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Reverse-phase protein array

Steven M Kornblau, Peter P Ruvolo, Rui-Yu Wang, V Lokesh Battula, Elisabeth J Shpall, Vivian R Ruvolo, Teresa McQueen, YiHua Qui, Zhihong Zeng, Sherry Pierce, Rodrigo Jacamo, Suk-Young Yoo, Phuong M Le, Jeffery Sun, Numsen Hail, Marina Konopleva, Michael Andreeff
Mesenchymal stromal cells support acute myeloid leukemia cell survival in the bone marrow microenvironment. Protein expression profiles of acute myeloid leukemia-derived mesenchymal stromal cells are unknown. Reverse phase protein array analysis was performed to compare expression of 151 proteins from acute myeloid leukemia mesenchymal stromal cells (n = 106) with mesenchymal stromal cells from healthy donors (n = 71). Protein expression differed significantly between the two groups with nineteen proteins overexpressed in leukemia stromal cells and nine overexpressed in normal stromal cells...
March 15, 2018: Haematologica
Jinho Lee, Gary K Geiss, Gokhan Demirkan, Christopher P Vellano, Brian Filanoski, Yiling Lu, Zhenlin Ju, Shuangxing Yu, Huifang Guo, Lisa Y Bogatzki, Warren E Carter, Rhonda K Meredith, Savitri Krishnamurthy, Zhiyong Ding, Joseph M Beechem, Gordon Mills
Molecular analysis of tumors forms the basis for personalized cancer medicine and increasingly guides patient selection for targeted therapy.  Future opportunities for personalized medicine are highlighted by the measurement of protein expression levels via immunohistochemistry, protein arrays, and other approaches; however, sample type, sample quantity, batch effects, and "time to result" are limiting factors for clinical application.  Here, we present a development pipeline for a novel multiplexed DNA-labeled antibody platform which digitally quantifies protein expression from lysate samples...
March 12, 2018: Molecular & Cellular Proteomics: MCP
Mehdi Moini
In the past few years, there has been a significant effort by the forensic science community to develop new scientific techniques for the analysis of forensic evidence. Forensic chemists have been spearheaded to develop information-rich confirmatory technologies and techniques and apply them to a broad array of forensic challenges. The purpose of these confirmatory techniques is to provide alternatives to presumptive techniques that rely on data such as color changes, pattern matching, or retention time alone, which are prone to more false positives...
March 12, 2018: Electrophoresis
Anneke D van Dijk, Chenyue W Hu, Eveline S J M de Bont, YiHua Qiu, Fieke W Hoff, Suk Young Yoo, Kevin R Coombes, Amina A Qutub, Steven M Kornblau
Post-translational histone tail modifications are known to play a role in leukemogenesis and are therapeutic targets. A global analysis of the level and patterns of expression of multiple histone modifying proteins (HMP) in acute myeloid leukemia (AML) and the effect of different patterns of expression on outcome and prognosis has not been investigated in AML patients. Here we analyzed 20 HMP by reverse phase protein array (RPPA) in a cohort of 205 newly diagnosed AML patients. Protein levels were correlated with patient and disease characteristics, including survival and mutational state...
March 5, 2018: Proteomics
Johnny R Ramroop, Mark N Stein, Justin M Drake
Prostate cancer is the most common malignancy in men in the United States. While androgen deprivation therapy results in tumor responses initially, there is relapse and progression to metastatic castration-resistant prostate cancer. Currently, all prostate cancer patients receive essentially the same treatment, and there is a need for clinically applicable technologies to provide predictive biomarkers toward personalized therapies. Genomic analyses of tumors are used for clinical applications, but with a paucity of obvious driver mutations in metastatic castration-resistant prostate cancer, other applications, such as phosphoproteomics, may complement this approach...
