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Gobena S, Admassu B, Kinde MZ, Gessese AT. Proteomics and Its Current Application in Biomedical Area: Concise Review. ScientificWorldJournal 2024; 2024:4454744. [PMID: 38404932 PMCID: PMC10894052 DOI: 10.1155/2024/4454744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024] Open
Abstract
Biomedical researchers tirelessly seek cutting-edge technologies to advance disease diagnosis, drug discovery, and therapeutic interventions, all aimed at enhancing human and animal well-being. Within this realm, proteomics stands out as a pivotal technology, focusing on extensive studies of protein composition, structure, function, and interactions. Proteomics, with its subdivisions of expression, structural, and functional proteomics, plays a crucial role in unraveling the complexities of biological systems. Various sophisticated techniques are employed in proteomics, including polyacrylamide gel electrophoresis, mass spectrometry analysis, NMR spectroscopy, protein microarray, X-ray crystallography, and Edman sequencing. These methods collectively contribute to the comprehensive understanding of proteins and their roles in health and disease. In the biomedical field, proteomics finds widespread application in cancer research and diagnosis, stem cell studies, and the diagnosis and research of both infectious and noninfectious diseases. In addition, it plays a pivotal role in drug discovery and the emerging frontier of personalized medicine. The versatility of proteomics allows researchers to delve into the intricacies of molecular mechanisms, paving the way for innovative therapeutic approaches. As infectious and noninfectious diseases continue to emerge and the field of biomedical research expands, the significance of proteomics becomes increasingly evident. Keeping abreast of the latest developments in proteomics applications becomes paramount for the development of therapeutics, translational research, and study of diverse diseases. This review aims to provide a comprehensive overview of proteomics, offering a concise outline of its current applications in the biomedical domain. By doing so, it seeks to contribute to the understanding and advancement of proteomics, emphasizing its pivotal role in shaping the future of biomedical research and therapeutic interventions.
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Affiliation(s)
- Semira Gobena
- College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Bemrew Admassu
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Mebrie Zemene Kinde
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Abebe Tesfaye Gessese
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
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Khadirnaikar S, Shukla S, Prasanna SRM. Machine learning based combination of multi-omics data for subgroup identification in non-small cell lung cancer. Sci Rep 2023; 13:4636. [PMID: 36944673 PMCID: PMC10030850 DOI: 10.1038/s41598-023-31426-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/11/2023] [Indexed: 03/23/2023] Open
Abstract
Non-small Cell Lung Cancer (NSCLC) is a heterogeneous disease with a poor prognosis. Identifying novel subtypes in cancer can help classify patients with similar molecular and clinical phenotypes. This work proposes an end-to-end pipeline for subgroup identification in NSCLC. Here, we used a machine learning (ML) based approach to compress the multi-omics NSCLC data to a lower dimensional space. This data is subjected to consensus K-means clustering to identify the five novel clusters (C1-C5). Survival analysis of the resulting clusters revealed a significant difference in the overall survival of clusters (p-value: 0.019). Each cluster was then molecularly characterized to identify specific molecular characteristics. We found that cluster C3 showed minimal genetic aberration with a high prognosis. Next, classification models were developed using data from each omic level to predict the subgroup of unseen patients. Decision‑level fused classification models were then built using these classifiers, which were used to classify unseen patients into five novel clusters. We also showed that the multi-omics-based classification model outperformed single-omic-based models, and the combination of classifiers proved to be a more accurate prediction model than the individual classifiers. In summary, we have used ML models to develop a classification method and identified five novel NSCLC clusters with different genetic and clinical characteristics.
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Affiliation(s)
- Seema Khadirnaikar
- Department of Electrical Engineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Sudhanshu Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India.
| | - S R M Prasanna
- Department of Electrical Engineering, Indian Institute of Technology Dharwad, Dharwad, India
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3
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Mir MA, Qayoom H, Sofi S, Jan N. Proteomics: A groundbreaking development in cancer biology. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00004-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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Proteomics: Application of next-generation proteomics in cancer research. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00016-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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5
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Functional Proteomic Profiling of Triple-Negative Breast Cancer. Cells 2021; 10:cells10102768. [PMID: 34685748 PMCID: PMC8535076 DOI: 10.3390/cells10102768] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/08/2021] [Accepted: 09/26/2021] [Indexed: 01/13/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a subtype of breast cancer that comprises various disease entities, all of which share a set of common features: a lack of expression of the estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2, respectively. Because of their receptor status, conventional chemotherapy remains the main therapeutic option for TNBC patients. We employed a reverse phase protein array approach (RPPA), complemented by immunohistochemistry, to quantitatively profile the activation state of 84 actionable key signaling intermediates and phosphoproteins in a set of 44 TNBC samples. We performed supervised and unsupervised approaches to proteomic data analysis to identify groups of samples sharing common characteristics that could be amenable to existing therapies. We found the heterogenous activation of multiple pathways, with PI3 K/AKT/mTOR signaling being the most common event. Some specific individualized therapeutic possibilities include the expression of oncogenic KIT in association with cytokeratin 15 and Erk1/2 positive tumors, both of which may have clinical value.
