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Clinical Proteomics

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https://www.readbyqxmd.com/read/29935335/top-down-characterization-of-chicken-core-histones
#1
Hao Wu, Kaijie Xiao, Zhixin Tian
Core histones and their PTMs play important roles in regulating gene transcription and other DNA-related processes. The study of core histones PTMs, their cross-talk and functional roles is not only of broad biological significance but also of wide pathological and clinical relevance. Having the strength of comprehensive proteoform identification with 100% amino acid sequence coverage and combinatorial PTMs, top-down proteomics has become the state-of-the-art analytical tool for combinatorial PTM characterization of core histones...
June 20, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29927718/multiomics-data-triangulation-for-asthma-candidate-biomarkers-and-precision-medicine
#2
Matija Pecak, Peter Korošec, Tanja Kunej
Asthma is a common complex disorder and has been subject to intensive omics research for disease susceptibility and therapeutic innovation. Candidate biomarkers of asthma and its precision treatment demand that they stand the test of multiomics data triangulation before they can be prioritized for clinical applications. We classified the biomarkers of asthma after a search of the literature and based on whether or not a given biomarker candidate is reported in multiple omics platforms and methodologies, using PubMed and Web of Science, we identified omics studies of asthma conducted on diverse platforms using keywords, such as asthma, genomics, metabolomics, and epigenomics...
June 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29925955/a-multiprotein-supercomplex-controlling-oncogenic-signalling-in-lymphoma
#3
James D Phelan, Ryan M Young, Daniel E Webster, Sandrine Roulland, George W Wright, Monica Kasbekar, Arthur L Shaffer, Michele Ceribelli, James Q Wang, Roland Schmitz, Masao Nakagawa, Emmanuel Bachy, Da Wei Huang, Yanlong Ji, Lu Chen, Yandan Yang, Hong Zhao, Xin Yu, Weihong Xu, Maryknoll M Palisoc, Racquel R Valadez, Theresa Davies-Hill, Wyndham H Wilson, Wing C Chan, Elaine S Jaffe, Randy D Gascoyne, Elias Campo, Andreas Rosenwald, German Ott, Jan Delabie, Lisa M Rimsza, Fausto J Rodriguez, Fayez Estephan, Matthias Holdhoff, Michael J Kruhlak, Stephen M Hewitt, Craig J Thomas, Stefania Pittaluga, Thomas Oellerich, Louis M Staudt
B cell receptor (BCR) signaling has emerged as a therapeutic target in B cell lymphomas, but inhibiting this pathway in diffuse large B cell lymphoma (DLBCL) has benefited only a subset of patients1 . Gene expression profiling identified two major DLBCL subtypes, known as germinal center (GC) B cell-like (GCB) and activated B cell-like (ABC)2,3 , with inferior outcomes following immunochemotherapy in ABC. Autoantigens drive BCR-dependent activation of NF-κB in ABC DLBCL through a kinase cascade of SYK, BTK and PKCβ to promote the assembly of the CARD11-BCL10-MALT1 (CBM) adapter complex that recruits and activates IκB kinase (IKK)4-6 ...
June 20, 2018: Nature
https://www.readbyqxmd.com/read/29925527/identification-of-fda-approved-oncology-drugs-with-selective-potency-in-high-risk-childhood-ependymoma
#4
Andrew M Donson, Vladimir Amani, Elliot A Warner, Andrea M Griesinger, Davis A Witt, Jean M Mulcahy Levy, Lindsey M Hoffman, Todd C Hankinson, Michael H Handler, Rajeev Vibhakar, Kathleen Dorris, Nicholas K Foreman
Children with ependymoma are cured in less than 50% of cases, with little improvement in outcome over the last several decades. Chemotherapy has not impacted survival in ependymoma, due in part to a lack of preclinical models that has precluded comprehensive drug testing. We recently developed two human ependymoma cell lines harboring high-risk phenotypes which provided us with an opportunity to execute translational studies. ependymoma and other pediatric brain tumor cell lines were subject to a large-scale comparative drug screen of ependymoma -approved oncology drugs for rapid clinical application...