2018: Frontiers in Oncology
Lynn Calvin Shaw, Sergio Li Calzi, Nan Li, Leni Moldovan, Nilanjana Sengupta-Caballero, Judith Lindsey Quigley, Mircea Ivan, Bokkyoo Jun, Nicolas G Bazan, Michael Edwin Boulton, Julia Busik, Josef Neu, Maria B Grant
Purpose: Low levels of the long chain polyunsaturated fatty acid (LCPUFA) docosahexaenoic acid (DHA) have been implicated in retinopathy of prematurity (ROP). However, oral DHA suffers from poor palatability and is associated with increased bleeding in premature infants. We asked whether oral administration of the neutraceutical arginine-glutamine (Arg-Glu) could increase retinal DHA and improve outcomes in a mouse model of oxygen-induced retinopathy (OIR). Methods: Postnatal day 7 (P7) pups were maintained at 75% oxygen for 5 days and then returned to room air on P12...
February 1, 2018: Investigative Ophthalmology & Visual Science
A Ranjitha Dhanasekaran, Katheleen J Gardiner
Reverse Phase Protein Arrays (RPPA) is a high-throughput technology used to profile levels of protein expression. Handling the large datasets generated by RPPA can be facilitated by appropriate software tools. Here, we describe RPPAware, a free and intuitive software suite that was developed specifically for analysis and visualization of RPPA data. RPPAware is a portable tool that requires no installation and was built using Java. Many modules of the tool invoke R to utilize the statistical features. To demonstrate the utility of RPPAware, data generated from screening brain regions of a mouse model of Down syndrome with 62 antibodies were used as a case study...
January 15, 2018: Journal of Bioinformatics and Computational Biology
Ignacio G Bressán, Mariana L Mendez, María I Gimenez
BACKGROUND: Voriconazole is a broad-spectrum triazole antifungal agent. It is widely used in the treatment of invasive fungal infections in immunocompromised patients. Because the pharmacokinetics of voriconazole demonstrates considerable variability, monitoring its serum levels plays an important role in optimizing therapies against many clinically relevant fungal pathogens. The aim of this study was to validate a simple and rapid U-HPLC-PDA method with minimal sample preparation for routine therapeutic drug monitoring (TDM) of voriconazole...
February 8, 2018: Therapeutic Drug Monitoring
Ozlem Aslan, Mattia Cremona, Clare Morgan, Lydia W Cheung, Gordon B Mills, Bryan T Hennessy
BACKGROUND: The phosphoinositide-3-kinase (PI3K) pathway is the most commonly activated pathway in cancers due to mutations at multiple nodes and loss of PTEN. Furthermore, in endometrial cancer (EC), PI3K and RAS/RAF/MEK/MAPK (RAS/MAPK herein) pathway mutations frequently co-exist. We examined the role of PI3K and RAS/MAPK pathway mutations in determining responsiveness to therapies targeted to these pathways in vitro in EC. METHODS: 13 EC cell lines were profiled for their PI3K pathway and KRAS mutational and PTEN protein status and treated with one MEK- and two PI3K- targeted inhibitors alone and in combination...
February 9, 2018: BMC Cancer
Mohammed Gagaoua, Muriel Bonnet, Marie-Pierre Ellies-Oury, Leanne De Koning, Brigitte Picard
The validation of biomarkers and tools for the prediction of beef texture remains a challenging task. In this study, reverse phase protein arrays (RPPA) quantified 29 protein biomarkers in the m. Longissimus thoracis of Charolais cattle sampled early post-mortem. Myosin heavy chain 1 (MHC1, slow-oxidative fibers) and Retinal dehydrogenase 1 (ALDH1A1, oxidative enzyme) discriminated between tender and juicy vs. tough meat with residues classes and are validated as prime biomarkers of beef texture. Several proteins belonging to energy metabolism, heat shock and oxidative stress, cytoskeletal, cell signaling and apoptosis were related with tenderness...
