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https://www.readbyqxmd.com/read/28231577/response-evaluation-in-head-and-neck-oncology-definition-and-prediction
#1
T K Hoffmann, P J Schuler, S Laban, R Grässlin, M Beer, A J Beer, U Friebe-Hoffmann, L Bullinger, P Möller, T Wiegel
Curative treatment of head and neck squamous cell carcinoma includes surgery and/or (chemo)radiation, whereas in the palliative setting, chemotherapy and/or immunotherapy represent(s) the standard approach. With regard to quality control, methods for determining treatment response are sorely needed. For surgical therapy, histopathology is the standard quality control. Established criteria for high-risk patients include resection margins of the primary tumor and extracapsular extension of lymph node metastases...
February 24, 2017: ORL; Journal for Oto-rhino-laryngology and its related Specialties
https://www.readbyqxmd.com/read/28231575/individual-biomarkers-using-molecular-personalized-medicine-approaches
#2
Hans P Zenner
Molecular personalized medicine tries to generate individual predictive biomarkers to assist doctors in their decision making. These are thought to improve the efficacy and lower the toxicity of a treatment. The molecular basis of the desired high-precision prediction is modern "omex" technologies providing high-throughput bioanalytical methods. These include genomics and epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, imaging, and functional analyses. In most cases, producing big data also requires a complex biomathematical analysis...
February 24, 2017: ORL; Journal for Oto-rhino-laryngology and its related Specialties
https://www.readbyqxmd.com/read/28227255/multi-omic-approaches-for-characterization-of-hepatocellular-carcinoma
#3
Habtom W Ressom, Cristina Di Poto, Alessia Ferrarini, Yunli Hu, Mohammad R Nezami Ranjbar, Ehwang Song, Rency S Varghese, Minkun Wang, Shiyue Zhou, Rui Zhu, Yiming Zuo, Mahlet G Tadesse, Yehia Mechref, Habtom W Ressom, Cristina Di Poto, Alessia Ferrarini, Yunli Hu, Mohammad R Nezami Ranjbar, Ehwang Song, Rency S Varghese, Minkun Wang, Shiyue Zhou, Rui Zhu, Yiming Zuo, Mahlet G Tadesse, Yehia Mechref, Mahlet G Tadesse, Shiyue ZhOU, Rui Zhu, Yehia Mechref, Alessia Ferrarini, Cristina Di Poto, Yiming Zuo, Habtom W Ressom, Mohammad R Nezami Ranjbar, Ehwang Song, Minkun Wang, Rency S Varghese, Yunli Hu
Multi-omic approaches offer the opportunity to characterize complex diseases such as cancer at various molecular levels. In this paper, we present transcriptomic, proteomic/glycoproteomic, glycomic, and metabolomic (TPGM) data we acquired by analysis of liver tissues from hepatocellular carcinoma (HCC) cases and patients with liver cirrhosis. We evaluated changes in the levels of transcripts, proteins, glycans, and metabolites between tumor and cirrhotic tissues by statistical methods. We demonstrated the potential of multi-omic approaches and network analysis to investigate the interactions among these biomolecules in the progression of liver cirrhosis to HCC...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28225828/systematic-analysis-of-non-structural-protein-features-for-the-prediction-of-ptm-function-potential-by-artificial-neural-networks
#4
Henry M Dewhurst, Matthew P Torres
Post-translational modifications (PTMs) provide an extensible framework for regulation of protein behavior beyond the diversity represented within the genome alone. While the rate of identification of PTMs has rapidly increased in recent years, our knowledge of PTM functionality encompasses less than 5% of this data. We previously developed SAPH-ire (Structural Analysis of PTM Hotspots) for the prioritization of eukaryotic PTMs based on function potential of discrete modified alignment positions (MAPs) in a set of 8 protein families...