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Tsang O, Wong JWH. Proteogenomic interrogation of cancer cell lines: an overview of the field. Expert Rev Proteomics 2021; 18:221-232. [PMID: 33877947 DOI: 10.1080/14789450.2021.1914594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Introduction: Cancer cell lines (CCLs) have been a major resource for cancer research. Over the past couple of decades, they have been instrumental in omic profiling method development and as model systems to generate new knowledge in cell and cancer biology. More recently, with the increasing amount of genomic, transcriptomic and proteomic data being generated in hundreds of CCLs, there is growing potential for integrative proteogenomic data analyses to be performed.Areas covered: In this review, we first describe the most commonly used proteome profiling methods in CCLs. We then discuss how these proteomics data can be integrated with genomics data for proteogenomics analyses. Finally, we highlight some of the recent biological discoveries that have arisen from proteogenomics analyses of CCLs.Expert opinion: Protegeonomics analyses of CCLs have so far enabled the discovery of novel proteins and proteoforms. It has also improved our understanding of biological processes including post-transcriptional regulation of protein abundance and the presentation of antigens by major histocompatibility complex alleles. With proteomics data to be generated in hundreds to thousands of CCLs in coming years, there will be further potential for large-scale proteogenomics analyses and data integration with the phenotypically well-characterized CCLs.
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Affiliation(s)
- Olson Tsang
- Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Jason W H Wong
- Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR.,School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
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Maity AK, Carroll RJ, Mallick BK. Integration of Survival and Binary Data for Variable Selection and Prediction: A Bayesian Approach. J R Stat Soc Ser C Appl Stat 2020; 68:1577-1595. [PMID: 33311813 DOI: 10.1111/rssc.12377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We consider the problem where the data consist of a survival time and a binary outcome measurement for each individual, as well as corresponding predictors. The goal is to select the common set of predictors which affect both the responses, and not just only one of them. In addition, we develop a survival prediction model based on data integration. This article is motivated by the Cancer Genomic Atlas (TCGA) databank, which is currently the largest genomics and transcriptomics database. The data contain cancer survival information along with cancer stages for each patient. Furthermore, it contains Reverse-phase Protein Array (RPPA) measurements for each individual, which are the predictors associated with these responses. The biological motivation is to identify the major actionable proteins associated with both survival outcomes and cancer stages. We develop a Bayesian hierarchical model to jointly model the survival time and the classification of the cancer stages. Moreover, to deal with the high dimensionality of the RPPA measurements, we use a shrinkage prior to identify significant proteins. Simulations and TCGA data analysis show that the joint integrated modeling approach improves survival prediction.
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Affiliation(s)
- Arnab Kumar Maity
- Early Clinical Development Oncology Statistics, 10777 Science Center Drive, Pfizer Inc., San Diego, CA 92121
| | - Raymond J Carroll
- Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX, 77843-3143, and School of Mathematical and Physical Sciences, University of Technology, Sydney, Broadway NSW 2007, Australia
| | - Bani K Mallick
- Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX, 77843-3143
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You Y, Ru X, Lei W, Li T, Xiao M, Zheng H, Chen Y, Zhang L. Developing the novel bioinformatics algorithms to systematically investigate the connections among survival time, key genes and proteins for Glioblastoma multiforme. BMC Bioinformatics 2020; 21:383. [PMID: 32938364 PMCID: PMC7646399 DOI: 10.1186/s12859-020-03674-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Glioblastoma multiforme (GBM) is one of the most common malignant brain tumors and its average survival time is less than 1 year after diagnosis. RESULTS Firstly, this study aims to develop the novel survival analysis algorithms to explore the key genes and proteins related to GBM. Then, we explore the significant correlation between AEBP1 upregulation and increased EGFR expression in primary glioma, and employ a glioma cell line LN229 to identify relevant proteins and molecular pathways through protein network analysis. Finally, we identify that AEBP1 exerts its tumor-promoting effects by mainly activating mTOR pathway in Glioma. CONCLUSIONS We summarize the whole process of the experiment and discuss how to expand our experiment in the future.