June 1, 2018: Food Chemistry
Cynthia de la Fuente, Chelsea Pinkham, Deemah Dabbagh, Brett Beitzel, Aura Garrison, Gustavo Palacios, Kimberley Alex Hodge, Emanuel F Petricoin, Connie Schmaljohn, Catherine E Campbell, Aarthi Narayanan, Kylene Kehn-Hall
Rift Valley fever virus (RVFV) infects both ruminants and humans leading to a wide variance of pathologies dependent on host background and age. Utilizing a targeted reverse phase protein array (RPPA) to define changes in signaling cascades after in vitro infection of human cells with virulent and attenuated RVFV strains, we observed high phosphorylation of Smad transcription factors. This evolutionarily conserved family is phosphorylated by and transduces the activation of TGF-β superfamily receptors. Moreover, we observed that phosphorylation of Smad proteins required active RVFV replication and loss of NSs impaired this activation, further corroborating the RPPA results...
2018: PloS One
Roberta Bortolozzi, Elena Mattiuzzo, Luca Trentin, Benedetta Accordi, Giuseppe Basso, Giampietro Viola
Dysregulation of the cyclin D1-CDK4/CDK6 complex is frequently observed in almost all human cancer and contributes to aberrant cell proliferation and consequent tumorigenesis. Although many reports described the importance of CDK4/CDK6 in different set of human tumors, only few studies have been performed on leukemia. By gene expression analysis performed in a cohort of childhood patients affected by B-acute lymphoblastic leukemia (B-ALL) we found that both CDK4 and CDK6 are highly expressed. Moreover, Reverse Phase Protein Array (RPPA) analysis showed that cyclin D1 levels are higher in patients undergoing relapse...
February 3, 2018: Biochemical Pharmacology
Malgorzata Milewska, Mattia Cremona, Clare Morgan, John O'Shea, Aoife Carr, Sri H Velanki, Ann M Hopkins, Sinead Toomey, Stephen F Madden, Bryan T Hennessy, Alex J Eustace
Background: The application of genomic technologies to patient tumor samples identified groups of signaling pathways which acquire activating mutations. Some cancers are dependent on these mutations and the aberrant proteins resulting from these mutations can be targeted by novel drugs which can eradicate the cancer. Methods: We used to determine the frequency of ERBB mutations in solid tumors. We then determined the sensitivity of a panel of cell lines to clinically available PI3K inhibitors...
2018: Therapeutic Advances in Medical Oncology
Dongze Zhang, Huiyin Tu, Liang Cao, Hong Zheng, Robert L Muelleman, Michael C Wadman, Yu-Long Li
BACKGROUND: Attenuated cardiac vagal activity is associated with ventricular arrhythmogenesis and related mortality in patients with chronic heart failure. Our recent study has shown that expression of N-type Ca2+ channel α-subunits (Cav2.2-α) and N-type Ca2+ currents are reduced in intracardiac ganglion neurons from rats with chronic heart failure. Rat intracardiac ganglia are divided into the atrioventricular ganglion (AVG) and sinoatrial ganglion. Ventricular myocardium receives projection of neuronal terminals only from the AVG...
January 15, 2018: Journal of the American Heart Association
H Rouhrazi, N Turgan, G Oktem
Unlike low tumorigenic bulk tumor cells (non-CSCs), cancer stem cells (CSCs) are a subset of tumor cells that can self-renew and differentiate into different cancer subtypes. CSCs are considered responsible for tumor recurrence, distant metastasis, angiogenesis, and drug or radiation resistance. CSCs also are resistant to apoptosis. Zoledronic acid (ZA) is a third generation bisphosphonate that reduces cell proliferation and exhibits anti-tumor effects by inducing cell death in some malignancies; however, the effects of ZA on CSCs are unclear...
