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https://www.readbyqxmd.com/read/28809001/reverse-phase-protein-arrays-and-drug-discovery
#1
Kenneth G Macleod, Bryan Serrels, Neil O Carragher
Reverse Phase Protein Arrays (RPPA) represent a sensitive antibody-based proteomic approach, which enables simultaneous quantification of the abundance of multiple proteins and posttranslational modifications across multiple samples. Here, we provide protocols for RPPA performed on two distinct protein-binding substrates associated with two most commonly used RPPA platform technologies. We compare and contrast the respective advantages and limitations of each platform within the context of drug discovery applications...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28781988/multiple-response-regression-analysis-links-magnetic-resonance-imaging-features-to-de-regulated-protein-expression-and-pathway-activity-in-lower-grade-glioma
#2
Michael Lehrer, Anindya Bhadra, Visweswaran Ravikumar, James Y Chen, Max Wintermark, Scott N Hwang, Chad A Holder, Erich P Huang, Brenda Fevrier-Sullivan, John B Freymann, Arvind Rao
BACKGROUND AND PURPOSE: Lower grade gliomas (LGGs), lesions of WHO grades II and III, comprise 10-15% of primary brain tumors. In this first-of-a-kind study, we aim to carry out a radioproteomic characterization of LGGs using proteomics data from the TCGA and imaging data from the TCIA cohorts, to obtain an association between tumor MRI characteristics and protein measurements. The availability of linked imaging and molecular data permits the assessment of relationships between tumor genomic/proteomic measurements with phenotypic features...
May 2017: Oncoscience
https://www.readbyqxmd.com/read/28759843/trim28-epigenetic-corepressor-is-indispensable-for-stable-induced-pluripotent-stem-cell-formation
#3
Marta Klimczak, Patrycja Czerwińska, Sylwia Mazurek, Barbara Sozańska, Przemysław Biecek, Andrzej Mackiewicz, Maciej Wiznerowicz
Cellular reprogramming proceeds in a stepwise pathway initiated by binding and transcription of pluripotency factors followed by genome-wide epigenetic changes. Priming events, such as erasure of DNA methylation and chromatin remodeling determines the success of pluripotency acquisition later. Therefore, growing efforts are made to understand epigenetic regulatory network that makes reprogramming possible and efficient. Here, we analyze the role of transcriptional corepressor TRIM28, involved in heterochromatin formation, during the process of reprogramming of mouse somatic cells into induced pluripotent stem cells (iPS cells)...
July 15, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28754817/multifaceted-role-of-btla-in-the-control-of-cd8-t-cell-fate-after-antigen-encounter
#4
Krit Ritthipichai, Cara Haymaker, Melisa Martinez-Paniagua, Andrew Aschenbrenner, Xiaohui Yi, Minying Zhang, Charuta Kale, Yared Hailemichael, Willem W Overwijk, Luis Vence, Jason Roszik, Navin Varadarajan, Roza Nurieva, Laszlo G Radvanyi, Patrick Hwu, Chantale Bernatchez
Adoptive T-cell therapy using autologous tumor-infiltrating lymphocytes (TIL) has shown an overall clinical response rate 40-50% in metastatic melanoma patients. BTLA (B-and-T lymphocyte attenuator) expression on transferred CD8(+) TIL was associated with better clinical outcome. The suppressive function of the ITIM and ITSM motifs of BTLA is well described. Here, we sought to determine the functional characteristics of the CD8(+)BTLA(+)TIL subset and define the contribution of the Grb2 motif of BTLA in T cell co-stimulation...
July 28, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28753272/colony-lysate-arrays-for-proteomic-profiling-of-drug-tolerant-persisters-of-cancer-cell
#5
Kohei Kume, Satoshi S Nishizuka
Functional heterogeneity of cancer cells is one of the key properties to understanding relapse after drug treatment. Hence, clarification is needed with regard to which types of subgroups of cancer cells dominantly contribute to the initiation of relapse. Recently, we established the colony lysate array (CoLA), which is a method that allows comparison of individual colonies at the protein level to assess the initiation of anticancer drug-tolerant persisters (DTPs) based on the reverse-phase protein array (RPPA) system...
