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Clinical Proteomics

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https://www.readbyqxmd.com/read/29691334/forward-genetic-dissection-of-biofilm-development-by-fusobacterium-nucleatum-novel-functions-of-cell-division-proteins-ftsx-and-envc
#1
Chenggang Wu, Abu Amar Mohamed Al Mamun, Truc Thanh Luong, Bo Hu, Jianhua Gu, Ju Huck Lee, Melissa D'Amore, Asis Das, Hung Ton-That
Fusobacterium nucleatum is a key member of the human oral biofilm. It is also implicated in preterm birth and colorectal cancer. To facilitate basic studies of fusobacterial virulence, we describe here a versatile transposon mutagenesis procedure and a pilot screen for mutants defective in biofilm formation. Out of 10 independent biofilm-defective mutants isolated, the affected genes included the homologs of the Escherichia coli cell division proteins FtsX and EnvC, the electron transport protein RnfA, and four proteins with unknown functions...
April 24, 2018: MBio
https://www.readbyqxmd.com/read/29691233/evaluation-of-biodistribution-of-sulforaphane-after-administration-of-oral-broccoli-sprout-extract-in-melanoma-patients-with-multiple-atypical-nevi
#2
Shawn Tahata, Shivendra V Singh, Yan Lin, Eun-Ryeong Hahm, Jan H Beumer, Susan M Christner, Uma N Rao, Cindy Sander, Ahmad A Tarhini, Hussein Tawbi, Laura K Ferris, Melissa Wilson, Amy Rose, Catherine M Dietz, Ellen K Hughes, Jed W Fahey, Sancy A Leachman, Pamela B Cassidy, Lisa H Butterfield, Hassane M Zarour, John M Kirkwood
Broccoli sprout extract containing sulforaphane (BSE-SFN) has been shown to inhibit ultraviolet radiation-induced damage and tumor progression in skin. This study evaluated the toxicity and potential effects of oral BSE-SFN at three dosages. Seventeen patients who each had at least 2 atypical nevi and a prior history of melanoma were randomly allocated to 50, 100, or 200 µmol oral BSE-SFN daily for 28 days. Atypical nevi were photographed on days 1 and 28, and plasma and nevus samples were taken on days 1, 2, and 28...
April 24, 2018: Cancer Prevention Research
https://www.readbyqxmd.com/read/29691073/microbiological-diagnosis-of-bacteraemia-and-fungaemia-blood-cultures-and-molecular-methods
#3
María Remedio Guna Serrano, Nieves Larrosa Escartín, Mercedes Marín Arriaza, Juan Carlos Rodríguez Díaz
OBJETIVE: In this review we try to update the new procedures applicable in the microbiological diagnosis of bacteriemia and fungemias. METHOD: Review of scientific literature. RESULTS AND CONCLUSIONS: After defining the process and indicating its fundamental principles, the main biomarkers used in clinical practice are reviewed. Subsequently, the particularities of the pre-analytical phase (collection and transport of samples) are highlighted and the steps to follow for the microbiological identification by classical methods are detailed, based on the culture of the blood samples...
April 21, 2018: Enfermedades Infecciosas y Microbiología Clínica
https://www.readbyqxmd.com/read/29687643/proteomic-analysis-of-exosomes-and-its-application-in-hiv-1-infection
#4
REVIEW
Collins Cheruiyot, Zemplen Pataki, Bharat Ramratnam, Ming Li
Exosomes are 30-100 nm extracellular vesicles secreted from late endosomes by various types of cells. Numerous studies have suggested that exosomes play significant roles in HIV-1 biogenesis. Proteomics coupled with exosome fractionation has been successfully used to identify various exosomal proteins and helped us to uncover the interactions between exosomes and HIV-1. To inform the current progress in the intersection of exosome, proteomics and HIV-1, this review is focused on: i) analyzing different exosome isolation, purification methods and their implications in HIV-1 studies; ii) evaluating the roles of various proteomic techniques in defining exosomal contents; iii) discussing the research and clinical applications of proteomics and exosome in HIV-1 biology...
April 23, 2018: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29684684/targeted-data-independent-acquisition-for-mass-spectrometric-detection-of-ras-mutations-in-formalin-fixed-paraffin-embedded-tumor-biopsies
#5
Yeoun Jin Kim, Andrew G Chambers, Fabiola Cecchi, Todd Hembrough
Genomic testing for KRAS and NRAS mutations in clinical biopsies of various cancers is routinely performed to predict futility of anti-epidermal growth factor receptor (anti-EGFR) therapies. We hypothesized that RAS mutations could be detected and quantified at the protein level for diagnostic purposes using data-independent acquisition (DIA)-based mass spectrometry in formalin-fixed, paraffin-embedded (FFPE) tumor samples. We developed a targeted DIA assay that surveys the specific mass range of all possible peptides harboring activating mutations in KRAS exon 2...