2017: PloS One
https://www.readbyqxmd.com/read/28225807/increased-liver-specific-proteins-in-circulating-extracellular-vesicles-as-potential-biomarkers-for-drug-and-alcohol-induced-liver-injury
#5
Young-Eun Cho, Eun-Ju Im, Pyong-Gon Moon, Esteban Mezey, Byoung-Joon Song, Moon-Chang Baek
Drug- and alcohol-induced liver injury are a leading cause of liver failure and transplantation. Emerging evidence suggests that extracellular vesicles (EVs) are a source of biomarkers because they contain unique proteins reflecting the identity and tissue-specific origin of the EV proteins. This study aimed to determine whether potentially hepatotoxic agents, such as acetaminophen (APAP) and binge alcohol, can increase the amounts of circulating EVs and evaluate liver-specific EV proteins as potential biomarkers for liver injury...
2017: PloS One
https://www.readbyqxmd.com/read/28224978/methylated-antibody-affinity-purification-to-improve-proteomic-identification-of-plant-rna-polymerase-pol-v-complex-and-the-interacting-proteins
#6
Guochen Qin, Jun Ma, Xiaomei Chen, Zhaoqing Chu, Yi-Min She
Affinity purification followed by enzymatic digestion and mass spectrometry has been widely utilized for the sensitive detection of interacting proteins and protein complexes in various organisms. In plants, the method is technically challenging due to the low abundance proteins, non-specific binding and difficulties of eluting interacting proteins from antibody beads. In this report, we describe a strategy to modify antibodies by reductive methylation of lysines without affecting their binding properties, followed by on-bead digestion of bound proteins with endoproteinase Lys-C...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28224023/evaluation-of-liver-cirrhosis-and-hepatocellular-carcinoma-using-protein-protein-interaction-networks
#7
Mohammad Javad Ehsani Ardakani, Akram Safaei, Afsaneh Arefi Oskouie, Hesam Haghparast, Mehrdad Haghazali, Hamid Mohaghegh Shalmani, Hassan Peyvandi, Nosratollah Naderi, Mohammad Reza Zali
AIM: In the current study, we analysised only the articles that investigate serum proteome profile of cirrhosis patients or HCC patients versus healthy controls. BACKGROUND: Increased understanding of cancer biology has enabled identification of molecular events that lead to the discovery of numerous potential biomarkers in diseases. Protein-protein interaction networks is one of aspect that could elevate the understanding level of molecular events and protein connections that lead to the identification of genes and proteins associated with diseases...
December 2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28223226/targeted-protein-degradation-by-protacs
#8
REVIEW
Taavi K Neklesa, James D Winkler, Craig M Crews
Targeted protein degradation using the PROTAC technology is emerging as a novel therapeutic method to address diseases driven by the aberrant expression of a disease-causing protein. PROTAC molecules are bifunctional small molecules that simultaneously bind a target protein and an E3-ubiquitin ligase, thus causing ubiquitination and degradation of the target protein by the proteasome. Like small molecules, PROTAC molecules possess good tissue distribution and the ability to target intracellular proteins. Herein, we highlight the advantages of protein degradation using PROTACs, and provide specific examples where degradation offers therapeutic benefit over classical enzyme inhibition...
February 13, 2017: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28223178/direct-experimental-manipulation-of-intestinal-cells-in-ascaris-suum-with-minor-influences-on-the-global-transcriptome
#9
Bruce A Rosa, Samantha N McNulty, Makedonka Mitreva, Douglas P Jasmer
Ascaris suum provides a powerful model for studying parasitic nematodes, including individual tissues such as the intestine, an established target for anthelmintic treatments. Here, we add a valuable experimental component to our existing functional, proteomic, transcriptomic and phylogenomic studies of the Ascaris suum intestine, by developing a method to manipulate intestinal cell functions via direct delivery of experimental treatments (in this case, double-stranded (ds)RNA) to the apical intestinal membrane...
February 18, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28223106/diagnosis-of-major-depressive-disorder-by-combining-multimodal-information-from-heart-rate-dynamics-and-serum-proteomics-using-machine-learning-algorithm
#10
Eun Young Kim, Min Young Lee, Se Hyun Kim, Kyooseob Ha, Kwang Pyo Kim, Yong Min Ahn
OBJECTIVE: Major depressive disorder (MDD) is a systemic and multifactorial disorder that involves abnormalities in multiple biochemical pathways and the autonomic nervous system. This study applied a machine-learning method to classify MDD and control groups by incorporating data from serum proteomic analysis and heart rate variability (HRV) analysis for the identification of novel peripheral biomarkers. METHODS: The study subjects consisted of 25 drug-free female MDD patients and 25 age- and sex-matched healthy controls...