June 20, 2018: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/29924981/quantitative-proteomic-analysis-and-antivenom-study-revealing-that-neurotoxic-phospholipase-a-2-enzymes-the-major-toxin-class-of-russell-s-viper-venom-from-southern-india-shows-the-least-immuno-recognition-and-neutralization-by-commercial-polyvalent-antivenom
#5
Bhargab Kalita, Sudeepa Singh, Aparup Patra, Ashis K Mukherjee
The proteome composition of Russell's viper venom (RVV) from southern India (SI) was investigated by 1D-SDS-PAGE of venom followed by tandem mass spectrometry analysis of protein bands. A total of 66 proteins belonging to 14 snake venom protein families were identified by LC-MS/MS analysis against Viperidae (taxid 8689) protein entries from the non-redundant NCBI database. Phospholipase A2 (43.25%) and snaclec (14.57%) represented the most abundant enzymatic and non-enzymatic proteins, respectively. SI RVV was characterized as containing a higher quantity of PLA2 and a lower amount of Kunitz-type serine protease inhibitors, in comparison to RVV from other regions of the Indian subcontinent...
June 17, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29924966/a-proteomic-variant-approach-provara-for-personalized-medicine-of-inherited-and-somatic-disease
#6
DarrenM Hutt, Salvatore Loguercio, Alexandre Rosa Campos, William E Balch
The advent of precision medicine for genetic diseases has been hampered by the large number of variants that cause familial and somatic disease, a complexity that is further confounded by the impact of genetic modifiers. To begin to understand differences in onset, progression and therapeutic response that exist among disease-causing variants, we present the proteomic variant approach (ProVarA), a proteomic method that integrates mass spectrometry with genomic tools to dissect the etiology of disease. To illustrate its value, we examined the impact of variation in cystic fibrosis (CF), where 2025 disease-associated mutations in the CF transmembrane conductance regulator (CFTR) gene have been annotated and where individual genotypes exhibit phenotypic heterogeneity and response to therapeutic intervention...
June 17, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29922073/identification-of-pgam1-as-a-putative-therapeutic-target-for-pancreatic-ductal-adenocarcinoma-metastasis-using-quantitative-proteomics
#7
Xinlu Liu, Yejing Weng, Peng Liu, Zhigang Sui, Lei Zhou, Yinpeng Huang, Lihua Zhang, Yukui Zhang, Xiaodong Tan
Background: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive gastrointestinal cancer characterized by an extremely low survival rate because of early metastasis. Identifying satisfactory therapeutic targets associated with metastasis is crucial to improve the treatment effect of PDAC. Materials and methods: In this research, we used stable isotope labeling by amino acids in cell culture, 1-dodecyl-3-methylimidazolium chloride-assisted sample preparation method preparing protein sample and nano-reversed-phase liquid chromatography-mass spectrometry/mass spectrometry analysis to perform the comparative proteomics of two homologous hamster pancreatic cancer cell lines that are different in metastatic ability: PC-1...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29921511/the-lncrna-snhg3-regulates-energy-metabolism-of-ovarian-cancer-by-an-analysis-of-mitochondrial-proteomes
#8
Na Li, Xiaohan Zhan, Xianquan Zhan
BACKGROUND: Malignant tumors are heterogeneous diseases characterized by different metabolic phenotypes. These were revealed by Warburg effect and reverse Warburg effect phenotypes. However, the molecular mechanism remains largely unknown. METHODS: Isobaric tag for relative and absolute quantification (iTRAQ) proteomics was used to identify mitochondrial differentially expressed proteins (DEPs) of ovarian cancers relative to controls, followed by bioinformatic analysis...
June 16, 2018: Gynecologic Oncology
https://www.readbyqxmd.com/read/29921293/chip-functions-as-an-oncogene-by-promoting-colorectal-cancer-metastasis-via-activation-of-mapk-and-akt-signaling-and-suppression-of-e-cadherin
#9
Jingjing Xu, Jun Zhou, Hanjue Dai, Fei Liu, Wenjing Li, Wenjuan Wang, Feng Guo
BACKGROUND: The carboxyl terminus of Hsc70-interacting protein (CHIP) is an E3 ubiquitin ligase that plays a controversial role in different cancers, either as a tumor suppressor or a tumor promoter. To date, the exact function and underlying mechanism of CHIP in colorectal cancer (CRC) is not yet clear. Here we aimed to determine whether CHIP could affect the biological behaviors of CRC cells and its underlying mechanisms. METHODS: Stably transfected CHIP overexpression and depletion DLD-1 and HT-29 cells were established using Lipofectamine 2000...