April 20, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29683367/insights-into-apoptotic-proteins-in-chemotherapy-quantification-techniques-and-informing-therapy-choice
#6
Janine Naß, Thomas Efferth
INTRODUCTION: Cancer is one of the leading causes of morbidity and mortality worldwide. A hallmark of cancer is evasion of apoptosis leading to tumor progression and drug resistance. Biomarker research has become a sign of the times, and proteins involved in apoptosis may be used for clinical diagnostic or prognostic purposes in cancer treatment. The recent progress in proteomic technology has triggered an emerging number of researchers to study the molecular mechanisms that regulate the apoptotic signal transduction pathways in cancer...
April 23, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29682908/tracking-disease-progression-non-invasively-in-duchenne-and-becker-muscular-dystrophies
#7
Pietro Spitali, Kristina Hettne, Roula Tsonaka, Mohammed Charrout, Janneke van den Bergen, Zaïda Koeks, Hermien E Kan, Melissa T Hooijmans, Andreas Roos, Volker Straub, Francesco Muntoni, Cristina Al-Khalili-Szigyarto, Marleen J A Koel-Simmelink, Charlotte E Teunissen, Hanns Lochmüller, Erik H Niks, Annemieke Aartsma-Rus
BACKGROUND: Analysis of muscle biopsies allowed to characterize the pathophysiological changes of Duchenne and Becker muscular dystrophies (D/BMD) leading to the clinical phenotype. Muscle tissue is often investigated during interventional dose finding studies to show in situ proof of concept and pharmacodynamics effect of the tested drug. Less invasive readouts are needed to objectively monitor patients' health status, muscle quality, and response to treatment. The identification of serum biomarkers correlating with clinical function and able to anticipate functional scales is particularly needed for personalized patient management and to support drug development programs...
April 16, 2018: Journal of Cachexia, Sarcopenia and Muscle
https://www.readbyqxmd.com/read/29681787/the-response-to-neoadjuvant-chemoradiotherapy-with-5-fluorouracil-in-locally-advanced-rectal-cancer-patients-a-predictive-proteomic-signature
#8
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/29680270/regulation-of-cancer-cell-signaling-pathways-by-mushrooms-and-their-bioactive-molecules-overview-of-the-journey-from-benchtop-to-clinical-trials
#9
Aliye Aras, Sumbul Khalid, Saima Jabeen, Ammad Ahmad Farooqi, Baojun Xu
Mushrooms represent a tremendous source of biologically useful and pharmacologically active molecules. Recent breakthroughs in cancer genetics, genomics, proteomics and translational research have helped us to develop a better understanding of the underlying mechanisms which are contributory in cancer development and progression. Different signaling pathways particularly, Wnt, SHH, TGF/SMAD and JAK/STAT have been shown to modulate cancer progression and development. Increasingly it is being realized that genetic/epigenetic mutations and loss of apoptosis also mandate a 'multi-molecular' perspective for the development of therapies to treat cancer...
April 19, 2018: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/29678717/a-tandem-mass-tag-tmt-proteomic-analysis-during-the-early-phase-of-experimental-pancreatitis-reveals-new-insights-in-the-disease-pathogenesis
#10
Violeta García-Hernández, Carmen Sánchez-Bernal, Domitille Schvartz, José J Calvo, Jean-Charles Sanchez, Jesús Sánchez-Yagüe
Changes in the protein expression occurring within the initiation phase of acute pancreatitis (AP) might be vital in the development of this complex disease. However, the exact mechanisms involved in the onset of AP remains elusive and most of our knowledge about the pathobiology of AP comes from animal models. We performed in a rat pancreatitic model a high-throughput shotgun proteomic profiling of the soluble and whole membrane fractions from the pancreas during the early phase of cerulein (Cer)-induced AP...
April 17, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29677503/revolutionizing-precision-oncology-through-collaborative-proteogenomics-and-data-sharing
#11
Henry Rodriguez, Stephen R Pennington
The integration of proteomics into precision oncology presents opportunities that may transform the molecular analysis of cancer and accelerate basic and clinical cancer research. This Commentary discusses the importance of international collaboration and data sharing inspired by the Cancer Moonshot to accelerate the progress of multi-omic precision medicine-an approach that addresses the global diversity of people and of cancers.
