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Clinical Proteomics

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https://www.readbyqxmd.com/read/27922620/relevance-of-necroptosis-in-cancer
#1
REVIEW
Najoua Lalaoui, Gabriela Brumatti
Resistance to caspase-dependent apoptosis is often responsible for treatment failures in cancer. Finding novel therapeutic strategies that can activate alternative cell death programs appears to be appealing. Necroptosis is a form of programmed necrosis that occurs under caspase deficient conditions. This alternative form of cell death has recently emerged as a potential anti-cancer therapy that could overcome apoptosis resistance. A growing understanding of the molecular events triggering necroptosis helped to examine its implication in cancer development and to define new therapeutic strategies...
December 6, 2016: Immunology and Cell Biology
https://www.readbyqxmd.com/read/27917957/refined-purification-strategy-for-reliable-proteomic-profiling-of-hdl2-3-impact-on-proteomic-complexity
#2
Michael Holzer, Sabine Kern, Ruth Birner-Grünberger, Sanja Curcic, Akos Heinemann, Gunther Marsche
Proteomics have extended the list of high-density lipoprotein (HDL) associated proteins to about 90. One of the major issues of global protein characterization is establishing specificity of association as opposed to contamination, a fact which has never been addressed for isolated HDL. We have developed a refined purification strategy to isolate HDL by density, followed by purification by size to generate "highly purified" fractions of HDL2/3, which allow the reliable quantification of the HDL proteome for biomarker discovery...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27916117/specific-mixing-facilitates-the-comparative-quantification-of-phosphorylation-sites-with-significant-dysregulations
#3
Jing Liu, Bo Xu, Zheyi Liu, Mingming Dong, Jiawei Mao, Ye Zhou, Jin Chen, Fangjun Wang, Hanfa Zou
Mass spectrometry (MS) based quantitative analyses of proteome and proteome post-translational modifications (PTMs) play more and more important roles in biological, pharmaceutical and clinical studies. However, it is still a big challenge to accurately quantify the proteins or proteins PTM sites with extreme relative abundances in comparative protein samples, such as the significantly dysregulated ones. Herein, a novel quantification strategy, Mixing at Specific Ratio (MaSR) before isotope labeling, had been developed to improve the quantification accuracy and coverage of extreme proteins and protein phosphorylation sites...
January 15, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/27915473/urine-proteomics-in-the-era-of-mass-spectrometry
#4
REVIEW
Ashley Beasley-Green
With the technological advances of mass spectrometry (MS)-based platforms, clinical proteomics is one of the most rapidly growing areas in biomedical research. Urine proteomics has become a popular subdiscipline of clinical proteomics because it is an ideal source for the discovery of noninvasive disease biomarkers. The urine proteome offers a comprehensive view of the local and systemic physiology since the proteome is primarily composed of proteins/peptides from the kidneys and plasma. The emergence of MS-based proteomic platforms as prominent bioanalytical tools in clinical applications has enhanced the identification of protein-based urinary biomarkers...
November 2016: International Neurourology Journal
https://www.readbyqxmd.com/read/27914711/proteomic-based-research-strategy-identified-laminin-subunit-alpha-2-as-a-potential-urinary-specific-biomarker-for-the-medullary-sponge-kidney-disease
#5
Antonia Fabris, Maurizio Bruschi, Laura Santucci, Giovanni Candiano, Simona Granata, Alessandra Dalla Gassa, Nadia Antonucci, Andrea Petretto, Gian Marco Ghiggeri, Giovanni Gambaro, Antonio Lupo, Gianluigi Zaza
Medullary sponge kidney (MSK) disease, a rare kidney malformation featuring recurrent renal stones and nephrocalcinosis, continues to be diagnosed using expensive and time-consuming clinical/instrumental tests (mainly urography). Currently, no molecular diagnostic biomarkers are available. To identify such we employed a proteomic-based research strategy utilizing urine from 22 patients with MSK and 22 patients affected by idiopathic calcium nephrolithiasis (ICN) as controls. Notably, two patients with ICN presented cysts...
