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Reverse-phase protein array

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https://www.readbyqxmd.com/read/28886403/increased-mapk1-3-phosphorylation-in-luminal-breast-cancer-related-with-pik3ca-hotspot-mutations-and-prognosis
#1
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...
September 5, 2017: Translational Oncology
https://www.readbyqxmd.com/read/28871817/cytotoxicity-in-vitro-anti-leishmanial-and-fingerprint-hplc-photodiode-array-analysis-of-the-roots-of-trillium-govanianum
#2
Kashif Maqbool Khan, Lutfun Nahar, Abdul Mannan, Ihsan Ul-Haq, Muhammad Arfan, Ghazanfar Ali Khan, Izhar Hussain, Satyajit D Sarker
Trillium govanianum Wall. ex D. Don (Melanthiaceae alt. Trilliaceae), commonly known as 'nagchhatry' or 'teen patra', distributed from Pakistan to Bhutan about 2500-3800 m altitude is indigenous to Himalayas region. In folk medicine the plant has been reported for the treatment of wound healing, sepsis and in various sexual disorders. This paper reports, for the first time, to evaluate the cytotoxicity, in vitro anti-leishmanial (promastigotes) and fingerprint HPLC-photodiode array analysis of the MeOH extract of the roots of T...
September 5, 2017: Natural Product Research
https://www.readbyqxmd.com/read/28809001/reverse-phase-protein-arrays-and-drug-discovery
#3
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/28791374/corilagin-sensitizes-epithelial-ovarian-cancer-to-chemotherapy-by-inhibiting-snail%C3%A2-glycolysis-pathways
#4
Luoqi Jia, Jiayi Zhou, Hongbo Zhao, Hongyan Jin, Minzhi Lv, Naiqing Zhao, Zhizhong Zheng, Yiling Lu, Yanlin Ming, Yinhua Yu
We identified that corilagin is a major component extracted from a well-known hepatoprotective and antiviral medicinal herb, Phyllanthus niruri L with antitumor activity. Our previous study found that corilagin inhibited the growth of ovarian cancer cells via the TGF-β/AKT/ERK signaling pathways. Recently, we demonstrated that corilagin enhanced the sensitivity of ovarian cancer cells to chemotherapy. Ovarian cancer cell lines, SKOv3ip, Hey and HO-8910PM-Snail, were treated with different concentrations of corilagin in combination with paclitaxel and carboplatin...
August 7, 2017: Oncology Reports
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
#5
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
#6
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
#7
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/28754127/predictive-biomarkers-of-resistance-to-hypofractionated-radiotherapy-in-high-grade-glioma
#8
Julian Biau, Emmanuel Chautard, Leanne De Koning, Frank Court, Bruno Pereira, Pierre Verrelle, Marie Dutreix
BACKGROUND: Radiotherapy plays a major role in the management of high grade glioma. However, the radioresistance of glioma cells limits its efficiency and drives recurrence inside the irradiated tumor volume leading to poor outcome for patients. Stereotactic hypofractionated radiotherapy is one option for recurrent high grade gliomas. Optimization of hypofractionated radiotherapy with new radiosensitizing agents requires the identification of robust druggable targets involved in radioresistance...
July 28, 2017: Radiation Oncology
https://www.readbyqxmd.com/read/28753272/colony-lysate-arrays-for-proteomic-profiling-of-drug-tolerant-persisters-of-cancer-cell
#9
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/28731187/isolation-and-purification-of-novel-peptides-derived-from-sepia-ink-effects-on-apoptosis-of-prostate-cancer-cell-pc%C3%A2-3
#10
Fangfang Huang, Yinwen Jing, Guofang Ding, Zuisu Yang
Novel prostate cancer therapeutics are in high demand. In order to identify potential therapeutic targets, protein from sepia ink was hydrolyzed by utilizing pepsin in an orthogonal array design. Pepsin hydrolysate (SH) obtained at optimal conditions exhibited the highest antitumor activity. Subsequently, a novel antitumor peptide, which was termed SHP, was isolated through ultrafiltration, gel filtration chromatography and reversed phase high‑performance liquid chromatography. The amino acid sequence of SHP was identified as Leu‑Lys‑Glu‑Glu‑Asn‑Arg‑Arg‑Arg‑Arg‑Asp with a molecular mass of 1371...