April 19, 2018: Cell
https://www.readbyqxmd.com/read/29677216/plasma-metabolomic-biomarkers-accurately-classify-acute-mild-traumatic-brain-injury-from-controls
#12
Massimo S Fiandaca, Mark Mapstone, Amin Mahmoodi, Thomas Gross, Fabio Macciardi, Amrita K Cheema, Kian Merchant-Borna, Jeffrey Bazarian, Howard J Federoff
Past and recent attempts at devising objective biomarkers for traumatic brain injury (TBI) in both blood and cerebrospinal fluid have focused on abundance measures of time-dependent proteins. Similar independent determinants would be most welcome in diagnosing the most common form of TBI, mild TBI (mTBI), which remains difficult to define and confirm based solely on clinical criteria. There are currently no consensus diagnostic measures that objectively define individuals as having sustained an acute mTBI. Plasma metabolomic analyses have recently evolved to offer an alternative to proteomic analyses, offering an orthogonal diagnostic measure to what is currently available...
2018: PloS One
https://www.readbyqxmd.com/read/29674508/combined-braf-and-hsp90-inhibition-in-patients-with-unresectable-braf-v600e-mutant-melanoma
#13
Zeynep Eroglu, Yian Ann Chen, Geoffrey T Gibney, Jeffrey S Weber, Ragini R Kudchadkar, Nikhil I Khushalani, Joseph Markowitz, Andrew S Brohl, Leticia F Tetteh, Howida Ramadan, Gina Arnone, Jiannong Li, Xiuhua Zhao, Ritin Sharma, Lancia N F Darville, Bin Fang, Inna Smalley, Jane L Messina, John M Koomen, Vernon K Sondak, Keiran S M Smalley
PURPOSE: BRAF inhibitors are clinically active in patients with advanced BRAFV600 -mutant melanoma, although acquired resistance remains common. Preclinical studies demonstrated that resistance could be overcome using concurrent treatment with the HSP90 inhibitor XL888. METHODS: Vemurafenib (960 mg PO BID) combined with escalating doses of XL888 (30, 45, 90 or 135 mg PO twice weekly) was investigated in 21 patients with advanced BRAFV600 -mutant melanoma. Primary endpoints were safety and determination of a maximum tolerated dose...
April 19, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29672976/dual-frequency-irradiation-cest-mri-of-endogenous-bulk-mobile-proteins
#14
Steffen Goerke, Johannes Breitling, Moritz Zaiss, Johannes Windschuh, Patrick Kunz, Patrick Schuenke, Daniel Paech, Dario L Longo, Karel D Klika, Mark E Ladd, Peter Bachert
A novel MRI contrast is proposed which enables the selective detection of endogenous bulk mobile proteins in vivo. Such a non-invasive imaging technique may be of particular interest for many diseases associated with pathological alterations of protein expression, such as cancer and neurodegenerative disorders. Specificity to mobile proteins was achieved by the selective measurement of intramolecular spin diffusion and the removal of semi-solid macromolecular signal components by a correction procedure. For this purpose, the approach of chemical exchange saturation transfer (CEST) was extended to a radiofrequency (RF) irradiation scheme at two different frequency offsets (dualCEST)...
April 19, 2018: NMR in Biomedicine
https://www.readbyqxmd.com/read/29672914/revisiting-the-nih-taskforce-on-the-research-needs-of-eosinophil-associated-diseases-re-tread
#15
REVIEW
Paneez Khoury, Praveen Akuthota, Steven J Ackerman, Joseph R Arron, Bruce S Bochner, Margaret H Collins, Jean-Emmanuel Kahn, Patricia C Fulkerson, Gerald J Gleich, Rashmi Gopal-Srivastava, Elizabeth A Jacobsen, Kristen M Leiferman, Levi-Schaffer Francesca, Sameer K Mathur, Michael Minnicozzi, Calman Prussin, Marc E Rothenberg, Florence Roufosse, Kathleen Sable, Dagmar Simon, Hans-Uwe Simon, Lisa A Spencer, Jonathan Steinfeld, Andrew J Wardlaw, Michael E Wechsler, Peter F Weller, Amy D Klion
BACKGROUND: Eosinophil-associated diseases (EADs) are rare, heterogeneous disorders characterized by the presence of eosinophils in tissues and/or peripheral blood resulting in immunopathology. The heterogeneity of tissue involvement, lack of sufficient animal models, technical challenges in working with eosinophils, and lack of standardized histopathologic approaches have hampered progress in basic research. Additionally, clinical trials and drug development for rare EADs are limited by the lack of primary and surrogate endpoints, biomarkers, and validated patient-reported outcomes...