August 11, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28706145/reverse-phase-protein-array-rppa-combined-with-computational-analysis-to-unravel-relevant-prognostic-factors-in-non-small-cell-lung-cancer-nsclc-a-pilot-study
#6
Vienna Ludovini, Rita Chiari, Lorenzo Tomassoni, Chiara Antonini, Elisa Baldelli, Sara Baglivo, Annamaria Sigillino, Francesca Romana Tofanetti, Guido Bellezza, K Alex Hodge, Emanuel Petricoin, Mariaelena Pierobon, Lucio Crinò, Fortunato Bianconi
In this work high throughput technology and computational analysis were used to study two stage IV lung adenocarcinoma patients treated with standard chemotherapy with markedly different survival (128 months vs 6 months, respectively) and whose tumor samples exhibit a dissimilar protein activation pattern of the signal transduction. Tumor samples of the two patients were subjected to Reverse Phase Protein Microarray (RPPA) analysis to explore the expression/activation levels of 51 signaling proteins. We selected the most divergent proteins based on the ratio of their RPPA values in the two patients with short (s-OS) and long (l-OS) overall survival (OS) and tested them against a EGFR-IGF1R mathematical model...
June 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28701032/bcl2-regulation-according-to-molecular-subtype-of-breast-cancer-by-analysis-of-the-cancer-genome-atlas-database
#7
Ki-Tae Hwang, Kwangsoo Kim, Ji Hyun Chang, Sohee Oh, Young A Kim, Jong Yoon Lee, Se Hee Jung, In Sil Choi
Purpose: We investigated BCL2 regulation across DNA, RNA, protein, and methylation status according to molecular subtype of breast cancer using The Cancer Genome Atlas (TCGA) database. Materials and Methods: We analyzed clinical and biological data on 1,096 breast cancers from the TCGA database. Biological data included reverse phase protein array (RPPA), mRNA sequencing (mRNA seq), mRNA microarray, methylation, copy number alteration linear, copy number alteration nonlinear, and mutation data...
July 4, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28698200/targeting-axl-and-mtor-pathway-overcomes-primary-and-acquired-resistance-to-wee1-inhibition-in-small-cell-lung-cancer
#8
Triparna Sen, Pan Tong, Lixia Diao, Lerong Li, Youhong Fan, Jennifer Hoff, John Heymach, Jing Wang, Lauren A Byers
Purpose: Drugs targeting DNA repair and cell cycle checkpoints have emerged as promising therapies for small cell lung cancer (SCLC). Among these, the WEE1 inhibitor AZD1775 has shown clinical activity in a subset of SCLC patients, but resistance is common. Understanding primary and acquired resistance mechanisms will be critical for developing effective WEE1 inhibitor combinations. <p>Experimental Design: AZD1775 sensitivity in SCLC cell lines was correlated with baseline expression level of 200 total or phosphorylated proteins measured by reverse phase protein array (RPPA) to identify predictive markers of primary resistance...
July 11, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28651964/protein-network-construction-using-reverse-phase-protein-array-data
#9
Rency S Varghese, Yiming Zuo, Yi Zhao, Yong-Wei Zhang, Sandra A Jablonski, Mariaelena Pierobon, Emanuel F Petricoin, Habtom W Ressom, Louis M Weiner
In this paper, we introduce a novel computational method for constructing protein networks based on reverse phase protein array (RPPA) data to identify complex patterns in protein signaling. The method is applied to phosphoproteomic profiles of basal expression and activation/phosphorylation of 76 key signaling proteins in three breast cancer cell lines (MCF7, LCC1, and LCC9). Temporal RPPA data are acquired at 48h, 96h, and 144h after knocking down four genes in separate experiments. These genes are selected from a previous study as important determinants for breast cancer survival...
June 24, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28648142/overcoming-intratumoural-heterogeneity-for-reproducible-molecular-risk-stratification-a-case-study-in-advanced-kidney-cancer
#10
Alexander L R Lubbock, Grant D Stewart, Fiach C O'Mahony, Alexander Laird, Peter Mullen, Marie O'Donnell, Thomas Powles, David J Harrison, Ian M Overton
BACKGROUND: Metastatic clear cell renal cell cancer (mccRCC) portends a poor prognosis and urgently requires better clinical tools for prognostication as well as for prediction of response to treatment. Considerable investment in molecular risk stratification has sought to overcome the performance ceiling encountered by methods restricted to traditional clinical parameters. However, replication of results has proven challenging, and intratumoural heterogeneity (ITH) may confound attempts at tissue-based stratification...
