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intact cell protein profiling

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https://www.readbyqxmd.com/read/28510335/proteoforms-in-peripheral-blood-mononuclear-cells-as-novel-rejection-biomarkers-in-liver-transplant-recipients
#1
T K Toby, M Abecassis, K Kim, P M Thomas, R T Fellers, R D LeDuc, N L Kelleher, J Demetris, J Levitsky
Biomarker profiles of acute rejection in liver transplant recipients could enhance the diagnosis and management of recipients. Our aim was to identify diagnostic proteoform signatures of acute rejection in circulating immune cells, using an emergent "top down" proteomics methodology. We prepared differentially processed and cryopreserved cell lysates from 26 non-viral liver transplant recipients by molecular weight-based fractionation and analyzed them by mass spectrometry of whole proteins in three steps: 1) Nanocapillary liquid chromatography coupled with high-resolution tandem mass spectrometry; 2) database searching to identify and characterize intact proteoforms; 3) data processing through a hierarchical linear model matching the study design to quantify proteoform fold changes in patients with rejection vs...
May 16, 2017: American Journal of Transplantation
https://www.readbyqxmd.com/read/28481867/the-rb-il-6-axis-controls-self-renewal-and-endocrine-therapy-resistance-by-fine-tuning-mitochondrial-activity
#2
S Kitajima, A Yoshida, S Kohno, F Li, S Suzuki, N Nagatani, Y Nishimoto, N Sasaki, H Muranaka, Y Wan, T C Thai, N Okahashi, F Matsuda, H Shimizu, T Nishiuchi, Y Suzuki, K Tominaga, N Gotoh, M Suzuki, M E Ewen, D A Barbie, O Hirose, T Tanaka, C Takahashi
Retinoblastoma (RB) protein inactivation during tumor progression is often associated with acquisition of immature phenotypes and resistance to therapy. Determination of an RB inactivation signature in a context of gaining undifferentiated phenotype in a p53-null sarcoma system revealed a critical role for interleukin (IL)-6. Using a Gene Set Enrichment Analysis (GSEA), we discovered that poorly differentiated breast cancers are enriched for this RB inactivation signature. Accelerated IL-6 secretion following RB inactivation in an RB-intact luminal-type breast cancer cell line MCF-7 promoted a positive feed forward loop between IL-6 and STAT3 driving tumor growth and endocrine therapy resistance...
May 8, 2017: Oncogene
https://www.readbyqxmd.com/read/28412815/high-throughput-analysis-of-intact-human-proteins-using-uvpd-and-hcd-on-an-orbitrap-mass-spectrometer
#3
Timothy P Cleland, Caroline J DeHart, Ryan T Fellers, Alexandra J VanNispen, Joseph B Greer, Richard D LeDuc, W Ryan Parker, Paul M Thomas, Neil L Kelleher, Jennifer S Brodbelt
The analysis of intact proteins (top-down strategy) by mass spectrometry has great potential to elucidate proteoform variation, including patterns of post-translational modifications (PTMs), which may not be discernible by analysis of peptides alone (bottom-up approach). To maximize sequence coverage and localization of PTMs, various fragmentation modes have been developed to produce fragment ions from deep within intact proteins. Ultraviolet photodissociation (UVPD) has recently been shown to produce high sequence coverage and PTM retention on a variety of proteins, with increasing evidence of efficacy on a chromatographic time scale...
May 5, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28385661/intact-cell-maldi-tof-mass-spectrometry-on-single-bovine-oocyte-and-follicular-cells-combined-with-top-down-proteomics-a-novel-approach-to-characterise-markers-of-oocyte-maturation
#4
Valérie Labas, Ana-Paula Teixeira-Gomes, Laura Bouguereau, Audrey Gargaros, Lucie Spina, Aurélie Marestaing, Svetlana Uzbekova
Intact cell MALDI-TOF mass spectrometry (ICM-MS) was adapted to bovine follicular cells from individual ovarian follicles to obtain the protein/peptide signatures (<17kDa) of single oocytes, cumulus cells (CC) and granulosa cells (GC), which shared a total of 439 peaks. By comparing the ICM-MS profiles of single oocytes and CC before and after in vitro maturation (IVM), 71 different peaks were characterised, and their relative abundance was found to vary depending on the stage of oocyte meiotic maturation...