June 19, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29915593/detection-of-glycan-shedding-in-the-blood-new-class-of-multiple-sclerosis-biomarkers
#10
Brian DellaValle, Alba Manresa-Arraut, Henrik Hasseldam, Allan Stensballe, Jørgen Rungby, Agnete Larsen, Casper Hempel
Introduction: Multiple sclerosis (MS) is a devastating autoimmune disease, afflicting people in the prime of their lives. Presently, after initial clinical presentation, there are no reliable markers for whether a patient will develop MS, or whether their prognosis will be aggressive or relapsing-remitting. Furthermore, many MS patients do not respond to treatment. Thus, markers for diagnosis, prognosis, and treatment-responsiveness are lacking for a disease, where a precision medicine approach would be valuable...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29915313/in-vitro-inhibition-of-hepatic-stellate-cell-activation-by-the-autophagy-related-lipid-droplet-protein-atg2a
#11
Yun Hong, Sirui Li, Jifeng Wang, Youming Li
Clinical studies have found that moderate intake of retinol or oleic acid can enlarge the lipid droplets of hepatic stellate cells and suppress their activation. However, the link between lipid droplets and cell activation is unknown. This study compared the dynamics of lipid droplet-associated protein expression between activated and reverted stellate cells. Reversion of the activated human stellate cell line LX-2 and inhibition of primary mouse stellate cell activation were induced by retinol or oleic acid, which resulted in larger lipid droplets and the downregulation of cell activation markers...
June 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29915149/glycomic-and-proteomic-changes-in-aging-brain-nigrostriatal-pathway
#12
Rekha Raghunathan, Nicole K Polinski, Joshua A Klein, John D Hogan, Chun Shao, Kshitij Khatri, Deborah R Leon, Mark E McComb, Fredric P Manfredsson, Caryl E Sortwell, Joseph Zaia
Parkinson's disease (PD) is a neurological disorder characterized by the progressive loss of functional dopaminergic neurons in the nigrostriatal pathway in the brain.  While current treatments provide only symptomatic relief, gene therapy has the potential to slow or halt the degeneration of nigrostriatal dopamine neurons in PD patients. Adeno-associated viruses (AAV) are vectors of choice in gene therapy due to their well-characterized safety and efficacy profiles; however, while gene therapy has been successful in preclinical models of the disease, clinical trials in humans have failed to demonstrate efficacy...
June 18, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29915101/proteomic-architecture-of-human-coronary-and-aortic-atherosclerosis
#13
David M Herrington, Chunhong Mao, Sarah J Parker, Zongming Fu, Guoqiang Yu, Lulu Chen, Vidya Venkatraman, Yi Fu, Yizhi Wang, Timothy D Howard, Goo Jun, Caroline F Zhao, Yongmei Liu, Georgia Saylor, Weston R Spivia, Grace B Athas, Dana Troxclair, James E Hixson, Richard S Vander Heide, Yue Wang, Jennifer E Van Eyk
BACKGOUND: The inability to detect premature atherosclerosis significantly hinders implementation of personalized therapy to prevent coronary heart disease. A comprehensive understanding of arterial protein networks and how they change in early atherosclerosis could identify new biomarkers for disease detection and improved therapeutic targets. METHODS: Here we describe the human arterial proteome and proteomic features strongly associated with early atherosclerosis based on mass spectrometry analysis of coronary artery and aortic specimens from 100 autopsied young adults (200 arterial specimens)...
June 19, 2018: Circulation
https://www.readbyqxmd.com/read/29905852/omics-studies-for-comprehensive-understanding-of-immunoglobulin-a-nephropathy-state-of-the-art-and-future-directions
#14
Francesco Paolo Schena, Grazia Serino, Fabio Sallustio, Mario Falchi, Sharon N Cox
Immunoglobulin A nephropathy (IgAN) is the most common worldwide primary glomerulonephritis with a strong autoimmune component. The disease shows variability in both clinical phenotypes and endpoints and can be potentially subdivided into more homogeneous subtypes through the identification of specific molecular biomarkers. This review focuses on the role of omics in driving the identification of potential molecular subtypes of the disease through the integration of multilevel data from genomics, transcriptomics, epigenomics, proteomics and metabolomics...
June 13, 2018: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/29905355/-radiomics-big-data-instead-of-biopsies-in-the-future
#15
Kathrin Scheckenbach
Precision medicine is increasingly pushed forward, also with respect to upcoming new targeted therapies. Individual characterization of diseases on the basis of biomarkers is a prerequisite for this development. So far, biomarkers are characterized clinically, histologically or on a molecular level. The implementation of broad screening methods ("Omics") and the analysis of big data - in addition to single markers - allow to define biomarker signatures. Next to "Genomics", "Proteomics", and "Metabolicis", "Radiomics" gained increasing interest during the last years...