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Affiliation(s)
- Yujie You
- College of Computer Science, Sichuan University, Chengdu, 610065 China
| | - Xufang Ru
- Department of Neurosurgery, Southwest Hospital, Third Military Medical University, Chongqing, P.R. China
| | - Wanjing Lei
- College of Computer Science, Sichuan University, Chengdu, 610065 China
| | - Tingting Li
- College of Mathematics and Statistics, Southwest University, Chongqing, 400715 P.R. China
| | - Ming Xiao
- College of Computer Science, Sichuan University, Chengdu, 610065 China
| | - Huiru Zheng
- School of Computing, Ulster University, Coleraine, Londonderry, Northern Ireland, UK
| | - Yujie Chen
- Department of Neurosurgery, Southwest Hospital, Third Military Medical University, Chongqing, P.R. China
| | - Le Zhang
- College of Computer Science, Sichuan University, Chengdu, 610065 China
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Sriskandarajah P, De Haven Brandon A, MacLeod K, Carragher NO, Kirkin V, Kaiser M, Whittaker SR. Combined targeting of MEK and the glucocorticoid receptor for the treatment of RAS-mutant multiple myeloma. BMC Cancer 2020; 20:269. [PMID: 32228485 PMCID: PMC7106683 DOI: 10.1186/s12885-020-06735-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/11/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Multiple myeloma (MM) remains incurable despite recent therapeutic advances. RAS mutations are frequently associated with relapsed/refractory disease. Efforts to target the mitogen-activated protein kinase (MAPK) pathway with the MEK inhibitor, trametinib (Tra) have been limited by toxicities and the development of resistance. Dexamethasone (Dex) is a corticosteroid commonly used in clinical practice, to enhance efficacy of anti-myeloma therapy. Therefore, we hypothesised that the combination of Tra and Dex would yield synergistic activity in RAS-mutant MM. METHODS The response of human MM cell lines to drug treatment was analysed using cell proliferation assays, Western blotting, Annexin V and propidium iodide staining by flow cytometry and reverse phase protein arrays. The efficacy of trametinib and dexamethasone treatment in the MM.1S xenograft model was assessed by measuring tumor volume over time. RESULTS The Tra/Dex combination demonstrated synergistic cytotoxicity in KRASG12A mutant lines MM.1S and RPMI-8226. The induction of apoptosis was associated with decreased MCL-1 expression and increased BIM expression. Reverse phase proteomic arrays revealed suppression of FAK, PYK2, FLT3, NDRG1 and 4EBP1 phosphorylation with the Tra/Dex combination. Notably, NDRG1 expression was associated with the synergistic response to Tra/Dex. MM cells were sensitive to PDK1 inhibition and IGF1-induced signalling partially protected from Tra/Dex treatment, highlighting the importance of this pathway. In the MM.1S tumor xenograft model, only the combination of Tra/Dex resulted in a significant inhibition of tumor growth. CONCLUSIONS Overall Tra/Dex demonstrates antiproliferative activity in RAS-mutant MM cell lines associated with suppression of pro-survival PDK1 signalling and engagement of apoptotic pathways. Our data support further investigation of this combination in RAS-mutant MM.
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Affiliation(s)
- Priya Sriskandarajah
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SW7 3RP, UK.,The Royal Marsden NHS Foundation Trust, London, UK
| | | | - Kenneth MacLeod
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Vladimir Kirkin
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Martin Kaiser
- The Royal Marsden NHS Foundation Trust, London, UK.,Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Steven R Whittaker
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SW7 3RP, UK.
