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https://www.readbyqxmd.com/read/29452276/application-of-targeted-mass-spectrometry-in-bottom-up-proteomics-for-systems-biology-research
#1
Nathan P Manes, Aleksandra Nita-Lazar
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples...
February 13, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29450702/establishment-and-characterization-of-the-ncc-ss1-c1-synovial-sarcoma-cell-line
#2
Fusako Kito, Rieko Oyama, Yoko Takai, Marimu Sakumoto, Kumiko Shiozawa, Zhiwei Qiao, Takenori Uehara, Akihiko Yoshida, Akira Kawai, Tadashi Kondo
Synovial sarcoma is an aggressive mesenchymal malignancy characterized by unique gene fusions. Tissue culture cells are essential tools for further understanding tumorigenesis and anti-cancer drug development; however, only a limited number of well-characterized synovial sarcoma cell lines exist. Thus, the objective of this study was to establish a patient-derived synovial sarcoma cell line. We established a synovial sarcoma cell line from tumor tissue isolated from a 72-year-old female patient. Prepared cells were analyzed for the presence of gene fusions by fluorescence in situ hybridization, RT-PCR, and karyotyping...
February 15, 2018: Human Cell
https://www.readbyqxmd.com/read/29450650/access-to-the-cns-biomarker-strategies-for-dopaminergic-treatments
#3
REVIEW
Willem Johan van den Brink, Semra Palic, Isabelle Köhler, Elizabeth Cunera Maria de Lange
Despite substantial research carried out over the last decades, it remains difficult to understand the wide range of pharmacological effects of dopaminergic agents. The dopaminergic system is involved in several neurological disorders, such as Parkinson's disease and schizophrenia. This complex system features multiple pathways implicated in emotion and cognition, psychomotor functions and endocrine control through activation of G protein-coupled dopamine receptors. This review focuses on the system-wide effects of dopaminergic agents on the multiple biochemical and endocrine pathways, in particular the biomarkers (i...
February 15, 2018: Pharmaceutical Research
https://www.readbyqxmd.com/read/29449793/clinical-proteomic-analysis-of-scrub-typhus-infection
#4
Edmond Changkyun Park, Sang-Yeop Lee, Sung Ho Yun, Chi-Won Choi, Hayoung Lee, Hyun Seok Song, Sangmi Jun, Gun-Hwa Kim, Chang-Seop Lee, Seung Il Kim
Background: Scrub typhus is an acute and febrile infectious disease caused by the Gram-negative α-proteobacterium Orientia tsutsugamushi from the family Rickettsiaceae that is widely distributed in Northern, Southern and Eastern Asia. In the present study, we analysed the serum proteome of scrub typhus patients to investigate specific clinical protein patterns in an attempt to explain pathophysiology and discover potential biomarkers of infection. Methods: Serum samples were collected from three patients (before and after treatment with antibiotics) and three healthy subjects...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29448056/proteomic-analysis-of-first-trimester-maternal-serum-to-identify-candidate-biomarkers-potentially-predictive-of-spontaneous-preterm-birth
#5
Arlene M D'Silva, Jon A Hyett, Jens R Coorssen
Spontaneous preterm birth (sPTB) remains a major clinical dilemma; current diagnostics and interventions have not reduced the rate of this serious healthcare burden. This study characterizes differential protein profiles and post-translational modifications (PTMs) in first trimester maternal serum using a refined top-down approach coupling two-dimensional gel electrophoresis (2DE) and mass spectrometry (MS) to directly compare subsequent term and preterm labour events and identify marked protein differences...
February 12, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29448055/proteomic-characterization-of-withaferin-a-targeted-protein-networks-for-the-treatment-of-monoclonal-myeloma-gammopathies
#6
Martin Dom, Fritz Offner, Wim Vanden Berghe, Xaveer Van Ostade
Withaferin A (WA), a natural steroid lactone from the plant Withania somnifera, is often studied because of its antitumor properties. Although many in vitro and in vivo studies have been performed, the identification of Withaferin A protein targets and its mechanism of antitumor action remain incomplete. We used quantitative chemoproteomics and differential protein expression analysis to characterize the WA antitumor effects on a multiple myeloma cell model. Identified relevant targets were further validated by Ingenuity Pathway Analysis and Western blot and indicate that WA targets protein networks that are specific for monoclonal gammopathy of undetermined significance (MGUS) and other closely related disorders, such as multiple myeloma (MM) and Waldenström macroglobulinemia (WM)...
