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Clinical Proteomics

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https://www.readbyqxmd.com/read/28326926/potential-protein-biomarkers-for-burning-mouth-syndrome-discovered-by-quantitative-proteomics
#1
Eoon Hye Ji, Cynthia Diep, Tong Liu, Hong Li, Robert Merrill, Diana Messadi, Shen Hu
Burning mouth syndrome (BMS) is a chronic pain disorder characterized by severe burning sensation in normal looking oral mucosa. Diagnosis of BMS remains to be a challenge to oral healthcare professionals because the method for definite diagnosis is still uncertain. In this study, a quantitative saliva proteomic analysis was performed in order to identify target proteins in BMS patients' saliva that may be used as biomarkers for simple, non-invasive detection of the disease. By using isobaric tags for relative and absolute quantitation labeling and liquid chromatography-tandem mass spectrometry to quantify 1130 saliva proteins between BMS patients and healthy control subjects, we found that 50 proteins were significantly changed in the BMS patients when compared to the healthy control subjects ( p ≤ 0...
January 2017: Molecular Pain
https://www.readbyqxmd.com/read/28323866/elevated-fecal-peptidase-d-at-onset-of-colitis-in-galphai2-mice-a-mouse-model-of-ibd
#2
Daniel Bergemalm, Robert Kruse, Maria Sapnara, Jonas Halfvarson, Elisabeth Hultgren Hörnquist
BACKGROUND: The identification of novel fecal biomarkers in inflammatory bowel disease (IBD) is hampered by the complexity of the human fecal proteome. On the other hand, in experimental mouse models there is probably less variation. We investigated the fecal protein content in mice to identify possible biomarkers and pathogenic mechanisms. METHODS: Fecal samples were collected at onset of inflammation in Galphai2-/- mice, a well-described spontaneous model of chronic colitis, and from healthy littermates...
2017: PloS One
https://www.readbyqxmd.com/read/28321390/metabonomics-research-progress-on-liver-diseases
#3
REVIEW
Mengqian Yu, Ying Zhu, Qingwei Cong, Chunyan Wu
Metabolomics as the new omics technique develops after genomics, transcriptomics, and proteomics and has rapid development at present. Liver diseases are worldwide public health problems. In China, chronic hepatitis B and its secondary diseases are the common liver diseases. They can be diagnosed by the combination of history, virology, liver function, and medical imaging. However, some patients seldom have relevant physical examination, so the diagnosis may be delayed. Many other liver diseases, such as drug-induced liver injury (DILI), alcoholic liver disease (ALD) and nonalcoholic fatty liver disease (NAFLD), and autoimmune liver diseases, still do not have definite diagnostic markers; the diagnosis consists of history, medical imaging, and the relevant score...
2017: Canadian Journal of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28319051/tissue-specific-exosome-biomarkers-for-noninvasively-monitoring-immunologic-rejection-of-transplanted-tissue
#4
Prashanth Vallabhajosyula, Laxminarayana Korutla, Andreas Habertheuer, Ming Yu, Susan Rostami, Chao-Xing Yuan, Sanjana Reddy, Chengyang Liu, Varun Korutla, Brigitte Koeberlein, Jennifer Trofe-Clark, Michael R Rickels, Ali Naji
In transplantation, there is a critical need for noninvasive biomarker platforms for monitoring immunologic rejection. We hypothesized that transplanted tissues release donor-specific exosomes into recipient circulation and that the quantitation and profiling of donor intra-exosomal cargoes may constitute a biomarker platform for monitoring rejection. Here, we have tested this hypothesis in a human-into-mouse xenogeneic islet transplant model and validated the concept in clinical settings of islet and renal transplantation...
March 20, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28319050/extracellular-matrix-proteomics-identifies-molecular-signature-of-symptomatic-carotid-plaques
#5
Sarah R Langley, Karin Willeit, Athanasios Didangelos, Ljubica Perisic Matic, Philipp Skroblin, Javier Barallobre-Barreiro, Mariette Lengquist, Gregor Rungger, Alexander Kapustin, Ludmilla Kedenko, Chris Molenaar, Ruifang Lu, Temo Barwari, Gonca Suna, Xiaoke Yin, Bernhard Iglseder, Bernhard Paulweber, Peter Willeit, Joseph Shalhoub, Gerard Pasterkamp, Alun H Davies, Claudia Monaco, Ulf Hedin, Catherine M Shanahan, Johann Willeit, Stefan Kiechl, Manuel Mayr
BACKGROUND: The identification of patients with high-risk atherosclerotic plaques prior to the manifestation of clinical events remains challenging. Recent findings question histology- and imaging-based definitions of the "vulnerable plaque," necessitating an improved approach for predicting onset of symptoms. METHODS: We performed a proteomics comparison of the vascular extracellular matrix and associated molecules in human carotid endarterectomy specimens from 6 symptomatic versus 6 asymptomatic patients to identify a protein signature for high-risk atherosclerotic plaques...
