Literature DB >> 24777629

Realizing the promise of reverse phase protein arrays for clinical, translational, and basic research: a workshop report: the RPPA (Reverse Phase Protein Array) society.

Rehan Akbani1, Karl-Friedrich Becker2, Neil Carragher3, Ted Goldstein4, Leanne de Koning5, Ulrike Korf6, Lance Liotta7, Gordon B Mills1, Satoshi S Nishizuka8, Michael Pawlak9, Emanuel F Petricoin7, Harvey B Pollard10, Bryan Serrels3, Jingchun Zhu4.   

Abstract

Reverse phase protein array (RPPA) technology introduced a miniaturized "antigen-down" or "dot-blot" immunoassay suitable for quantifying the relative, semi-quantitative or quantitative (if a well-accepted reference standard exists) abundance of total protein levels and post-translational modifications across a variety of biological samples including cultured cells, tissues, and body fluids. The recent evolution of RPPA combined with more sophisticated sample handling, optical detection, quality control, and better quality affinity reagents provides exquisite sensitivity and high sample throughput at a reasonable cost per sample. This facilitates large-scale multiplex analysis of multiple post-translational markers across samples from in vitro, preclinical, or clinical samples. The technical power of RPPA is stimulating the application and widespread adoption of RPPA methods within academic, clinical, and industrial research laboratories. Advances in RPPA technology now offer scientists the opportunity to quantify protein analytes with high precision, sensitivity, throughput, and robustness. As a result, adopters of RPPA technology have recognized critical success factors for useful and maximum exploitation of RPPA technologies, including the following: preservation and optimization of pre-analytical sample quality, application of validated high-affinity and specific antibody (or other protein affinity) detection reagents, dedicated informatics solutions to ensure accurate and robust quantification of protein analytes, and quality-assured procedures and data analysis workflows compatible with application within regulated clinical environments. In 2011, 2012, and 2013, the first three Global RPPA workshops were held in the United States, Europe, and Japan, respectively. These workshops provided an opportunity for RPPA laboratories, vendors, and users to share and discuss results, the latest technology platforms, best practices, and future challenges and opportunities. The outcomes of the workshops included a number of key opportunities to advance the RPPA field and provide added benefit to existing and future participants in the RPPA research community. The purpose of this report is to share and disseminate, as a community, current knowledge and future directions of the RPPA technology.
© 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

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Year:  2014        PMID: 24777629      PMCID: PMC4083105          DOI: 10.1074/mcp.O113.034918

Source DB:  PubMed          Journal:  Mol Cell Proteomics        ISSN: 1535-9476            Impact factor:   5.911


  113 in total

1.  RPPanalyzer: Analysis of reverse-phase protein array data.

Authors:  Heiko A Mannsperger; Stephan Gade; Frauke Henjes; Tim Beissbarth; Ulrike Korf
Journal:  Bioinformatics       Date:  2010-07-15       Impact factor: 6.937

Review 2.  Antibody-based proteomics: analysis of signaling networks using reverse protein arrays.

Authors:  Hans Voshol; Markus Ehrat; Jens Traenkle; Eric Bertrand; Jan van Oostrum
Journal:  FEBS J       Date:  2009-10-26       Impact factor: 5.542

3.  Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum.

Authors:  Tujin Shi; Thomas L Fillmore; Xuefei Sun; Rui Zhao; Athena A Schepmoes; Mahmud Hossain; Fang Xie; Si Wu; Jong-Seo Kim; Nathan Jones; Ronald J Moore; Ljiljana Pasa-Tolić; Jacob Kagan; Karin D Rodland; Tao Liu; Keqi Tang; David G Camp; Richard D Smith; Wei-Jun Qian
Journal:  Proc Natl Acad Sci U S A       Date:  2012-09-04       Impact factor: 11.205

4.  Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells.

Authors:  Raoul Tibes; Yihua Qiu; Yiling Lu; Bryan Hennessy; Michael Andreeff; Gordon B Mills; Steven M Kornblau
Journal:  Mol Cancer Ther       Date:  2006-10       Impact factor: 6.261

Review 5.  Mapping molecular networks using proteomics: a vision for patient-tailored combination therapy.

Authors:  Emanuel F Petricoin; Verena E Bichsel; Valerie S Calvert; Virginia Espina; Mary Winters; Lynn Young; Claudio Belluco; Bruce J Trock; Marc Lippman; David A Fishman; Dennis C Sgroi; Peter J Munson; Laura J Esserman; Lance A Liotta
Journal:  J Clin Oncol       Date:  2005-05-20       Impact factor: 44.544

6.  A pilot characterization of human lung NSCLC by protein pathway activation mapping.

Authors:  Angela Zupa; Giuseppina Improta; Alessandra Silvestri; Elisa Pin; Jianghong Deng; Michele Aieta; Pellegrino Musto; Donato Nitti; Enzo Mammano; Lance Liotta; Claudio Belluco; Julia Wulfkuhle; Emanuel Petricoin
Journal:  J Thorac Oncol       Date:  2012-12       Impact factor: 15.609

7.  Molecular analysis of HER2 signaling in human breast cancer by functional protein pathway activation mapping.

Authors:  Julia D Wulfkuhle; Daniela Berg; Claudia Wolff; Rupert Langer; Kai Tran; Julie Illi; Virginia Espina; Mariaelena Pierobon; Jianghong Deng; Angela DeMichele; Axel Walch; Holger Bronger; Ingrid Becker; Christine Waldhör; Heinz Höfler; Laura Esserman; Lance A Liotta; Karl-Friedrich Becker; Emanuel F Petricoin
Journal:  Clin Cancer Res       Date:  2012-10-08       Impact factor: 12.531

8.  IGFBP2 is a candidate biomarker for Ink4a-Arf status and a therapeutic target for high-grade gliomas.

Authors:  Lynette M Moore; Kristen M Holmes; Sarah M Smith; Ying Wu; Elena Tchougounova; Lene Uhrbom; Raymond Sawaya; Janet M Bruner; Gregory N Fuller; Wei Zhang
Journal:  Proc Natl Acad Sci U S A       Date:  2009-09-16       Impact factor: 11.205

9.  Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks.