February 18, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28222617/presynaptic-calmodulin-targets-lessons-from-structural-proteomics
#11
Noa Lipstein, Melanie Göth, Christine Piotrowski, Kevin Pagel, Andrea Sinz, Olaf Jahn
Calmodulin (CaM) is a highly conserved Ca(2+)-binding protein that is exceptionally abundant in the brain. In the presynaptic compartment of neurons, CaM transduces changes in Ca(2+) concentration into the regulation of synaptic transmission dynamics. Areas covered: We review selected literature including published CaM interactor screens and outline established and candidate presynaptic CaM targets. We present a workflow of biochemical and structural proteomic methods that were used to identify and characterize the interactions between CaM and Munc13 proteins...
March 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28221766/proteoform-profile-mapping-of-the-human-serum-complement-component-c9-reveals-unexpected-new-features-of-n-o-and-c-glycosylation
#12
Vojtech Franc, Yang Yang, Albert J R Heck
The human complement C9 protein (~65 kDa) is a member of the complement pathway. It plays an essential role in the membrane attack complex (MAC), which forms a lethal pore on the cellular surface of pathogenic bacteria. Here, we charted in detail the structural micro-heterogeneity of C9 purified from human blood serum, using an integrative workflow combining high-resolution native mass spectrometry and (glyco)peptide-centric proteomics. The proteoform profile of C9 was acquired by high-resolution native mass spectrometry, which revealed the co-occurrence of ~50 distinct MS signals...
February 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28221344/chemoproteomic-profiling-and-discovery-of-protein-electrophiles-in-human-cells
#13
Megan L Matthews, Lin He, Benjamin D Horning, Erika J Olson, Bruno E Correia, John R Yates, Philip E Dawson, Benjamin F Cravatt
Activity-based protein profiling (ABPP) serves as a chemical proteomic platform to discover and characterize functional amino acids in proteins on the basis of their enhanced reactivity towards small-molecule probes. This approach, to date, has mainly targeted nucleophilic functional groups, such as the side chains of serine and cysteine, using electrophilic probes. Here we show that 'reverse-polarity' (RP)-ABPP using clickable, nucleophilic hydrazine probes can capture and identify protein-bound electrophiles in cells...
March 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28220420/identification-of-mapk-substrates-using-quantitative-phosphoproteomics
#14
Tong Zhang, Jacqueline D Schneider, Ning Zhu, Sixue Chen
Activation of mitogen-activated protein kinases (MAPKs) under diverse biotic and abiotic factors and identification of an array of downstream MAPK target proteins are hot topics in plant signal transduction. Through interactions with a plethora of substrate proteins, MAPK cascades regulate many physiological processes in the course of plant growth, development, and response to environmental factors. Identification and quantification of potential MAPK substrates are essential, but have been technically challenging...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28216224/targeted-proteomics-driven-verification-of-biomarker-candidates-associated-with-breast-cancer-aggressiveness
#15
Iva Procházková, Juraj Lenčo, Alena Fučíková, Jiří Dresler, Lenka Čápková, Roman Hrstka, Rudolf Nenutil, Pavel Bouchal
Breast cancer is the most common and molecularly relatively well characterized malignant disease in women, however, its progression to metastatic cancer remains lethal for 78% of patients 5years after diagnosis. Novel markers could identify the high risk patients and their verification using quantitative methods is essential to overcome genetic, inter-tumor and intra-tumor variability and translate novel findings into cancer diagnosis and treatment. We recently identified 13 proteins associated with estrogen receptor, tumor grade and lymph node status, the key factors of breast cancer aggressiveness, using untargeted proteomics...