October 2017: Molecular Medicine Reports
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
#11
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
#12
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
#13
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/28674890/high-density-serum-plasma-reverse-phase-protein-arrays
#14
Cecilia Hellström, Tea Dodig-Crnković, Mun-Gwan Hong, Jochen M Schwenk, Peter Nilsson, Ronald Sjöberg
In-depth exploration and characterization of human serum and plasma proteomes is an attractive strategy for the identification of potential prognostic or diagnostic biomarkers. The possibility of analyzing larger numbers of samples in a high-throughput fashion has markedly increased with affinity-based microarrays, thus providing higher statistical power to these biomarker studies. Here, we describe a protocol for high-density serum and plasma reverse phase protein arrays (RPPAs). We demonstrate how a biobank of 12,392 samples was immobilized and analyzed on a single microarray slide, allowing high-quality profiling of abundant target proteins across all samples in one assay...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28659338/high-throughput-profiling-of-signaling-networks-identifies-mechanism-based-combination-therapy-to-eliminate-microenvironmental-resistance-in-acute-myeloid-leukemia
#15
Zhihong Zeng, Wenbin Liu, Twee Tsao, YiHua Qiu, Yang Zhao, Ismael Samudio, Dos D Sarbassov, Steven M Kornblau, Keith A Baggerly, Hagop M Kantarjian, Marina Konopleva, Michael Andreeff
The bone marrow microenvironment is known to provide a survival advantage to residual acute myeloid leukemia cells, possibly contributing to disease recurrence. The mechanisms by which stroma in the microenvironment regulates leukemia survival remain largely unknown. Using reverse phase-protein array technology, we profiled 53 key protein molecules in 11 signaling pathways in 20 primary acute myeloid leukemia samples and two cell lines, aiming to understand stroma-mediated signaling modulation in response to the targeted agents temsirolimus (MTOR), ABT737 (BCL2/BCL-XL), and Nutlin-3a (MDM2), and to identify the effective combination therapy targeting acute myeloid leukemia in the context of the leukemia microenvironment...
June 28, 2017: Haematologica
https://www.readbyqxmd.com/read/28651964/protein-network-construction-using-reverse-phase-protein-array-data
#16
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
#17
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
#18
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
#19
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/28627414/akt-hyperactivation-and-the-potential-of-akt-targeted-therapy-in-diffuse-large-b-cell-lymphoma
#20
Jinfen Wang, Zijun Y Xu-Monette, Kausar J Jabbar, Qi Shen, Ganiraju C Manyam, Alexandar Tzankov, Carlo Visco, Jing Wang, Santiago Montes-Moreno, Karen Dybkær, Wayne Tam, Govind Bhagat, Eric D Hsi, J Han van Krieken, Maurilio Ponzoni, Andrés J M Ferreri, Shi Wang, Michael B Møller, Miguel A Piris, L Jeffrey Medeiros, Yong Li, Lan V Pham, Ken H Young
AKT signaling is important for proliferation and survival of tumor cells. The clinical significance of AKT activation in diffuse large B-cell lymphoma (DLBCL) is not well analyzed. Here, we assessed expression of phosphorylated AKT (p-AKT) in 522 DLBCL patients. We found that high levels of p-AKT nuclear expression, observed in 24.3% of the study cohort, were associated with significantly worse progression-free survival and Myc and Bcl-2 overexpression. However, multivariate analysis indicated that AKT hyperactivation was not an independent factor...
August 2017: American Journal of Pathology
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