February 12, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29447837/analyses-of-the-molecular-mechanisms-associated-with-salinity-adaption-of-trachidermus-fasciatus-through-combined-itraq-based-proteomics-and-rna-sequencing-based-transcriptomics
#7
REVIEW
Qian Ma, Xinfu Liu, Wenrong Feng, Shufang Liu, Zhimeng Zhuang
Osmoregulation mechanism underlying acclimation and adaptation of migratory fish to different salinities has been studied for decades. Recently developed transcriptomic and proteomic techniques would make it possible to provide more reliable data to decipher the mechanism study at a molecular level. Here in this study, an integrative analysis of the kidney-specific transcriptome and proteome was performed to identify important regulators and pathways involved in salinity adaption of roughskin sculpin (Trachidermus fasciatus)...
February 12, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/29445034/the-skp1-cullin-f-box-e3-ligase-%C3%AE-trcp-and-cdk2-cooperate-to-control-stil-abundance-and-centriole-number
#8
Christian Arquint, Fabien Cubizolles, Agathe Morand, Alexander Schmidt, Erich A Nigg
Deregulation of centriole duplication has been implicated in cancer and primary microcephaly. Accordingly, it is important to understand how key centriole duplication factors are regulated. E3 ubiquitin ligases have been implicated in controlling the levels of several duplication factors, including PLK4, STIL and SAS-6, but the precise mechanisms ensuring centriole homeostasis remain to be fully understood. Here, we have combined proteomics approaches with the use of MLN4924, a generic inhibitor of SCF E3 ubiquitin ligases, to monitor changes in the cellular abundance of centriole duplication factors...
February 2018: Open Biology
https://www.readbyqxmd.com/read/29444441/initiating-events-in-direct-cardiomyocyte-reprogramming
#9
Kimberly Sauls, Todd M Greco, Li Wang, Meng Zou, Michelle Villasmil, Li Qian, Ileana M Cristea, Frank L Conlon
Direct reprogramming of fibroblasts into cardiomyocyte-like cells (iCM) holds great potential for heart regeneration and disease modeling and may lead to future therapeutic applications. Currently, application of this technology is limited by our lack of understanding of the molecular mechanisms that drive direct iCM reprogramming. Using a quantitative mass spectrometry-based proteomic approach, we identified the temporal global changes in protein abundance that occur during initial phases of iCM reprogramming...
February 13, 2018: Cell Reports
https://www.readbyqxmd.com/read/29442729/genomic-and-proteomic-evidences-for-exopolysaccharide-biosynthesis-in-sphingobium-chungbukense-dj77
#10
Soo Youn Lee, Simranjeet Singh Sekhon, Mihye Kim, Ji-Young Ahn, Hyung Cheol Kim, Young-Chang Kim, Yang-Hoon Kim
Sphingobium chungbukense DJ77 is a Gram-negative bacterium has metabolic capability of producing exopolysaccharide (EPS) as a potential reducing and stabilizing agent for metallic nanoparticle synthesis. In this study, we investigated the genomic and proteomic analysis to verify metabolic pathway and involved genes and enzymes related to EPS biosynthesis in S. chungbukense DJ77. End-sequencing results of randomly selected fosmid library, which were prepared from high molecular weight DNA of S. chungbukense DJ77, showed identity to sequences from genes related the EPS biosynthesis pathways in several bacteria...
June 1, 2018: Journal of Nanoscience and Nanotechnology
https://www.readbyqxmd.com/read/29442498/proteostasis-and-the-regulation-of-intra-and-extracellular-protein-aggregation-by-atp-independent-molecular-chaperones-lens-%C3%AE-crystallins-and-milk-caseins
#11
John A Carver, Heath Ecroyd, Roger J W Truscott, David C Thorn, Carl Holt
Molecular chaperone proteins perform a diversity of roles inside and outside the cell. One of the most important is the stabilization of misfolding proteins to prevent their aggregation, a process that is potentially detrimental to cell viability. Diseases such as Alzheimer's, Parkinson's, and cataract are characterized by the accumulation of protein aggregates. In vivo, many proteins are metastable and therefore under mild destabilizing conditions have an inherent tendency to misfold, aggregate, and hence lose functionality...
