaluated by enzyme-linked immunosorbent assays. Additionally, targeted proteomic assays (LC-PRM) were used to evaluate the expression of the activation peptide of F13A1 (AP-F13A1) in a further 113 serum samples...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29588628/a-robust-mass-spectrometry-method-for-rapid-profiling-of-erythrocyte-ghost-membrane-proteomes
#9
Haddy K S Fye, Paul Mrosso, Lesley Bruce, Marie-Laëtitia Thézénas, Simon Davis, Roman Fischer, Gration L Rwegasira, Julie Makani, Benedikt M Kessler
Background: Red blood cell (RBC) physiology is directly linked to many human disorders associated with low tissue oxygen levels or anemia including chronic obstructive pulmonary disease, congenital heart disease, sleep apnea and sickle cell anemia. Parasites such as Plasmodium spp. and phylum Apicomplexa directly target RBCs, and surface molecules within the RBC membrane are critical for pathogen interactions. Proteomics of RBC membrane 'ghost' fractions has therefore been of considerable interest, but protocols described to date are either suboptimal or too extensive to be applicable to a larger set of clinical cohorts...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29541007/proteomics-based-insights-into-mitogen-activated-protein-kinase-inhibitor-resistance-of-cerebral-melanoma-metastases
#10
Nina Zila, Andrea Bileck, Besnik Muqaku, Lukas Janker, Ossia M Eichhoff, Phil F Cheng, Reinhard Dummer, Mitchell P Levesque, Christopher Gerner, Verena Paulitschke
Background: MAP kinase inhibitor (MAPKi) therapy for BRAF mutated melanoma is characterized by high response rates but development of drug resistance within a median progression-free survival (PFS) of 9-12 months. Understanding mechanisms of resistance and identifying effective therapeutic alternatives is one of the most important scientific challenges in melanoma. Using proteomics, we want to specifically gain insight into the pathophysiological process of cerebral metastases. Methods: Cerebral metastases from melanoma patients were initially analyzed by a LC-MS shotgun approach performed on a QExactive HF hybrid quadrupole-orbitrap mass spectrometer...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29541006/change-of-ranibizumab-induced-human-vitreous-protein-profile-in-patients-with-proliferative-diabetic-retinopathy-based-on-proteomics-analysis
#11
Chen Zou, Changjing Han, Minjie Zhao, Jingjing Yu, Lin Bai, Yuan Yao, Shuaixin Gao, Hui Cao, Zhi Zheng
Background: Preoperative treatment of anti-vascular endothelial growth factor (VEGF) agents is extensively used in proliferative diabetic retinopathy (PDR), but the molecular mechanism is not fully understood. The objective of this research is to observe change of protein profile induced by ranibizumab (an anti-VEGF agent) in vitreous humor from PDR patients and reveal the effects of anti-VEGF treatment on PDR. Methods: A proteomic method was used to identify differentially expressed proteins in vitreous humor...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29527141/reproducible-proteomics-sample-preparation-for-single-ffpe-tissue-slices-using-acid-labile-surfactant-and-direct-trypsinization
#12
Melanie Christine Föll, Matthias Fahrner, Victor Oginga Oria, Markus Kühs, Martin Lothar Biniossek, Martin Werner, Peter Bronsert, Oliver Schilling
Background: Proteomic analyses of clinical specimens often rely on human tissues preserved through formalin-fixation and paraffin embedding (FFPE). Minimal sample consumption is the key to preserve the integrity of pathological archives but also to deal with minimal invasive core biopsies. This has been achieved by using the acid-labile surfactant RapiGest in combination with a direct trypsinization (DTR) strategy. A critical comparison of the DTR protocol with the most commonly used filter aided sample preparation (FASP) protocol is lacking...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29527140/proteomic-characterization-of-high-density-lipoprotein-particles-in-patients-with-non-alcoholic-fatty-liver-disease
#13
Prahlad K Rao, Kate Merath, Eugene Drigalenko, Avinash Y L Jadhav, Richard A Komorowski, Matthew I Goldblatt, Anand Rohatgi, Mark A Sarzynski, Samer Gawrieh, Michael Olivier
Background: Metabolic diseases such as obesity and diabetes are associated with changes in high-density lipoprotein (HDL) particles, including changes in particle size and protein composition, often resulting in abnormal function. Recent studies suggested that patients with non-alcoholic fatty liver disease (NAFLD), including individuals with non-alcoholic steatohepatitis (NASH), have smaller HDL particles when compared to individuals without liver pathologies. However, no studies have investigated potential changes in HDL particle protein composition in patients with NAFLD, in addition to changes related to obesity, to explore putative functional changes of HDL which may increase the risk of cardiovascular complications...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29507546/glycan-analysis-of-colorectal-cancer-samples-reveals-stage-dependent-changes-in-cea-glycosylation-patterns
#14
Qianqian Zhao, Tiancheng Zhan, Zaian Deng, Qianqian Li, Yaming Liu, Shaojie Yang, Dengbo Ji, Yan Li
Background: Carcinoembryonic antigen (CEA) is a glycoprotein associated with colorectal cancer (CRC). While the functions of its gene and protein have been fully characterized, its post-translational modifications in the context of CRC development remain undefined. Methods: To show the correlation between the different stages of CRC development and changes in the glycosylation patterns of CEA, we analyzed CEA in tumor tissues (CEA-T) and paired tumor-adjacent normal tissues (CEA-A) from 53 colorectal cancer patients using a high-density lectin microarray containing 56 plant lectins...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29507545/current-applications-of-antibody-microarrays
#15
REVIEW
Ziqing Chen, Tea Dodig-Crnković, Jochen M Schwenk, Sheng-Ce Tao
The concept of antibody microarrays is one of the most versatile approaches within multiplexed immunoassay technologies. These types of arrays have increasingly become an attractive tool for the exploratory detection and study of protein abundance, function, pathways, and potential drug targets. Due to the properties of the antibody microarrays and their potential use in basic research and clinical analytics, various types of antibody microarrays have already been developed. In spite of the growing number of studies utilizing this technique, few reviews about antibody microarray technology have been presented to reflect the quality and future uses of the generated data...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29449793/clinical-proteomic-analysis-of-scrub-typhus-infection
#16
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
#17
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
#18
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
#19
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
#20
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
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