March 2018: Laryngo- Rhino- Otologie
https://www.readbyqxmd.com/read/29904612/proteomic-identification-of-potential-markers-of-myosteatosis-in-human-urine
#16
Holger Husi, Alisdair MacDonald, Richard J E Skipworth, Janice Miller, Andrew Cronshaw, Kenneth C H Fearon, James A Ross
Myosteatosis, the infiltration of fat in skeletal muscle, is associated with lower skeletal muscle density (SMD) as detected by computed tomography (CT). It increases with aging and obesity and is thought to play a role in the aetiology of insulin resistance and type II diabetes. The clinical significance of myosteatosis in cancer cachexia, however, remains to be determined. Along with demonstrable subcutaneous and visceral lipolysis, myosteatosis may also be a key component of the syndrome. We aimed to investigate the use of human urine as a non-invasive way to screen for molecular biomarkers of myosteatosis/reduced SMD using SELDI-TOF mass spectrometry...
June 2018: Biomedical Reports
https://www.readbyqxmd.com/read/29904611/urinary-diagnostic-proteomic-markers-for-dynapenia-in-cancer-patients
#17
Holger Husi, Alisdair MacDonald, Richard J E Skipworth, Janice Miller, Andrew Cronshaw, Carolyn Greig, Kenneth C H Fearon, James A Ross
Dynapenia is defined as the age-related loss of muscle strength, and plays a significant role in the loss of physical function and increased risk of disability among older individuals. The need for an early diagnosis supports the search for a biomarker that reflects muscle 'weakening'. This has previously proven difficult due to patient heterogeneity at presentation and lack of understanding of the underlying molecular mechanisms. The aim of the present study was to identify potential urinary biomarkers of dynapenia in patients undergoing potentially curative surgery for upper gastrointestinal cancer...
June 2018: Biomedical Reports
https://www.readbyqxmd.com/read/29904594/towards-precision-medicine-the-application-of-omics-technologies-in-asthma-management
#18
Chiara Scelfo, Carla Galeone, Francesca Bertolini, Marco Caminati, Patrizia Ruggiero, Nicola Facciolongo, Francesco Menzella
Asthma is a chronic obstructive respiratory disease characterised by bronchial inflammation. Its biological and clinical features have been widely explored and a number of pharmacological treatments are currently available. Currently several aspects of asthma pathophysiological background remain unclear, and this is crucial for the traditional asthma phenotype approach as well as for new endotype definition. In this scenario, the identification of new molecular and clinical biomarkers may be helpful in order to better understand the disease, define specific diagnostic tools and highlight relevant novel targets for pharmacology treatments...
2018: F1000Research
https://www.readbyqxmd.com/read/29904402/identification-of-csf-biomarkers-by-proteomics-in-guillain-barr%C3%A3-syndrome
#19
Pei Li, Sujie Wang, Ruili Zhang, Jian Pei, Lili Chen, Yibin Cao, Haoliang Zhang, Guofeng Yang
The purpose of the present study was to screen for differentially expressed proteins in the cerebrospinal fluid (CSF) of patients with Guillain-Barré syndrome (GBS). The identification of differentially expressed protein can provide new targets for understanding the pathogenic mechanism, early clinical diagnosis, prognosis and for measuring the effectiveness of interventions. We enrolled 50 GBS patients and 50 meningitis patients (control group) to compare protein expression in CSF. The GBS cases included 28 cases of acute inflammatory demyelinating polyneuropathy (AIDP) and 22 cases of acute motor axonal neuropathy (AMAN)...
June 2018: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29903999/high-throughput-identification-of-mammalian-secreted-proteins-using-species-specific-scheme-and-application-to-human-proteome
#20
Jian Zhang, Haiting Chai, Song Guo, Huaping Guo, Yanling Li
Secreted proteins are widely spread in living organisms and cells. Since secreted proteins are easy to be detected in body fluids, urine, and saliva in clinical diagnosis, they play important roles in biomarkers for disease diagnosis and vaccine production. In this study, we propose a novel predictor for accurate high-throughput identification of mammalian secreted proteins that is based on sequence-derived features. We combine the features of amino acid composition, sequence motifs, and physicochemical properties to encode collected proteins...
June 14, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
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