February 14, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29439554/pilot-study-on-mass-spectrometry-based-analysis-of-the-proteome-of-cd34%C3%A2-%C2%BAcd123%C3%A2-%C2%BA-progenitor-cells-for-the-identification-of-potential-targets-for-immunotherapy-in-acute-myeloid-leukemia
#12
Johannes R Schmidt, Elke Rücker-Braun, Katharina Heidrich, Malte von Bonin, Friedrich Stölzel, Christian Thiede, Jan M Middeke, Gerhard Ehninger, Martin Bornhäuser, Johannes Schetelig, Kristin Schubert, Martin von Bergen, Falk Heidenreich
Targeting of leukemic stem cells with specific immunotherapy would be an ideal approach for the treatment of myeloid malignancies, but suitable epitopes are unknown. The comparative proteome-level characterization of hematopoietic stem and progenitor cells from healthy stem cell donors and patients with acute myeloid leukemia has the potential to reveal differentially expressed proteins which can be used as surface-markers or as proxies for affected molecular pathways. We employed mass spectrometry methods to analyze the proteome of the cytosolic and the membrane fraction of CD34 and CD123 co-expressing FACS-sorted leukemic progenitors from five patients with acute myeloid leukemia...
February 12, 2018: Proteomes
https://www.readbyqxmd.com/read/29439246/cyclic-mechanical-stretch-induced-smooth-muscle-cell-changes-in-cerebral-aneurysm-progress-by-reducing-collagen-type-iv-and-collagen-type-vi-levels
#13
Peixi Liu, Yaying Song, Yingjie Zhou, Yingjun Liu, Tianming Qiu, Qingzhu An, Jianping Song, Peiliang Li, Yuan Shi, Sichen Li, Kai Quan, Guo-Yuan Yang, Wei Zhu
BACKGROUND/AIMS: Cerebral aneurysm growth is characterized by continuous structural weakness of local smooth muscle cells, though the mechanism is unclear. In this study, we examine protein changes in cerebral aneurysm and human brain vascular smooth muscle cells after cyclic mechanical stretch. We further explore the relationship between the smooth muscle cell changes and reductions in the levels of collagen types IV and VI. METHODS: Saccular cerebral aneurysms (n=10) were collected, and temporal artery samples were used as controls...
February 7, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29438996/global-identification-of-sumo-substrates-reveals-crosstalk-between-sumoylation-and-phosphorylation-promotes-cell-migration
#14
Ijeoma Uzoma, Jianfei Hu, Eric Cox, Shuli Xia, Jianying Zhou, Hee-Sool Rho, Catherine Guzzo, Corry Paul, Olutobi Ajala, C Rory Goodwin, Junseop Jeong, Cedric Moore, Hui Zhang, Pamela Meluh, Seth Blackshaw, Michael Matunis, Jiang Qian, Heng Zhu
Proteomics studies have revealed that SUMOylation is widely used posttranslational modification (PTM) in eukaryotes. However, how SUMO E1/2/3 complexes use different SUMO isoforms and recognize substrates remains largely unknown.  Using a human proteome microarray-based activity screen, we identified over 2,500 proteins that undergo SUMO E3-dependent SUMOylation.  We next constructed a SUMO isoform- and E3 ligase-dependent enzyme-substrate relationship network. Protein kinases were significantly enriched among SUMOylation substrates, suggesting crosstalk between tyrosine phosphorylation and SUMOylation...
February 8, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29438453/the-role-of-silicon-in-plant-biology-a-paradigm-shift-in-research-approach
#15
Adam Frew, Leslie A Weston, Olivia L Reynolds, Geoff M Gurr
Background: Silicon (Si) is known to have numerous beneficial effects on plants, alleviating diverse forms of abiotic and biotic stress. Research on this topic has accelerated in recent years and revealed multiple effects of Si in a range of plant species. Available information regarding the impact of Si on plant defence, growth and development is fragmented, discipline-specific, and usually focused on downstream, distal phenomena rather than underlying effects. Accordingly, there is a growing need for studies that address fundamental metabolic and regulatory processes, thereby allowing greater unification and focus of current research across disciplines...
February 9, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29437671/pharmacological-tlr4-antagonism-using-topical-resatorvid-blocks-solar-uv-induced-skin-tumorigenesis-in-skh-1-mice
#16
Karen Blohm-Mangone, Nichole B Burkett, Shekha Tahsin, Paul B Myrdal, Alhassan Aodah, Brenda Ho, Jaroslav Janda, Michelle McComas, Kathylynn Saboda, Denise J Roe, Zigang Dong, Ann M Bode, Emanuel F Petricoin, Valerie S Calvert, Clara Curiel-Lewandrowski, David S Alberts, Georg T Wondrak, Sally E Dickinson
An urgent need exists for the development of more efficacious molecular strategies targeting non-melanoma skin cancer (NMSC), the most common malignancy worldwide. Inflammatory signaling downstream of Toll-like receptor 4 (TLR4) has been implicated in several forms of tumorigenesis, yet its role in solar UV-induced skin carcinogenesis remains undefined. We have previously shown in keratinocyte cell culture and SKH-1 mouse epidermis that topical application of the specific TLR4 antagonist resatorvid (TAK-242) blocks acute UV-induced AP-1 and NF-κB signaling, associated with downregulation of inflammatory mediators and MAP Kinase phosphorylation...