March 20, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28317069/deciphering-the-role-of-ectosomes-in-cancer-development-and-progression-focus-on-the-proteome
#6
REVIEW
Magdalena Surman, Ewa Stępień, Dorota Hoja-Łukowicz, Małgorzata Przybyło
Ectosomes are small heterogeneous membrane vesicles generated by budding from the plasma membrane in a variety of cell types and, more frequently, in tumor cells. They are shed into the extracellular space and are proposed as a novel form of intracellular communication in which information is transmitted from the originating cell to recipient cells without direct cell-to-cell contact. This review focuses on a single population of extracellular vesicles-ectosomes. We summarize recent studies of tumor-derived ectosomes which examine their biogenesis and protein cargo, and their influence on different aspects of cancer progression...
March 19, 2017: Clinical & Experimental Metastasis
https://www.readbyqxmd.com/read/28315483/functional-proteomic-analysis-of-corticosteroid-pharmacodynamics-in-rat-liver-relationship-to-hepatic-stress-signaling-energy-regulation-and-drug-metabolism
#7
Vivaswath S Ayyar, Richard R Almon, Debra C DuBois, Siddharth Sukumaran, Jun Qu, William J Jusko
Corticosteroids (CS) are anti-inflammatory agents that cause extensive pharmacogenomic and proteomic changes in multiple tissues. An understanding of the proteome-wide effects of CS in liver and its relationships to altered hepatic and systemic physiology remains incomplete. Here, we report the application of a functional pharmacoproteomic approach to gain integrated insight into the complex nature of CS responses in liver in vivo. An in-depth functional analysis was performed using rich pharmacodynamic (temporal-based) proteomic data measured over 66h in rat liver following a single dose of methylprednisolone (MPL)...
March 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28315253/prediction-of-proteases-involved-in-peptide-generation
#8
Mercedes Arguello Casteleiro, Robert Stevens, Julie Klein
Clinical proteomics has led to the identification of a substantial number of disease-associated peptides and protein fragments in several conditions such as cancer, kidney, or cardiovascular diseases. In silico prediction tools that can facilitate linking of identified peptide biomarkers to predicted protease activity might therefore significantly contribute to the understanding of pathophysiological mechanisms of these diseases. Proteasix is an open-source, peptide-centric tool that can be used to predict in silico the proteases involved in naturally occurring peptide generation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28314843/quantitative-proteome-heterogeneity-in-myeloproliferative-neoplasm-subtypes-and-association-with-jak2-mutation-status
#9
Nuria Socoro-Yuste, Cokic Vladan P, Julie Mondet, Isabelle Plo, Pascal Mossuz
Apart from well-known genetic abnormalities, several studies have reported variations in protein expression in Philadelphia negative (Ph-) Myeloproliferative Neoplasm (MPN) patients that could contribute towards their clinical phenotype. In this context, a quantitative mass spectrometry proteomics protocol was used to identify differences in the granulocyte proteome with the goal to characterize the pathogenic role of aberrant protein expression in MPNs. LC MS/MS (LTQ Orbitrap) coupled to iTRAQ labeling showed significant and quantitative differences in protein content among various MPN subtypes [polycythemia vera (PV), essential thrombocythemia (ET) and primary myelofibrosis (PMF)], and according to the genetic status of JAK2 (JAK2V617F presence and JAK2V617F allele burden)...
March 17, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28314116/secretory-proteome-analysis-of-streptomycin-resistant-mycobacterium-tuberculosis-clinical-isolates
#10
Divakar Sharma, Deepa Bisht
Tuberculosis still remains one of the most fatal infectious diseases. Streptomycin (SM) is the drug of choice, especially for patients with multidrug-resistant tuberculosis or category II patients, because it targets the protein synthesis machinery by interacting with steps of translation. Several mechanisms have been proposed to explain the resistance, but our knowledge is inadequate. Secretome often plays an important role in pathogenesis and is considered an attractive reservoir for the development of novel diagnostic markers and targets...