June 26, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28647089/reverse-phase-protein-arrays-elucidate-mechanisms-of-action-and-phenotypic-response-in-2d-and-3d-models
#11
REVIEW
Michael Pawlak, Neil O Carragher
The development of new 2D and 3D phenotypic screening assays combined with high-throughput genomic and proteomic technologies are well placed to advance a new era of molecular pathway informed Phenotypic Drug Discovery. We describe the application of Reverse Phase Protein Array (RPPA) technology to elucidate the mechanism-of-action of small molecules at the post-translational pathway level. We propose that profiling of phenotypic hits and lead molecules in increasingly more complex 3D in vitro and ex vivo models at the post-translational pathway network level represents an effective strategy to both triage and progress the preclinical development of phenotypic screening hits...
March 2017: Drug Discovery Today. Technologies
https://www.readbyqxmd.com/read/28634413/topical-fibronectin-improves-wound-healing-of-irradiated-skin
#12
Maxwell B Johnson, Brandon Pang, Daniel J Gardner, Solmaz Niknam-Benia, Vinaya Soundarajan, Athanasios Bramos, David P Perrault, Kian Banks, Gene K Lee, Regina Y Baker, Gene H Kim, Sunju Lee, Yang Chai, Mei Chen, Wei Li, Lawrence Kwong, Young-Kwon Hong, Alex K Wong
Wound healing is significantly delayed in irradiated skin. To better understand global changes in protein expression after radiation, we utilized a reverse phase protein array (RPPA) to identify significant changes in paired samples of normal and irradiated human skin. Of the 210 proteins studied, fibronectin was the most significantly and consistently downregulated in radiation-damaged skin. Using a murine model, we confirmed that radiation leads to decreased fibronectin expression in the skin as well as delayed wound healing...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28621158/signaling-pathway-profiling-using-reverse-phase-protein-array-and-its-clinical-applications
#13
Mari Masuda, Tesshi Yamada
Increased accessibility to next-generation sequencing within the last decade has led to a paradigm shift in cancer treatment from one-size-fits-all medicine to precision medicine providing therapeutic strategies tailored to the requirements of individual patients. However, the effect of even the most successful agent yet tested is only transient, and durable efficacy has yet to be achieved. Genome- and transcriptome-based approaches cannot fully predict the diversity of protein expression patterns or post-translational modifications that directly contribute to cancer pathogenesis and physiology...
June 22, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28526811/proteomic-analysis-of-cerebrospinal-fluid-from-children-with-central-nervous-system-tumors-identifies-candidate-proteins-relating-to-tumor-metastatic-spread
#14
Filippo Spreafico, Italia Bongarzone, Sara Pizzamiglio, Ruben Magni, Elena Taverna, Maida De Bortoli, Chiara M Ciniselli, Elena Barzanò, Veronica Biassoni, Alessandra Luchini, Lance A Liotta, Weidong Zhou, Michele Signore, Paolo Verderio, Maura Massimino
Central nervous system (CNS) tumors are the most common solid tumors in childhood. Since the sensitivity of combined cerebrospinal fluid (CSF) cytology and radiological neuroimaging in detecting meningeal metastases remains relatively low, we sought to characterize the CSF proteome of patients with CSF tumors to identify biomarkers predictive of metastatic spread. CSF samples from 27 children with brain tumors and 13 controls (extra-CNS non-Hodgkin lymphoma) were processed using core-shell hydrogel nanoparticles, and analyzed with reverse-phase liquid chromatography/electrospray tandem mass spectrometry (LC-MS/MS)...