February 1, 2018: Cancer Prevention Research
https://www.readbyqxmd.com/read/29437267/pharmacoproteomics-profile-in-response-to-acamprosate-treatment-of-an-alcoholism-animal-model
#17
Caroline E Germany, Ashlie N Reker, David J Hinton, Alfredo Oliveros, Xinggui Shen, Lindsey G Andres-Beck, Katheryn M Wininger, Marjan Trutchul, Urska Cvek, Doo-Sup Choi, Hyung W Nam
Acamprosate is an FDA-approved medication for the treatment of alcoholism that is unfortunately only effective in certain patients. Although acamprosate known to stabilize the hyper-glutamatergic state in alcoholism, pharmacological mechanisms of action in brain tissue remains unknown. To investigate the mechanism of acamprosate efficacy, we employed a pharmacoproteomics approach using an animal model of alcoholism, type 1 equilibrative nucleoside transporter (ENT1) null mice. Our results demonstrated that acamprosate treatment significantly decreased both ethanol drinking and preference in ENT1 null mice compared to that of wild-type mice...
February 13, 2018: Proteomics
https://www.readbyqxmd.com/read/29436780/autosomal-tubulointerstitial-kidney-disease-muc1-type-differential-proteomics-suggests-that-mutated-muc1-insc-affects-vesicular-transport-in-renal-epithelial-cells
#18
Simon Staubach, Andrea Wenzel, Bodo B Beck, Markus M Rinschen, Stefan Müller, Franz-Georg Hanisch
Autosomal dominant tubulointerstitial kidney disease associated to the MUC1 gene (ADTKD-MUC1; formerly MCKD1) belongs to a heterogenous group of rare hereditary kidney diseases that is prototypically caused by frameshift mutations in the MUC1 repeat domain. The mutant MUC1(insC) lacks the transmembrane domaine, exhibits aberant cellular topology and hence might gain a function during the pathological process. To get insight into potential pathomechanisms we performed differential proteomics of extracellular vesicles shed by renal epithelia into the urine of patients...
February 13, 2018: Proteomics
https://www.readbyqxmd.com/read/29436741/targeting-epithelial-to-mesenchymal-transition-in-prostate-cancer-by-a-novel-compound-plectranthoic-acid-isolated-from-ficus-microcarpa
#19
Nosheen Akhtar, Deeba N Syed, Rahul K Lall, Bushra Mirza, Hasan Mukhtar
Epithelial-to-mesenchymal transition (EMT) plays a crucial role in prostate cancer (PCa) metastasis. This has led to a surge in the efforts for identification of safer and more effective compounds which can modulate EMT and consequently inhibiting migration and invasion of PCa cells. We reported previously that Plectranthoic acid (PA), a natural compound isolated from the extracts of Ficus microcarpa, has the capability to induce cell cycle arrest and apoptosis in PCa cells. Here, we determined the effects of PA on EMT, migration and invasion of PCa cells...
February 13, 2018: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/29436656/early-quantitative-profiling-of-differential-retinal-protein-expression-in-lens-induced-myopia-in-guinea-pig-using-fluorescence-difference-two-dimensional-gel-electrophoresis
#20
Yi Wu, Carly Siu-Yin Lam, Dennis Yan-Yin Tse, Chi Ho To, Quan Liu, Sally A McFadden, Rachel Ka-Man Chun, King Kit Li, Jianfang Bian, Chuen Lam
The current study aimed to investigate the differential protein expression in guinea pig retinas in response to lens-induced myopia (LIM) before fully compensated eye growth. Four days old guinea pigs (n=5) were subjected to ‑4D LIM for 8 days. Refractive errors were measured before and at the end of the lens wear period. Ocular dimensions were also recorded using high‑frequency A‑scan ultrasonography. After the LIM treatment, retinas of both eyes were harvested and soluble proteins were extracted. Paired retinal protein expressions in each animal were profiled and compared using a sensitive fluorescence difference two‑dimensional gel electrophoresis...
February 8, 2018: Molecular Medicine Reports
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