March 1, 2017: SLAS Discov
https://www.readbyqxmd.com/read/28314077/comparative-subproteomic-analysis-of-clinically-acquired-fluoroquinolone-resistance-and-ciprofloxacin-stress-in-salmonella-typhimurium-dt104b
#11
Susana Correia, Michel Hébraud, Ingrid Chafsey, Christophe Chambon, Didier Viala, Yolanda Sáenz, José Luis Capelo, Patrícia Poeta, Gilberto Igrejas
PURPOSE: Antimicrobial resistance is a worldwide public health threat and Salmonella enterica subsp. enterica serotype Typhimurium phage type DT104B multiresistant strains with additional quinolone resistance have been responsible for global outbreaks and high mortality. Quinolone resistance is known to be multifactorial but is still far from a complete understanding. To give new insights about the resistance mechanisms involved, this work aimed to evaluate subproteome changes between a S...
March 17, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28303493/the-effect-of-molecular-diagnostics-on-the-treatment-of-glioma
#12
REVIEW
Nancy Ann Oberheim Bush, Nicholas Butowski
PURPOSE OF REVIEW: This review summarizes the use of molecular diagnostics in glioma and its effect on the development of novel therapeutics and management decisions. RECENT FINDINGS: Genomic and proteomic profiling of brain tumors has provided significant expansion of our understanding of oncogenesis, characterization, and prognostication of brain tumors. Molecular markers such as MGMT, EGFR, IDH, 1p19q, ATRX, TERT, FGFR-TACC, and BRAF are now being used to classify brain tumors as well as influence management decisions...
April 2017: Current Oncology Reports
https://www.readbyqxmd.com/read/28302922/covariation-of-peptide-abundances-accurately-reflects-protein-concentration-differences
#13
Bo Zhang, Mohammad Pirmoradian, Roman Zubarev, Lukas Käll
Most implementations of mass spectrometry-based proteomics involve enzymatic digestion of proteins, expanding the analysis to multiple proteolytic peptides for each protein. Currently, there is no consensus of how to summarize peptides' abundances to protein concentrations, and such efforts are complicated by the fact that error control is normally applied to the identification process, and do not directly control errors linking peptide abundance measures to protein concentration. Peptides resulting from suboptimal digestion or being partially modified are not representative of the protein concentration...
March 16, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28301983/applying-systems-biology-methodology-to-identify-genetic-factors-possibly-associated-with-recovery-after-traumatic-brain-injury
#14
Brad G Kurowski, Amery Treble-Barna, Alexis J Pitzer, Shari L Wade, Lisa J Martin, Ranjit S Chima, Anil Jegga
Traumatic brain injury (TBI) is one of the leading causes of morbidity and mortality worldwide. It is linked with a number of medical, neurological, cognitive, and behavioral sequelae. The influence of genetic factors on the biology and related recovery after TBI is poorly understood. Studies that seek to elucidate the impact of genetic influences on neurorecovery after TBI will lead to better individualization of prognosis and inform development of novel treatments, which are considerably lacking. Current genetic studies related to TBI have focused on specific candidate genes...
March 16, 2017: Journal of Neurotrauma
https://www.readbyqxmd.com/read/28301386/kidney-perfusion-some-like-it-hot-others-prefer-to-keep-it-cool
#15
Ina Jochmans, Michael L Nicholson, Sarah A Hosgood
PURPOSE OF REVIEW: Machine perfusion technologies provide an opportunity for improved preservation, organ assessment, and resuscitation of damaged kidneys. This review summarizes the recent advances in hypothermic and normothermic kidney machine perfusion technologies. RECENT FINDINGS: Modifications to the perfusion conditions with the addition of oxygen during hypothermic machine perfusion can support a low level of metabolism, which in experimental settings improves graft function...
