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https://www.readbyqxmd.com/read/29030353/rad50-expression-is-associated-with-poor-clinical-outcomes-after-radiotherapy-for-resected-non-small-cell-lung-cancer
#1
Yifan Wang, Jayanthi Gudikote, Uma Giri, Jun Yan, Weiye Deng, Rui Ye, Wen Jiang, Nan Li, Brian Hobbs, Jing Wang, Stephen G Swisher, Junya Fujimoto, Ignacio Ivan Wistuba, Ritsuko Komaki, John Heymach, Steven H Lin
PURPOSE: Although postoperative radiotherapy is often used to maintain local control after surgical resection and chemotherapy for locally advanced non-small cell lung cancer (NSCLC), both locoregional failure and distant metastasis remain problematic.  The mechanisms of therapeutic resistance remain poorly understood.    Experimental Design: We used reverse-phase protein arrays (RPPAs) to profile the baseline expression of 170 total and phosphorylated proteins in 70 NSCLC cell lines to categorize pathways that may contribute to radiation resistance...
October 13, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29020998/proteomic-profiling-of-breast-cancer-metabolism-identifies-shmt2-and-asct2-as-prognostic-factors
#2
Stephan Bernhardt, Michaela Bayerlová, Martina Vetter, Astrid Wachter, Devina Mitra, Volker Hanf, Tilmann Lantzsch, Christoph Uleer, Susanne Peschel, Jutta John, Jörg Buchmann, Edith Weigert, Karl-Friedrich Bürrig, Christoph Thomssen, Ulrike Korf, Tim Beissbarth, Stefan Wiemann, Eva Johanna Kantelhardt
BACKGROUND: Breast cancer tumors are known to be highly heterogeneous and differences in their metabolic phenotypes, especially at protein level, are less well-understood. Profiling of metabolism-related proteins harbors the potential to establish new patient stratification regimes and biomarkers promoting individualized therapy. In our study, we aimed to examine the relationship between metabolism-associated protein expression profiles and clinicopathological characteristics in a large cohort of breast cancer patients...
October 11, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28986799/protein-arrays-iii-reverse-phase-protein-arrays
#3
Yulin Yuan, Xia Hong, Zuan-Tao Lin, Hongting Wang, Mikala Heon, Tianfu Wu
The reverse-phase protein array (RPPA) is to use highly specific antibodies to interrogate pan or posttranslationally modified protein targets, such as phosphorylated proteins, particularly the proteins involved in cell signaling pathways. In this protocol we will cover the preparation of cell (or tissue) lysates, sample printing, antibody validation, antibody interrogation, signal amplification steps, imaging and data analysis. In this protocol, colorimetric catalyzed signal amplification (CSA) chemistry, fluorescence and near-infrared (NIR) based detection methods will be described...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28984208/unique-protein-expression-signatures-of-survival-time-in-kidney-renal-clear-cell-carcinoma-through-a-pan-cancer-screening
#4
Guangchun Han, Wei Zhao, Xiaofeng Song, Patrick Kwok-Shing Ng, Jose A Karam, Eric Jonasch, Gordon B Mills, Zhongming Zhao, Zhiyong Ding, Peilin Jia
BACKGROUND: In 2016, it is estimated that there will be 62,700 new cases of kidney cancer in the United States, and 14,240 patients will die from the disease. Because the incidence of kidney renal clear cell carcinoma (KIRC), the most common type of kidney cancer, is expected to continue to increase in the US, there is an urgent need to find effective diagnostic biomarkers for KIRC that could help earlier detection of and customized treatment strategies for the disease. Accordingly, in this study we systematically investigated KIRC's prognostic biomarkers for survival using the reverse phase protein array (RPPA) data and the high throughput sequencing data from The Cancer Genome Atlas (TCGA)...
October 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28955722/the-progestin-receptor-interactome-in-the-female-mouse-hypothalamus-interactions-with-synaptic-proteins-are-isoform-specific-and-ligand-dependent
#5
Kalpana D Acharya, Sabin A Nettles, Katherine J Sellers, Dana D Im, Moriah Harling, Cassandra Pattanayak, Didem Vardar-Ulu, Cheryl F Lichti, Shixia Huang, Dean P Edwards, Deepak P Srivastava, Larry Denner, Marc J Tetel
Progestins bind to the progestin receptor (PR) isoforms, PR-A and PR-B, in brain to influence development, female reproduction, anxiety, and stress. Hormone-activated PRs associate with multiple proteins to form functional complexes. In the present study, proteins from female mouse hypothalamus that associate with PR were isolated using affinity pull-down assays with glutathione S-transferase-tagged mouse PR-A and PR-B. Using complementary proteomics approaches, reverse phase protein array (RPPA) and mass spectrometry, we identified hypothalamic proteins that interact with PR in a ligand-dependent and isoform-specific manner and were confirmed by Western blot...
September 2017: ENeuro
https://www.readbyqxmd.com/read/28949454/a-pilot-study-exploring-the-molecular-architecture-of-the-tumor-microenvironment-in-human-prostate-cancer-using-laser-capture-microdissection-and-reverse-phase-protein-microarray
#6
(no author information available yet)
The cross-talk between tumor epithelium and surrounding stromal/immune microenvironment is essential to sustain tumor growth and progression and provides new opportunities for the development of targeted treatments focused on disrupting the tumor ecology. Identification of novel approaches to study these interactions is of primary importance. Using laser capture microdissection (LCM) coupled with reverse phase protein microarray (RPPA) based protein signaling activation mapping we explored the molecular interconnection between tumor epithelium and surrounding stromal microenvironment in 18 prostate cancer (PCa) specimens...