April 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28369609/4-bromodiphenyl-ether-bde-3-induces-germ-cell-apoptosis-by-induction-of-ros-and-dna-damage-in-caenorhabditis-elegans
#5
Xinyue You, Jing Xi, Yiyi Cao, Jinfu Zhang, Yang Luan
Polybrominated diphenyl ethers (PBDEs) may affect male reproductive function; however, the underlying mechanism is still uncertain. By using Caenorhabditis elegans (C. elegans), a commonly used model to study basic biological processes in apoptosis, we investigated the toxic effects of 4-bromodiphenyl ether (BDE-3), the most fundamental mono-BDE generated from degradation of PBDEs in the environment. We found that BDE-3 treated worms exhibited decreased life spans, impaired fecundity and delayed egg laying...
March 27, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28291811/systematic-identification-and-characterization-of-long-non-coding-rnas-in-mouse-mature-sperm
#6
Xiaoning Zhang, Fengxin Gao, Jianbo Fu, Peng Zhang, Yuqing Wang, Xuhui Zeng
Increasing studies have shown that mature spermatozoa contain many transcripts including mRNAs and miRNAs. However, the expression profile of long non-coding RNAs (lncRNAs) in mammalian sperm has not been systematically investigated. Here, we used highly purified RNA to investigate lncRNA expression profiles in mouse mature sperm by stranded-specific RNA-seq. We identified 20,907 known and 4,088 novel lncRNAs transcripts, and the existence of intact lncRNAs was confirmed by RT-PCR and fluorescence in situ hybridization on two representative lncRNAs...
2017: PloS One
https://www.readbyqxmd.com/read/28280261/non-kinase-targets-of-protein-kinase-inhibitors
#7
REVIEW
Lenka Munoz
Kinome-wide profiling platforms have comprehensively identified the relevant kinases that are targeted by numerous protein kinase inhibitors. However, recent projects have begun to discover non-kinase targets of kinase inhibitors. These non-kinase targets can contribute to the desired or undesired activities of inhibitors, or act as silent bystanders. As a full awareness of a drug's mechanism of action is crucial for the interpretation of results and for successful preclinical and clinical drug development, these discoveries highlight the importance of understanding the pharmacology of kinase inhibitors beyond the kinome...
March 10, 2017: Nature Reviews. Drug Discovery
https://www.readbyqxmd.com/read/28263231/appendix-derived-pseudomyxoma-peritonei-pmp-molecular-profiling-toward-treatment-of-a-rare-malignancy
#8
Elizabeth M Gleeson, Rebecca Feldman, Beth L Mapow, Lynn T Mackovick, Kristine M Ward, William F Morano, Rene R Rubin, Wilbur B Bowne
OBJECTIVES: Pseudomyxoma peritonei (PMP) is a rare malignancy originating from the appendix, characterized by disseminated mucinous tumor implants on peritoneal surfaces. We examined the role of multiplatform molecular profiling to study biomarker-guided treatment strategies for this rare malignancy. METHODS: A total of 54 patients with appendix-derived PMP were included in the study. Tests included one or more of the following: gene sequencing (Sanger or next generation sequencing), protein expression (immunohistochemistry), and gene amplification (C/fluorescent in situ hybridization)...
March 3, 2017: American Journal of Clinical Oncology
https://www.readbyqxmd.com/read/28244757/development-of-isotag-a-chemical-glycoproteomics-technique-for-profiling-intact-n-and-o-glycopeptides-from-whole-cell-proteomes
#9
Christina M Woo, Alejandra Felix, William E Byrd, Devon K Zuegel, Mayumi Ishihara, Parastoo Azadi, Anthony T Iavarone, Sharon J Pitteri, Carolyn R Bertozzi
Protein glycosylation can have an enormous variety of biological consequences, reflecting the molecular diversity encoded in glycan structures. This same structural diversity has imposed major challenges on the development of methods to study the intact glycoproteome. We recently introduced a method termed isotope-targeted glycoproteomics (IsoTaG), which utilizes isotope recoding to characterize azidosugar-labeled glycopeptides bearing fully intact glycans. Here, we describe the broad application of the method to analyze glycoproteomes from a collection of tissue-diverse cell lines...
April 7, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28243547/analysis-of-gene-expression-profiles-of-lactobacillus-paracasei-induced-by-direct-contact-with-saccharomyces-cerevisiae-through-recognition-of-yeast-mannan
#10
Shino Yamasaki-Yashiki, Hiroshi Sawada, Masahiro Kino-Oka, Yoshio Katakura
Co-culture of lactic acid bacteria (LAB) and yeast induces specific responses that are not observed in pure culture. Gene expression profiles of Lactobacillus paracasei ATCC 334 co-cultured with Saccharomyces cerevisiae IFO 0216 were analyzed by DNA microarray, and the responses induced by direct contact with the yeast cells were investigated. Coating the LAB cells with recombinant DnaK, which acts as an adhesive protein between LAB and yeast cells, enhanced the ratio of adhesion of the LAB cells to the yeast cells...