November 30, 2016: Kidney International
https://www.readbyqxmd.com/read/27906678/humoral-immune-responses-toward-tumor-derived-antigens-in-previously-untreated-patients-with-chronic-lymphocytic-leukemia
#6
Valentina Griggio, Giorgia Mandili, Candida Vitale, Michela Capello, Paolo Macor, Sara Serra, Barbara Castella, Silvia Peola, Myriam Foglietta, Daniela Drandi, Paola Omedé, Daniele Sblattero, Paola Cappello, Roberto Chiarle, Silvia Deaglio, Mario Boccadoro, Francesco Novelli, Massimo Massaia, Marta Coscia
In chronic lymphocytic leukemia (CLL) the occurrence and the impact of antibody responses toward tumor-derived antigens are largely unexplored. Our serological proteomic data show that antibodies toward 47 identified antigens are detectable in 29 out of 35 patients (83%) with untreated CLL. The glycolytic enzyme alpha-enolase (ENO1) is the most frequently recognized antigen (i.e. 54% of CLL sera). We show that ENO1 is upregulated in the proliferating B-cell fraction of CLL lymph nodes. In CLL cells of the peripheral blood, ENO1 is exclusively expressed at the intracellular level, whereas it is exposed on the surface of apoptotic leukemic cells...
November 30, 2016: Oncotarget
https://www.readbyqxmd.com/read/27903834/saliva-diagnostics-current-views-and-directions
#7
Karolina Elżbieta Kaczor-Urbanowicz, Carmen Martin Carreras-Presas, Katri Aro, Michael Tu, Franklin Garcia-Godoy, David Tw Wong
In this review, we provide an update on the current and future applications of saliva for diagnostic purposes. There are many advantages of using saliva as a biofluid. Its collection is fast, easy, inexpensive, and non-invasive. In addition, saliva, as a "mirror of the body," can reflect the physiological and pathological state of the body. Therefore, it serves as a diagnostic and monitoring tool in many fields of science such as medicine, dentistry, and pharmacotherapy. Introduced in 2008, the term "Salivaomics" aimed to highlight the rapid development of knowledge about various "omics" constituents of saliva, including: proteome, transcriptome, micro-RNA, metabolome, and microbiome...
November 29, 2016: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/27903678/adnp-is-a-therapeutically-inducible-repressor-of-wnt-signaling-in-colorectal-cancer
#8
Cristina Blaj, Agnes Bringmann, Eva Marina Schmidt, Manuela Urbischek, Sebastian Lamprecht, Thomas Fröhlich, Georg J Arnold, Stefan Krebs, Helmut Blum, Heiko Hermeking, Andreas Jung, Thomas Kirchner, David Horst
PURPOSE: Constitutively active WNT signaling is hallmark of colorectal cancers and driver of malignant tumor progression. Therapeutic targeting of WNT signaling is difficult due to high pathway complexity and its role in tissue homeostasis. Here we identify the transcription factor ADNP as a pharmacologically inducible repressor of WNT signaling in colon cancer. EXPERIMENTAL DESIGN: We used transcriptomic, proteomic, and in situ analyses to identify ADNP expression in colorectal cancer, and cell biology approaches to determine its function...
November 30, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27900411/inflammatory-protein-response-in-cdkl5-rett-syndrome-evidence-of-a-subclinical-smouldering-inflammation
#9
Alessio Cortelazzo, Claudio de Felice, Silvia Leoncini, Cinzia Signorini, Roberto Guerranti, Roberto Leoncini, Alessandro Armini, Luca Bini, Lucia Ciccoli, Joussef Hayek
BACKGROUND: Mutations in the cyclin-dependent kinase-like 5 gene cause a clinical variant of Rett syndrome (CDKL5-RTT). A role for the acute-phase response (APR) is emerging in typical RTT caused by methyl-CpG-binding protein 2 gene mutations (MECP2-RTT). No information is, to date, available on the inflammatory protein response in CDKL5-RTT. We evaluated, for the first time, the APR protein response in CDKL5-RTT. METHODS: Protein patterns in albumin- and IgG-depleted plasma proteome from CDKL5-RTT patients were evaluated by two-dimensional gel electrophoresis/mass spectrometry...