December 2016: Molecular Oncology
https://www.readbyqxmd.com/read/28936799/proteomic-features-of-colorectal-cancer-identify-tumor-subtypes-independent-of-oncogenic-mutations-and-independently-predict-relapse-free-survival
#7
Callisia N Clarke, Michael S Lee, Wei Wei, Ganiraju Manyam, Zhi-Qin Jiang, Yiling Lu, Jeffrey Morris, Bradley Broom, David Menter, Eduardo Vilar-Sanchez, Kanwal Raghav, Cathy Eng, George J Chang, Iris Simon, Rene Bernards, Michael Overman, Gordon B Mills, Dipen Maru, Scott Kopetz
BACKGROUND: The directed study of the functional proteome in colorectal cancer (CRC) has identified critical protein markers and signaling pathways; however, the prognostic relevance of many of these proteins remains unclear. METHODS: We determined the prognostic implications of the functional proteome in 263 CRC tumor samples from patients treated at MD Anderson Cancer Center (MDACC) and 462 patients from The Cancer Genome Atlas (TCGA) to identify patterns of protein expression that drive tumorigenesis...
September 21, 2017: Annals of Surgical Oncology
https://www.readbyqxmd.com/read/28886403/increased-mapk1-3-phosphorylation-in-luminal-breast-cancer-related-with-pik3ca-hotspot-mutations-and-prognosis
#8
Diana Ramirez-Ardila, A Mieke Timmermans, Jean A Helmijr, John W M Martens, Els M J J Berns, Maurice P H M Jansen
INTRODUCTION: While mutations in PIK3CA are most frequently (45%) detected in luminal breast cancer, downstream PI3K/AKT/mTOR pathway activation is predominantly observed in the basal subtype. The aim was to identify proteins activated in PIK3CA mutated luminal breast cancer and the clinical relevance of such a protein in breast cancer patients. MATERIALS AND METHODS: Expression levels of 171 signaling pathway (phospho-)proteins established by The Cancer Genome Atlas (TCGA) using reverse phase protein arrays (RPPA) were in silico examined in 361 breast cancers for their relation with PIK3CA status...
October 2017: Translational Oncology
https://www.readbyqxmd.com/read/28869900/integration-of-rna-seq-and-rppa-data-for-survival-time-prediction-in-cancer-patients
#9
Zerrin Isik, Muserref Ece Ercan
Integration of several types of patient data in a computational framework can accelerate the identification of more reliable biomarkers, especially for prognostic purposes. This study aims to identify biomarkers that can successfully predict the potential survival time of a cancer patient by integrating the transcriptomic (RNA-Seq), proteomic (RPPA), and protein-protein interaction (PPI) data. The proposed method -RPBioNet- employs a random walk-based algorithm that works on a PPI network to identify a limited number of protein biomarkers...
August 26, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28860008/a-signalome-screening-approach-in-the-autoinflammatory-disease-tnf-receptor-associated-periodic-syndrome-traps-highlights-the-anti-inflammatory-properties-of-drugs-for-repurposing
#10
Ian Todd, Ola H Negm, Jenna Reps, Paul Radford, Grazziela Figueredo, Elizabeth M McDermott, Elizabeth Drewe, Richard J Powell, Susan Bainbridge, Mohamed Hamed, Sharon Crouch, Jon Garibaldi, Steve St-Gallay, Lucy C Fairclough, Patrick J Tighe
TNF receptor associated periodic syndrome (TRAPS) is an autoinflammatory disease caused by mutations in TNF Receptor 1 (TNFR1). Current therapies for TRAPS are limited and do not target the pro-inflammatory signalling pathways that are central to the disease mechanism. Our aim was to identify drugs for repurposing as anti-inflammatories based on their ability to down-regulate molecules associated with inflammatory signalling pathways that are activated in TRAPS. This was achieved using rigorously optimized, high through-put cell culture and reverse phase protein microarray systems to screen compounds for their effects on the TRAPS-associated inflammatory signalome...
August 30, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/28809001/reverse-phase-protein-arrays-and-drug-discovery
#11
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
#12
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
#13
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)...
August 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
#14
Krit Ritthipichai, Cara L Haymaker, Melisa Martinez, Andrew Aschenbrenner, Xiaohui Yi, Minying Zhang, Charuta Kale, Luis M Vence, Jason Roszik, Yared Hailemichael, Willem W Overwijk, Navin Varadarajan, Roza Nurieva, Laszlo G Radvanyi, Patrick Hwu, Chantale Bernatchez
Purpose: 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 associated) expression on transferred CD8(+) TILs 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 costimulation...
October 15, 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
#15
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...
September 5, 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
#16
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
#17
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
#18
Triparna Sen, Pan Tong, Lixia Diao, Lerong Li, Youhong Fan, Jennifer Hoff, John V Heymach, Jing Wang, Lauren Averett 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.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...
October 15, 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
#19
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...
July 15, 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
#20
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
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