2017: Bioscience of Microbiota, Food and Health
https://www.readbyqxmd.com/read/28213525/conformational-profiling-of-the-at1-angiotensin-ii-receptor-reflects-biased-agonism-g-protein-coupling-and-cellular-context
#11
Dominic Devost, Rory Sleno, Darlaine Pétrin, Alice Zhang, Yuji Shinjo, Rakan Okde, Junken Aoki, Asuka Inoue, Terence E Hébert
Here, we report the design and use of G protein-coupled receptor-based biosensors to monitor ligand-mediated conformational changes in receptors in intact cells. These biosensors use bioluminescence resonance energy transfer with Renilla luciferase (RlucII) as an energy donor, placed at the distal end of the receptor C-tail, and the small fluorescent molecule FlAsH as an energy acceptor, its binding site inserted at different positions throughout the intracellular loops and C-terminal tail of the angiotensin II type I receptor...
March 31, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28158294/deep-proteome-mapping-of-wm-266-4-human-metastatic-melanoma-cells-from-oncogenic-addiction-to-druggable-targets
#12
Eumorphia G Konstantakou, Athanassios D Velentzas, Athanasios K Anagnostopoulos, Zoi I Litou, Ourania A Konstandi, Aikaterini F Giannopoulou, Ema Anastasiadou, Gerassimos E Voutsinas, George Th Tsangaris, Dimitrios J Stravopodis
Cutaneous melanoma is a malignant tumor of skin melanocytes that are pigment-producing cells located in the basal layer (stratum basale) of epidermis. Accumulation of genetic mutations within their oncogenes or tumor-suppressor genes compels melanocytes to aberrant proliferation and spread to distant organs of the body, thereby resulting in severe and/or lethal malignancy. Metastatic melanoma's heavy mutational load, molecular heterogeneity and resistance to therapy necessitate the development of novel biomarkers and drug-based protocols that target key proteins involved in perpetuation of the disease...
2017: PloS One
https://www.readbyqxmd.com/read/28151945/antigenic-characterization-of-the-human-immunodeficiency-virus-hiv-1-envelope-glycoprotein-precursor-incorporated-into-nanodiscs
#13
Kristen C Witt, Luis Castillo-Menendez, Haitao Ding, Nicole Espy, Shijian Zhang, John C Kappes, Joseph Sodroski
The entry of human immunodeficiency virus (HIV-1) into host cells is mediated by the viral envelope glycoproteins (Envs), which are derived by the proteolytic cleavage of a trimeric gp160 Env precursor. The mature Env trimer is a major target for entry inhibitors and vaccine-induced neutralizing antibodies. Env interstrain variability, conformational flexibility and heavy glycosylation contribute to evasion of the host immune response, and create challenges for structural characterization and vaccine development...
2017: PloS One
https://www.readbyqxmd.com/read/28145808/characterization-of-the-l-glutamate-clearance-pathways-across-the-blood-brain-barrier-and-the-effect-of-astrocytes-in-an-in%C3%A2-vitro-blood-brain-barrier-model
#14
Hans Cc Helms, Blanca I Aldana, Simon Groth, Morten M Jensen, Helle S Waagepetersen, Carsten U Nielsen, Birger Brodin
The aim was to characterize the clearance pathways for L-glutamate from the brain interstitial fluid across the blood-brain barrier using a primary in vitro bovine endothelial/rat astrocyte co-culture. Transporter profiling was performed using uptake studies of radiolabeled L-glutamate with co-application of transporter inhibitors and competing amino acids. Endothelial abluminal L-glutamate uptake was almost abolished by co-application of an EAAT-1 specific inhibitor, whereas luminal uptake was inhibited by L-glutamate and L-aspartate (1 mM)...
January 1, 2017: Journal of Cerebral Blood Flow and Metabolism
https://www.readbyqxmd.com/read/28130393/irradiation-affects-germ-and-somatic-cells-in-prepubertal-monkey-testis-xenografts
#15
I Tröndle, B Westernströer, J Wistuba, N Terwort, S Schlatt, N Neuhaus
Study question: Does irradiation evoke adverse effects in germ and somatic cells in testis xenografts from prepubertal monkeys? Summary answer: In addition to the expected depletion of germ cells, a dose-dependent effect of irradiation was observed at the mRNA and protein level in Sertoli and peritubular myoid cells. What is known already: Testicular irradiation studies in monkeys have focused on the dose-dependent effects on germ cells. Previous studies using intact animals or xenografts reported that germ cells are highly sensitive to irradiation...