April 19, 2018: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/29671787/proteomic-identification-of-the-galectin-1-involved-molecular-pathways-in-urinary-bladder-urothelial-carcinoma
#16
Chien-Feng Li, Kun-Hung Shen, Lan-Hsiang Chien, Cheng-Hao Huang, Ting-Feng Wu, Hong-Lin He
Among various heterogeneous types of bladder tumors, urothelial carcinoma is the most prevalent lesion. Some of the urinary bladder urothelial carcinomas (UBUCs) develop local recurrence and may cause distal invasion. Galectin-1 de-regulation significantly affects cell transformation, cell proliferation, angiogenesis, and cell invasiveness. In continuation of our previous investigation on the role of galectin-1 in UBUC tumorigenesis, in this study, proteomics strategies were implemented in order to find more galectin-1-associated signaling pathways...
April 19, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29669750/current-challenges-and-opportunities-in-treating-glioblastoma
#17
Andrea Shergalis, Armand Bankhead, Urarika Luesakul, Nongnuj Muangsin, Nouri Neamati
Glioblastoma multiforme (GBM), the most common and aggressive primary brain tumor, has a high mortality rate despite extensive efforts to develop new treatments. GBM exhibits both intra- and intertumor heterogeneity, lending to resistance and eventual tumor recurrence. Large-scale genomic and proteomic analysis of GBM tumors has uncovered potential drug targets. Effective and "druggable" targets must be validated to embark on a robust medicinal chemistry campaign culminating in the discovery of clinical candidates...
July 2018: Pharmacological Reviews
https://www.readbyqxmd.com/read/29668468/clinical-proteomics-in-kidney-disease-from-discovery-to-clinical-application
#18
Martin Pejchinovski, Harald Mischak
Proteome analysis has been applied in multiple studies in the context of chronic kidney disease, aiming at improving our knowledge on the molecular pathophysiology of the disease. The approach is generally based on the hypothesis that proteins are key in maintaining kidney function, and disease is a clinical consequence of a significant change of the protein level. Knowledge on critical proteins and their alteration in disease should in turn enable identification of ideal biomarkers that could guide patient management...
December 1, 2017: Prilozi (Makedonska Akademija Na Naukite i Umetnostite. Oddelenie za Medicinski Nauki)
https://www.readbyqxmd.com/read/29667783/phap1-promotes-glioma-cell-proliferation-by-regulating-the-akt-p27-stathmin-pathway
#19
Manyi Xie, Zhe Ji, Yaxing Bao, Yufu Zhu, Yang Xu, Lei Wang, Shangfeng Gao, Zhiyi Liu, Zilu Tian, Qingming Meng, Hengliang Shi, Rutong Yu
PHAP1 (Putative HLA-DR-associated protein 1), also termed acidic leucine-rich nuclear phosphoprotein 32A (ANP32A), Phosphoprotein 32 (pp32) or protein phosphatase 2A inhibitor (I1PP2A), is a multifunctional protein aberrantly expressed in multiple types of human cancers. However, its expression pattern and clinical relevance in human glioma remain unknown. In this study, Western blotting and immunohistochemistry analysis demonstrated PHAP1 protein was highly expressed in glioma patients, especially in those with high-grade disease...
April 18, 2018: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/29667544/proteomic-markers-in-cervical-mucus
#20
Yolanda Fernandez-Hermida, Giuseppe Grande, Micaela Menarguez, Anna Laura Astorri, Rafael Azagra
Cervical Mucus (CM) is a viscous fluid produced by the cervical glands. It plays a key role in the transport and capacitation of sperm through the female genital tract. The CM undergoes modifications that make it have different biophysical and biochemical characteristics throughout the cycle, becoming an important element for the identification of ovulation. Since CM is rich in secreted proteins, it may represent moreover a source of putative biomarkers for female reproductive tract diseases. This review is an attempt to collect relevant knowledge about the physicochemical properties and functions of the cervical mucus, including its important role as a clinical marker of female fertility, and draws attention to CM as a source of potential proteomic biomarkers...
April 18, 2018: Protein and Peptide Letters
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