Authors:  Michael J Lee; Albert S Ye; Alexandra K Gardino; Anne Margriet Heijink; Peter K Sorger; Gavin MacBeath; Michael B Yaffe
Journal:  Cell       Date:  2012-05-11       Impact factor: 41.582

10.  An heregulin-EGFR-HER3 autocrine signaling axis can mediate acquired lapatinib resistance in HER2+ breast cancer models.

Authors:  Wenle Xia; Emanual F Petricoin; Sumin Zhao; Leihua Liu; Takuya Osada; Qing Cheng; Julia D Wulfkuhle; William R Gwin; Xiaoyi Yang; Rosa I Gallagher; Sarah Bacus; H Kim Lyerly; Neil L Spector
Journal:  Breast Cancer Res       Date:  2013       Impact factor: 6.466

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  58 in total

Review 1.  Moonshot Objectives: Catalyze New Scientific Breakthroughs-Proteogenomics.

Authors:  Karin D Rodland; Paul Piehowski; Richard D Smith
Journal:  Cancer J       Date:  2018 May/Jun       Impact factor: 3.360

2.  Peptide Immunoaffinity Enrichment and Targeted Mass Spectrometry Enables Multiplex, Quantitative Pharmacodynamic Studies of Phospho-Signaling.

Authors:  Jeffrey R Whiteaker; Lei Zhao; Ping Yan; Richard G Ivey; Uliana J Voytovich; Heather D Moore; Chenwei Lin; Amanda G Paulovich
Journal:  Mol Cell Proteomics       Date:  2015-05-18       Impact factor: 5.911

3.  Multiscale analysis of the murine intestine for modeling human diseases.

Authors:  Jesse Lyons; Charles A Herring; Amrita Banerjee; Alan J Simmons; Ken S Lau
Journal:  Integr Biol (Camb)       Date:  2015-07       Impact factor: 2.192

4.  Proteomics for cancer drug design.

Authors:  Amanda Haymond; Justin B Davis; Virginia Espina
Journal:  Expert Rev Proteomics       Date:  2019-08-04       Impact factor: 3.940

5.  A pilot study exploring the molecular architecture of the tumor microenvironment in human prostate cancer using laser capture microdissection and reverse phase protein microarray.

Authors:  Elisa Pin; Steven Stratton; Claudio Belluco; Lance Liotta; Ray Nagle; K Alex Hodge; Jianghong Deng; Ting Dong; Elisa Baldelli; Emanuel Petricoin; Mariaelena Pierobon
Journal:  Mol Oncol       Date:  2016-10-14       Impact factor: 6.603

6.  MAPK Activation Predicts Poor Outcome and the MEK Inhibitor, Selumetinib, Reverses Antiestrogen Resistance in ER-Positive High-Grade Serous Ovarian Cancer.

Authors:  Karina E Hew; Philip C Miller; Dorraya El-Ashry; Jun Sun; Alexandra H Besser; Tan A Ince; Mengnan Gu; Zhi Wei; Gao Zhang; Patricia Brafford; Wei Gao; Yiling Lu; Gordon B Mills; Joyce M Slingerland; Fiona Simpkins
Journal:  Clin Cancer Res       Date:  2015-10-19       Impact factor: 12.531

7.  Beclin 1 Promotes Endosome Recruitment of Hepatocyte Growth Factor Tyrosine Kinase Substrate to Suppress Tumor Proliferation.

Authors:  Asia N Matthew-Onabanjo; Jenny Janusis; Jose Mercado-Matos; Anne E Carlisle; Dohoon Kim; Fayola Levine; Peter Cruz-Gordillo; Ryan Richards; Michael J Lee; Leslie M Shaw
Journal:  Cancer Res       Date:  2019-11-19       Impact factor: 12.701

8.  Evaluation of Protein Profiles From Treated Xenograft Tumor Models Identifies an Antibody Panel for Formalin-fixed and Paraffin-embedded (FFPE) Tissue Analysis by Reverse Phase Protein Arrays (RPPA).

Authors:  Sabine Bader; Magdalena Zajac; Thomas Friess; Elisabeth Ruge; Natascha Rieder; Berthold Gierke; Yvonne Heubach; Marlene Thomas; Michael Pawlak
Journal:  Mol Cell Proteomics       Date:  2015-06-23       Impact factor: 5.911

Review 9.  Using reverse-phase protein arrays as pharmacodynamic assays for functional proteomics, biomarker discovery, and drug development in cancer.

Authors:  Yiling Lu; Shiyun Ling; Apurva M Hegde; Lauren A Byers; Kevin Coombes; Gordon B Mills; Rehan Akbani
Journal:  Semin Oncol       Date:  2016-06-15       Impact factor: 4.929

Review 10.  Translating pharmacodynamic biomarkers from bench to bedside: analytical validation and fit-for-purpose studies to qualify multiplex immunofluorescent assays for use on clinical core biopsy specimens.

Authors:  Allison Marrero; Scott Lawrence; Deborah Wilsker; Andrea Regier Voth; Robert J Kinders
Journal:  Semin Oncol       Date:  2016-06-14       Impact factor: 4.929

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