July 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28502001/clustering-and-network-analysis-of-reverse-phase-protein-array-data
#15
Adam Byron
Molecular profiling of proteins and phosphoproteins using a reverse phase protein array (RPPA) platform, with a panel of target-specific antibodies, enables the parallel, quantitative proteomic analysis of many biological samples in a microarray format. Hence, RPPA analysis can generate a high volume of multidimensional data that must be effectively interrogated and interpreted. A range of computational techniques for data mining can be applied to detect and explore data structure and to form functional predictions from large datasets...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28502000/reverse-phase-protein-microarrays
#16
Elisa Baldelli, Valerie Calvert, Alex Hodge, Amy VanMeter, Emanuel F Petricoin, Mariaelena Pierobon
While genes and RNA encode information about cellular status, proteins are considered the engine of the cellular machine, as they are the effective elements that drive all cellular functions including proliferation, migration, differentiation, and apoptosis. Consequently, investigations of the cellular protein network are considered a fundamental tool for understanding cellular functions.Alteration of the cellular homeostasis driven by elaborate intra- and extracellular interactions has become one of the most studied fields in the era of personalized medicine and targeted therapy...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28491035/proteomic-analysis-reveals-autophagy-as-pro-survival-pathway-elicited-by-long-term-exposure-with-5-azacitidine-in-high-risk-myelodysplasia
#17
Alessandra Romano, Cesarina Giallongo, Piera La Cava, Nunziatina L Parrinello, Antonella Chiechi, Calogero Vetro, Daniele Tibullo, Francesco Di Raimondo, Lance A Liotta, Virginia Espina, Giuseppe A Palumbo
Azacytidine (5-AZA) is the standard first-choice treatment for high-risk myelodysplasia (MDS) patients. However, the clinical outcome for those patients who interrupt treatment or whose disease failed to respond is very poor. In order to identify the cellular pathways that are modified by long-term exposure to 5-AZA, we evaluated key proteins associated with the autophagy pathway by reverse-phase microarray (RPPA). Comparing bone marrow mononucleated cells (BMMCs) obtained from 20 newly-diagnosed patients and after four 5-AZA cycles we found an increased autophagy signaling...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28476872/integrative-analysis-identifies-a-novel-axl-pi3-kinase-pd-l1-signaling-axis-associated-with-radiation-resistance-in-head-and-neck-cancer
#18
Heath D Skinner, Uma Giri, Liang P Yang, Manish Kumar, Ying Liu, Michael D Story, Curtis R Pickering, Lauren A Byers, Michelle D Williams, Jing Wang, Li Shen, Suk Y Yoo, You Hong Fan, David P Molkentine, Beth M Beadle, Raymond E Meyn, Jeffrey N Myers, John V Heymach
Purpose: The primary cause of death due to head and neck squamous cell carcinoma (HNSCC) is local treatment failure. The goal of this study was to examine this phenomenon using an unbiased approach.Experimental Design: We utilized human papilloma virus (HPV)-negative cell lines rendered radiation-resistant (RR) via repeated exposure to radiation, a panel of HPV-negative HNSCC cell lines and three cohorts of HPV-negative HNSCC tumors (n = 68, 97, and 114) from patients treated with radiotherapy and subjected to genomic, transcriptomic, and proteomic analysis...
June 1, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28446508/enrichment-of-pi3k-akt-mtor-pathway-activation-in-hepatic-metastases-from-breast-cancer
#19
Mariaelena Pierobon, Corinne Ramos, Shukmei Wong, K Alex Hodge, Jessica Aldrich, Sara Byron, Stephen P Anthony, Nicholas J Robert, Donald W Northfelt, Mohammad Jahanzeb, Linda Vocila, Julia Wulfkuhle, Guido Gambara, Rosa I Gallagher, Bryant Dunetz, Nicholas Hoke, Ting Dong, David W Craig, Massimo Cristofanilli, Brian Leyland-Jones, Lance A Liotta, Joyce A O'Shaughnessy, John D Carpten, Emanuel F Petricoin
Purpose: Little is known about the molecular signatures associated with specific metastatic sites in breast cancer. Using comprehensive multi-omic molecular profiling, we assessed whether alterations or activation of the PI3K-AKT-mTOR pathway is associated with specific sites of breast cancer metastasis.Experimental Design: Next-generation sequencing-based whole-exome sequencing was coupled with reverse-phase protein microarray (RPPA) functional signaling network analysis to explore the PI3K-AKT-mTOR axis in 32 pretreated breast cancer metastases...
August 15, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28442428/rapamycin-modulation-of-p70-s6-kinase-signaling-inhibits-rift-valley-fever-virus-pathogenesis
#20
Todd M Bell, Virginia Espina, Svetlana Senina, Caitlin Woodson, Ashwini Brahms, Brian Carey, Shih-Chao Lin, Lindsay Lundberg, Chelsea Pinkham, Alan Baer, Claudius Mueller, Elizabeth A Chlipala, Faye Sharman, Cynthia de la Fuente, Lance Liotta, Kylene Kehn-Hall
Despite over 60 years of research on antiviral drugs, very few are FDA approved to treat acute viral infections. Rift Valley fever virus (RVFV), an arthropod borne virus that causes hemorrhagic fever in severe cases, currently lacks effective treatments. Existing as obligate intracellular parasites, viruses have evolved to manipulate host cell signaling pathways to meet their replication needs. Specifically, translation modulation is often necessary for viruses to establish infection in their host. Here we demonstrated phosphorylation of p70 S6 kinase, S6 ribosomal protein, and eIF4G following RVFV infection in vitro through western blot analysis and in a mouse model of infection through reverse phase protein microarrays (RPPA)...
July 2017: Antiviral Research
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