November 29, 2016: Inflammation Research: Official Journal of the European Histamine Research Society ... [et Al.]
https://www.readbyqxmd.com/read/27899996/quantitative-label-free-mass-spectrometry-analysis-of-formalin-fixed-paraffin-embedded-tissue-representing-the-invasive-cutaneous-malignant-melanoma-proteome
#10
Paul Dowling, Benvon Moran, Edel McAuley, Paula Meleady, Michael Henry, Martin Clynes, Mairin McMenamin, Niamh Leonard, Mary Monks, Bairbre Wynne, Patrick Ormond, Annemarie Larkin
Understanding the events at a protein level that govern the progression from melanoma in situ to invasive melanoma are important areas of current research to be developed. Recent advances in the analysis of formalin-fixed, paraffin-embedded tissue by proteomics, particularly using the filter-aided sample preparation protocol, has opened up the possibility of studying vast archives of clinical material and associated medical records. In the present study, quantitative protein profiling was performed using tandem mass spectrometry, and the proteome differences between melanoma in situ and invasive melanoma were compared...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27899155/comparative-sequence-analysis-of-cyclospora-cayetanensis-apicoplast-genomes-originating-from-diverse-geographical-regions
#11
Hediye Nese Cinar, Yvonne Qvarnstrom, Yuping Wei-Pridgeon, Wen Li, Fernanda S Nascimento, Michael J Arrowood, Helen R Murphy, AhYoung Jang, Eunje Kim, RaeYoung Kim, Alexandre da Silva, Gopal R Gopinath
BACKGROUND: Cyclospora cayetanensis is an emerging coccidian parasite that causes endemic and epidemic diarrheal disease called cyclosporiasis, and this infection is associated with consumption of contaminated produce or water in developed and developing regions. Food-borne outbreaks of cyclosporiasis have occurred almost every year in the USA since the 1990s. Investigations of these outbreaks are currently hampered due to lack of molecular epidemiological tools for trace back analysis...
November 29, 2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27898657/serum-proteomic-test-in-advanced-non-squamous-non-small-cell-lung-cancer-treated-in-first-line-with-standard-chemotherapy
#12
F Grossi, E Rijavec, C Genova, G Barletta, F Biello, C Maggioni, G Burrafato, C Sini, M G Dal Bello, K Meyer, J Roder, H Roder, J Grigorieva
BACKGROUND: VeriStrat is a blood-based proteomic test with predictive and prognostic significance in second-line treatments for non-small cell lung cancer (NSCLC). This trial was designed to investigate the role of VeriStrat in first-line treatment of advanced NSCLC with standard chemotherapy. Here we present the results for 76 non-squamous patients treated with a combination of carboplatin or cisplatin with pemetrexed. METHODS: The test-assigned classifications of VeriStrat Good or VeriStrat Poor to samples collected at baseline...
November 29, 2016: British Journal of Cancer
https://www.readbyqxmd.com/read/27898018/combating-ebola-with-repurposed-therapeutics-using-the-cando-platform
#13
Gaurav Chopra, Sashank Kaushik, Peter L Elkin, Ram Samudrala
Ebola virus disease (EVD) is extremely virulent with an estimated mortality rate of up to 90%. However, the state-of-the-art treatment for EVD is limited to quarantine and supportive care. The 2014 Ebola epidemic in West Africa, the largest in history, is believed to have caused more than 11,000 fatalities. The countries worst affected are also among the poorest in the world. Given the complexities, time, and resources required for a novel drug development, finding efficient drug discovery pathways is going to be crucial in the fight against future outbreaks...
November 25, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27896965/identification-of-discriminative-imaging-proteomics-associations-in-alzheimer-s-disease-via-a-novel-sparse-correlation-model
#14
Jingwen Yan, Shannon L Risacher, Kwangsik Nho, Andrew J Saykin, L I Shen
Brain imaging and protein expression, from both cerebrospinal fluid and blood plasma, have been found to provide complementary information in predicting the clinical outcomes of Alzheimer's disease (AD). But the underlying associations that contribute to such a complementary relationship have not been previously studied yet. In this work, we will perform an imaging proteomics association analysis to explore how they are related with each other. While traditional association models, such as Sparse Canonical Correlation Analysis (SCCA), can not guarantee the selection of only disease-relevant biomarkers and associations, we propose a novel discriminative SCCA (denoted as DSCCA) model with new penalty terms to account for the disease status information...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896820/ppar%C3%AE-targeted-oral-cancer-treatment-and-additional-utility-of-genomics-analytic-techniques
#15
Nathan Handley, Jacob Eide, Randall Taylor, Beverly Wuertz, Patrick Gaffney, Frank Ondrey
OBJECTIVE: Peroxisome proliferator-activated receptor γ (PPARγ) agonists have been shown to have anti-proliferative, anti-angiogenic, and proapoptotic effects, leading to interest in their use as cancer therapeutics. Pioglitazone, a U.S. Food and Drug Administration-approved type II diabetes medication and PPARγ agonist, may have a role in adjuvant head-and-neck squamous cell carcinoma treatment or prevention. Therefore, the purpose of this study was: 1) to treat oral cavity cancer cells with the PPARγ activator, pioglitazone, to analyze gene expression changes; and 2) to compare those changes with our preexisting genomic data for development of hypothesis-driven additional basic and clinical studies...