March 1, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/28109117/lipid-profiling-of-parkin-mutant-human-skin-fibroblasts
#16
Simona Lobasso, Paola Tanzarella, Daniele Vergara, Michele Maffia, Tiziana Cocco, Angela Corcelli
Parkin mutations are a major cause of early-onset Parkinson's disease (PD). The impairment of protein quality control system together with defects in mitochondria and autophagy process are consequences of the lack of parkin, which leads to neurodegeneration. Little is known about the role of lipids in these alterations of cell functions. In the present study, parkin-mutant human skin primary fibroblasts have been considered as cellular model of PD to investigate on possible lipid alterations associated with the lack of parkin protein...
January 21, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28095896/screening-for-potential-genes-associated-with-bone-overgrowth-after-mid-shaft-femur-fracture-in-a-rat-model
#17
Chibing Liu, Yanting Liu, Weizhong Zhang, Xiuxin Liu
BACKGROUND: We investigated the underlying molecular mechanisms of bone overgrowth after femoral fracture by using high-throughput bioinformatics approaches. METHODS: The gene expression profile of GSE3298 (accession number) was obtained from the Gene Expression Omnibus database. Sixteen femoral growth plate samples, including nine samples without fracture and seven fracture samples for seven time points, were used for analysis. The Limma package was applied to identify differentially expressed genes (DEGs) between fractured and intact samples...
January 17, 2017: Journal of Orthopaedic Surgery and Research
https://www.readbyqxmd.com/read/28011869/pcom-db-update-a-protein-co-migration-database-for-photosynthetic-organisms
#18
Atsushi Takabayashi, Saeka Takabayashi, Kaori Takahashi, Mai Watanabe, Hiroko Uchida, Akio Murakami, Tomomichi Fujita, Masahiko Ikeuchi, Ayumi Tanaka
The identification of protein complexes is important for the understanding of protein structure and function and the regulation of cellular processes. We used blue-native PAGE and tandem mass spectrometry to identify protein complexes systematically, and built a web database, the protein co-migration database (PCoM-DB, http://pcomdb.lowtem.hokudai.ac.jp/proteins/top), to provide prediction tools for protein complexes. PCoM-DB provides migration profiles for any given protein of interest, and allows users to compare them with migration profiles of other proteins, showing the oligomeric states of proteins and thus identifying potential interaction partners...
December 22, 2016: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28001444/vitamin-d-receptor-expression-in-plasmablastic-lymphoma-and-myeloma-cells-confers-susceptibility-to-vitamin-d
#19
Duncan M Gascoyne, Linden Lyne, Hayley Spearman, Francesca M Buffa, Elizabeth J Soilleux, Alison H Banham
Plasmablastic B-cell malignancies include plasmablastic lymphoma and subsets of multiple myeloma and diffuse large B-cell lymphomaDLBCL. These diseases can be difficult to diagnose and treat, and they lack well-characterized cell line models. Here, immunophenotyping and FOXP1 expression profiling identified plasmablastic characteristics in DLBCL cell lines HLY-1 and SU-DHL-9, associated with CTNNAL1, HPGD, RORA, IGF1, and/or vitamin D receptor (VDR) transcription. We demonstrated VDR protein expression in primary plasmablastic tumor cells and confirmed in cell lines expression of both VDR and the metabolic enzyme CYP27B1, which catalyzes active vitamin D3 production...
March 1, 2017: Endocrinology
https://www.readbyqxmd.com/read/27986537/meaningful-respirometric-measurements-of-ucp1-mediated-thermogenesis
#20
REVIEW
Yongguo Li, Tobias Fromme, Martin Klingenspor
Regarding the enormous interest in brown and brite/beige adipose tissue in the context of metabolic disease, reliable quantification of thermogenesis in these adipocytes is a central issue. This requires an assay specific for uncoupling protein 1 (UCP1) mediated thermogenesis in adherent intact cells. In a recent study we identified a major pitfall associated with established procedures generally applied for this purpose. Meaningful respirometry of UCP1-mediated thermogenesis imperatively requires activation of UCP1 and control over free fatty acid levels...
March 2017: Biochimie
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