March 15, 2017: Current Opinion in Organ Transplantation
https://www.readbyqxmd.com/read/28299657/runx1-eto-leukemia
#16
Shan Lin, James C Mulloy, Susumu Goyama
AML1-ETO leukemia is the most common cytogenetic subtype of acute myeloid leukemia, defined by the presence of t(8;21). Remarkable progress has been achieved in understanding the molecular pathogenesis of AML1-ETO leukemia. Proteomic surveies have shown that AML-ETO forms a stable complex with several transcription factors, including E proteins. Genome-wide transcriptome and ChIP-seq analyses have revealed the genes directly regulated by AML1-ETO, such as CEBPA. Several lines of evidence suggest that AML1-ETO suppresses endogenous DNA repair in cells to promote mutagenesis, which facilitates acquisition of cooperating secondary events...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28298630/proteomic-analysis-of-proteome-and-histone-post-translational-modifications-in-heat-shock-protein-90-inhibition-mediated-bladder-cancer-therapeutics
#17
Qingdi Quentin Li, Jian-Jiang Hao, Zheng Zhang, L Spencer Krane, Kai H Hammerich, Thomas Sanford, Jane B Trepel, Len Neckers, Piyush K Agarwal
Heat shock protein 90 (HSP90) inhibition is an attractive strategy for cancer treatment. Several HSP90 inhibitors have shown promising effects in clinical oncology trials. However, little is known about HSP90 inhibition-mediated bladder cancer therapy. Here, we report a quantitative proteomic study that evaluates alterations in protein expression and histone post-translational modifications (PTMs) in bladder carcinoma in response to HSP90 inhibition. We show that 5 HSP90 inhibitors (AUY922, ganetespib, SNX2112, AT13387, and CUDC305) potently inhibited the proliferation of bladder cancer 5637 cells in a dose- and time-dependent manner...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28298564/proteomic-analysis-of-sera-from-individuals-with-diffuse-cutaneous-systemic-sclerosis-reveals-a-multianalyte-signature-associated-with-clinical-improvement-during-imatinib-mesylate-treatment
#18
D James Haddon, Hannah E Wand, Justin A Jarrell, Robert F Spiera, Paul J Utz, Jessica K Gordon, Lorinda S Chung
OBJECTIVE: Imatinib has been investigated for the treatment of systemic sclerosis (SSc) because of its ability to inhibit the platelet-derived growth factor receptor and transforming growth factor-β signaling pathways, which have been implicated in SSc pathogenesis. In a 12-month open-label clinical trial assessing the safety and efficacy of imatinib in the treatment of diffuse cutaneous SSc (dcSSc), significant improvements in skin thickening were observed. Here, we report our analysis of sera collected during the clinical trial...
March 15, 2017: Journal of Rheumatology
https://www.readbyqxmd.com/read/28298427/systematic-protein-protein-interaction-mapping-for-clinically-relevant-human-gpcrs
#19
Kate Sokolina, Saranya Kittanakom, Jamie Snider, Max Kotlyar, Pascal Maurice, Jorge Gandía, Abla Benleulmi-Chaachoua, Kenjiro Tadagaki, Atsuro Oishi, Victoria Wong, Ramy H Malty, Viktor Deineko, Hiroyuki Aoki, Shahreen Amin, Zhong Yao, Xavier Morató, David Otasek, Hiroyuki Kobayashi, Javier Menendez, Daniel Auerbach, Stephane Angers, Natasa Pržulj, Michel Bouvier, Mohan Babu, Francisco Ciruela, Ralf Jockers, Igor Jurisica, Igor Stagljar
G-protein-coupled receptors (GPCRs) are the largest family of integral membrane receptors with key roles in regulating signaling pathways targeted by therapeutics, but are difficult to study using existing proteomics technologies due to their complex biochemical features. To obtain a global view of GPCR-mediated signaling and to identify novel components of their pathways, we used a modified membrane yeast two-hybrid (MYTH) approach and identified interacting partners for 48 selected full-length human ligand-unoccupied GPCRs in their native membrane environment...
March 15, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28297797/-research-advances-in-diagnosis-of-non-alcoholic-fatty-liver-disease
#20
J H Wang, C H Yu
Non-alcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases in clinical practice, and the spectrum of NAFLD includes nonalcoholic simple fatty liver, nonalcoholic steatohepatitis, and liver cirrhosis. Some patients may even progress to hepatocellular carcinoma. At present, the gold standard for the diagnosis of NAFLD is liver biopsy, but since this is an invasive examination and has high costs, its application is limited in clinical practice. More and more studies have focused on noninvasive diagnostic methods for NAFLD, including serological markers, fatty liver predictive model, and imaging examinations...
February 20, 2017: Zhonghua Gan Zang Bing za Zhi, Zhonghua Ganzangbing Zazhi, Chinese Journal of Hepatology
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