January 4, 2018: Biotechnic & Histochemistry: Official Publication of the Biological Stain Commission
Karen Klepsland Mauland, Zhenlin Ju, Ingvild Løberg Tangen, Anna Berg, Karl-Henning Kalland, Anne Margrete Øyan, Line Bjørge, Shannon N Westin, Camilla Krakstad, Jone Trovik, Gordon B Mills, Erling A Hoivik, Henrica Maria Johanna Werner
Endometrial cancer development is strongly linked to obesity, but knowledge regarding the influence of excess weight on endometrial tumor signaling pathways remains scarce. We therefore analyzed reverse phase protein array (RPPA) data for obesity-related protein expression patterns, using one training (n=272) and two test cohorts (n=68; n=178) of well-annotated samples from women treated for endometrioid endometrial cancer. Gene expression profiling and immunohistochemistry were used for cross-platform validation...
December 5, 2017: Oncotarget
Stefanie Avril, Yasemin Dincer, Katharina Malinowsky, Claudia Wolff, Sibylle Gündisch, Alexander Hapfelmeier, Melanie Boxberg, Holger Bronger, Karl-Friedrich Becker, Barbara Schmalfeldt
Despite frequent initial response rates of epithelial ovarian cancer to platinum-based chemotherapy the majority of patients develop drug resistance. Our aim was to evaluate differential expression of signaling-pathway proteins in platinum-sensitive versus platinum-resistant primary epithelial ovarian cancer specimens to identify predictive biomarkers for treatment response. 192 patients were studied comprising of independent training ( n = 89) and validation ( n = 103) cohorts. Full-length proteins were extracted from paraffin-embedded samples including multiple regions per tumor to account for intratumoral heterogeneity...
November 17, 2017: Oncotarget
Mehreen Ali, Suleiman A Khan, Krister Wennerberg, Tero Aittokallio
Motivation: Proteomics profiling is increasingly being used for molecular stratification of cancer patients and cell-line panels. However, systematic assessment of the predictive power of large-scale proteomic technologies across various drug classes and cancer types is currently lacking. To that end, we carried out the first pan-cancer, multi-omics comparative analysis of the relative performance of two proteomic technologies, targeted reverse phase protein array (RPPA) and global mass spectrometry (MS), in terms of their accuracy for predicting the sensitivity of cancer cells to both cytotoxic chemotherapeutics and molecularly-targeted anticancer compounds...
November 27, 2017: Bioinformatics
John O'Shea, Mattia Cremona, Clare Morgan, Malgorzata Milewska, Frankie Holmes, Virginia Espina, Lance Liotta, Joyce O'Shaughnessy, Sinead Toomey, Stephen F Madden, Aoife Carr, Naomi Elster, Bryan T Hennessy, Alex J Eustace
Purpose: The MEK/MAPK pathway is commonly activated in HER2-positive breast cancer, but little investigation of targeting this pathway has been undertaken. Here we present the results of an in vitro preclinical evaluation of refametinib, an allosteric MEK1/2 inhibitor, in HER2-positive breast cancer cell lines including models of acquired resistance to trastuzumab or lapatinib. Methods: A panel of HER2-positive breast cancer cells were profiled for mutational status and also for anti-proliferative response to refametinib alone and in combination with the PI3K inhibitor (PI3Ki) copanlisib and the HER2-targeted therapies trastuzumab and lapatinib...
October 17, 2017: Oncotarget
James L Ross, Lee A D Cooper, Jun Kong, David Gutman, Merete Williams, Carol Tucker-Burden, Myles R McCrary, Alexandros Bouras, Milota Kaluzova, William D Dunn, Duc Duong, Constantinos G Hadjipanayis, Daniel J Brat
Glioblastoma (GBM) contains diverse microenvironments with uneven distributions of oncogenic alterations and signaling networks. The diffusely infiltrative properties of GBM result in residual tumor at neurosurgical resection margins, representing the source of relapse in nearly all cases and suggesting that therapeutic efforts should be focused there. To identify signaling networks and potential druggable targets across tumor microenvironments (TMEs), we utilized 5-ALA fluorescence-guided neurosurgical resection and sampling, followed by proteomic analysis of specific TMEs...
November 15, 2017: Scientific Reports
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