November 29, 2016: Laryngoscope
https://www.readbyqxmd.com/read/27896757/lc-ms-e-multiplex-ms-ms-ion-mobility-and-label-free-quantitation-in-clinical-proteomics
#16
Gustavo Henrique Martins Ferreira Souza, Paul C Guest, Daniel Martins-de-Souza
Proteomic tools can only be implemented in clinical settings if high-throughput, automated, sensitive, and accurate methods are developed. This has driven researchers to the edge of mass spectrometry (MS)-based proteomics capacity. Here we provide an overview of recent achievements in mass spectrometric technologies and instruments. This includes development of high and ultra definition-MS(E) (HDMS(E) and UDMS(E)) through implementation of ion mobility (IM) MS towards sensitive and accurate label-free proteomics using ultra performance liquid chromatography (UPLC)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896605/personalized-medicine-in-a-new-genomic-era-ethical-and-legal-aspects
#17
Maria Shoaib, Mansoor Ali Merchant Rameez, Syed Ather Hussain, Mohammed Madadin, Ritesh G Menezes
The genome of two completely unrelated individuals is quite similar apart from minor variations called single nucleotide polymorphisms which contribute to the uniqueness of each and every person. These single nucleotide polymorphisms are of great interest clinically as they are useful in figuring out the susceptibility of certain individuals to particular diseases and for recognizing varied responses to pharmacological interventions. This gives rise to the idea of 'personalized medicine' as an exciting new therapeutic science in this genomic era...
November 28, 2016: Science and Engineering Ethics
https://www.readbyqxmd.com/read/27895643/azithromycin-attenuates-pseudomonas-induced-lung-inflammation-by-targeting-bacterial-proteins-secreted-in-the-cultured-medium
#18
Teresinha Leal, Gabriella Bergamini, François Huaux, Nadtha Panin, Sabrina Noel, Barbara Dhooghe, Jeremy B Haaf, Pierluigi Mauri, Sara Motta, Dario Di Silvestre, Paola Melotti, Claudio Sorio
BACKGROUND: Pseudomonas aeruginosa airway infections are a major cause of morbidity and mortality in patients with cystic fibrosis (CF). Azithromycin improves the related clinical outcomes, but its mechanisms of action remain poorly understood. We tested the hypothesis that azithromycin downregulates P. aeruginosa-induced pro-inflammatory responses by modifying release of bacterial proteins. METHODS: We monitored inflammatory markers in lungs of CF mutant mice and their littermate controls in response to conditioned media (CM) collected from the reference P...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27895634/cytosolic-proteome-profiling-of-aminoglycosides-resistant-mycobacterium-tuberculosis-clinical-isolates-using-maldi-tof-ms
#19
Divakar Sharma, Manju Lata, Rananjay Singh, Nirmala Deo, Krishnamurthy Venkatesan, Deepa Bisht
Emergence of extensively drug resistant tuberculosis (XDR-TB) is the consequence of the failure of second line TB treatment. Aminoglycosides are the important second line anti-TB drugs used to treat the multi drug resistant tuberculosis (MDR-TB). Main known mechanism of action of aminoglycosides is to inhibit the protein synthesis by inhibiting the normal functioning of ribosome. Primary target of aminoglycosides are the ribosomal RNA and its associated proteins. Various mechanisms have been proposed for aminoglycosides resistance but still some are unsolved...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27895219/primer-in-genetics-and-genomics-article-1-dna-genes-and-chromosomes
#20
Janice S Dorman, Mandy J Schmella, Susan W Wesmiller
Precision medicine refers to the practice of determining a patient's unique genetic, biomarker, and other characteristics for the purpose of improving his or her clinical outcomes. Not all patients with the same clinical diagnosis respond equally to identical treatment regimens. By examining patients at the molecular level, health-care providers will be better able to apply the most effective therapies that each individual requires. To understand precision medicine, nurses must have a solid understanding of genomics and proteomics...
November 28, 2016: Biological Research for Nursing
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