February 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28214294/ptk6-localized-at-the-plasma-membrane-promotes-cell-proliferation-and-migration-through-phosphorylation-of-eps8
#16
Won-Sik Shin, Hyun Jae Shim, Young Hun Lee, Minju Pyo, Jun Sang Park, So Yun Ahn, Seung-Taek Lee
Protein tyrosine kinase 6 (PTK6; also known as Brk) is closely related to the Src family kinases, but lacks a membrane-targeting myristoylation signal. Sublocalization of PTK6 at the plasma membrane enhances its oncogenic potential. To understand the mechanism(s) underlying the oncogenic property of plasma-membrane-associated PTK6, proteins phosphorylated by membrane-targeted myristoylated PTK6 (Myr-PTK6) were enriched and analyzed using a proteomics approach. Eps8 which was identified by this method is phosphorylated by Myr-PTK6 in HEK293 cells...
February 18, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28213880/detection-of-digestive-malignancies-and-post-gastrectomy-complications-via-gastrointestinal-fluid-examination
#17
REVIEW
Lei Huang, Aman Xu
To date, gastric carcinoma (GC) is one of the common and fatal digestive malignancies worldwide. The prognosis of GC is not always satisfactory because of late diagnosis. Scholars are keen on discovering novel accurate and economical biomarkers in body liquids for GC screening to detect and evaluate the lesion before the results of imaging techniques are obtained. While traditional serum assays have limited sensitivity and specificity, gastrointestinal juice may provide relevant specific biomarkers because of its close contact with the tumor...
February 17, 2017: Frontiers of Medicine
https://www.readbyqxmd.com/read/28213128/quantitative-proteomic-analysis-of-human-testis-reveals-system-wide-molecular-and-cellular-pathways-associated-with-non-obstructive-azoospermia
#18
Mehdi Alikhani, Mehdi Mirzaei, Marjan Sabbaghian, Pouria Parsamatin, Razieh Karamzadeh, Samane Adib, Niloofar Sodeifi, Mohammad Ali Sadighi Gilani, Masoud Zabet-Moghaddam, Lindsay Parker, Yunqi Wo, Vivek Gupta, Paul A Haynes, Hamid Gourabi, Hossein Baharvand, Ghasem Hosseini Salekdeh
: Male infertility accounts for half of the infertility problems experienced by couples. Azoospermia, having no measurable level of sperm in seminal fluid, is one of the known conditions resulting in male infertility. In order to elucidate the complex molecular mechanisms causing male azoospermia, label-free quantitative shotgun proteomics was carried out on testicular tissue specimens from patients with obstructive azoospermia and non-obstructive azoospermia, including maturation arrest (MA) and Sertoli cell only syndrome (SCOS)...
February 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28210565/label-free-proteome-analysis-of-plasma-from-patients-with-breast-cancer-stage-specific-protein-expression
#19
Marina Duarte Pinto Lobo, Frederico Bruno Mendes Batista Moreno, Gustavo Henrique Martins Ferreira Souza, Sara Maria Moreira Lima Verde, Renato de Azevedo Moreira, Ana Cristina de Oliveira Monteiro-Moreira
Breast cancer is one of the most commonly diagnosed types of cancer among women. Breast cancer mortality rates remain high probably because its diagnosis is hampered by inaccurate detection methods. Since changes in protein expression as well as modifications in protein glycosylation have been frequently reported in cancer development, the aim of this work was to study the differential expression as well as modifications of glycosylation of proteins from plasma of women with breast cancer at different stages of disease (n = 30) compared to healthy women (n = 10)...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/28208246/combined-proteome-and-eicosanoid-profiling-approach-for-revealing-implications-of-human-fibroblasts-in-chronic-inflammation
#20
Ammar Tahir, Andrea Bileck, Besnik Muqaku, Laura Niederstaetter, Dominique Kreutz, Rupert L Mayer, Denise Wolrab, Samuel M Meier, Astrid Slany, Christopher Gerner
During inflammation, proteins and lipids act in a concerted fashion, calling for combined analyses. Fibroblasts are powerful mediators of chronic inflammation. However, little is known about eicosanoid formation by human fibroblasts. The aim of this study was to analyze the formation of the most relevant inflammation mediators including proteins and lipids in human fibroblasts upon inflammatory stimulation and subsequent treatment with dexamethasone, a powerful antiphlogistic drug. Label-free quantification was applied for proteome profiling, while an in-house established data-dependent analysis method based on high-resolution mass spectrometry was applied for eicosadomics...
February 7, 2017: Analytical Chemistry
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