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10
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Ecoy GAU, Chamni S, Suwanborirux K, Chanvorachote P, Chaotham C. Jorunnamycin A from Xestospongia sp. Suppresses Epithelial to Mesenchymal Transition and Sensitizes Anoikis in Human Lung Cancer Cells. JOURNAL OF NATURAL PRODUCTS 2019; 82:1861-1873. [PMID: 31260310 DOI: 10.1021/acs.jnatprod.9b00102] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Metastasis is a key driving force behind the high mortality rate associated with lung cancer. Herein, we report the first study revealing the antimetastasis activity of jorunnamycin A, a bistetrahydroisoquinolinequinone isolated from a Thai blue sponge Xestospongia sp. evidenced by its inhibition of epithelial to mesenchymal transition (EMT), sensitization of anoikis, and suppression of anchorage-independent survival in human lung cancer cells. Treatment with jorunnamycin A (0.05-0.5 μM) altered the expression of p53 and Bcl-2 family proteins, particularly causing the down-regulation of antiapoptosis Bcl-2 and Mcl-1 proteins. Under detachment conditions for 12 h, jorunnamycin A-treated cells exhibited diminution of pro-survival proteins p-Akt and p-Erk as well as the survival-promoting factor caveolin-1. Corresponding with the inhibition on the Akt and Erk pathway as well as activation of p53, there was an increase in the epithelial marker E-cadherin and a remarkable decrease of EMT markers and associated proteins including vimentin, snail, and claudin-1. As the loss of anchorage dependence is an important barrier to metastasis, the observed inhibitory effects of jorunnamycin A on the coordinating networks of EMT and anchorage-independent growth emphasize the potential development of jorunnamycin A as an effective agent against lung cancer metastasis.
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11
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Dutil J, Chen Z, Monteiro AN, Teer JK, Eschrich SA. An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines. Cancer Res 2019; 79:1263-1273. [PMID: 30894373 DOI: 10.1158/0008-5472.can-18-2747] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/08/2018] [Accepted: 12/26/2018] [Indexed: 12/21/2022]
Abstract
Recent work points to a lack of diversity in genomics studies from genome-wide association studies to somatic (tumor) genome analyses. Yet, population-specific genetic variation has been shown to contribute to health disparities in cancer risk and outcomes. Immortalized cancer cell lines are widely used in cancer research, from mechanistic studies to drug screening. Larger collections of cancer cell lines better represent the genomic heterogeneity found in primary tumors. Yet, the genetic ancestral origin of cancer cell lines is rarely acknowledged and often unknown. Using genome-wide genotyping data from 1,393 cancer cell lines from the Catalogue of Somatic Mutations in Cancer (COSMIC) and Cancer Cell Line Encyclopedia (CCLE), we estimated the genetic ancestral origin for each cell line. Our data indicate that cancer cell line collections are not representative of the diverse ancestry and admixture characterizing human populations. We discuss the implications of genetic ancestry and diversity of cellular models for cancer research and present an interactive tool, Estimated Cell Line Ancestry (ECLA), where ancestry can be visualized with reference populations of the 1000 Genomes Project. Cancer researchers can use this resource to identify cell line models for their studies by taking ancestral origins into consideration.
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Affiliation(s)
- Julie Dutil
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, Puerto Rico.
| | - Zhihua Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Alvaro N Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Steven A Eschrich
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
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O'Farrell AC, Miller IS, Evans R, Alamanou M, Cary M, Mallya Udupi G, Lafferty A, Monsefi N, Cremona M, Prehn JHM, Verheul HM, Gallagher WM, Gehrmann M, Byrne AT. Implementing Reverse Phase Protein Array Profiling as a Sensitive Method for the Early Pre-Clinical Detection of Off-Target Toxicities Associated with Sunitinib Malate. Proteomics Clin Appl 2019; 13:e1800159. [PMID: 30768761 DOI: 10.1002/prca.201800159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/23/2019] [Indexed: 11/12/2022]
Abstract
PURPOSE The tyrosine kinase inhibitor (TKI) sunitinib is a multi-targeted agent approved across multiple cancer indications. Nevertheless, since approval, data has emerged to describe a worrisome side effect profile including hypertension, hand-foot syndrome, fatigue, diarrhea, mucositis, proteinuria, and (rarely) congestive heart failure. It has been hypothesized that the observed multi-parameter toxicity profile is related to "on-target" kinase inhibition in "off-target" tissues. EXPERIMENTAL DESIGN To interrogate off-target effects in pre-clinical studies, a reverse phase protein array (RPPA) approach is employed. Mice are treated with sunitinib (40 mg kg-1 ) for 4 weeks, following which critical organs are removed. The Zeptosens RPPA platform is employed for protein expression analysis. RESULTS Differentially expressed proteins associated with damage and/or stress are found in the majority of organs from treated animals. Proteins differentially expressed in the heart are associated with myocardial hypertrophy, ischaemia/reperfusion, and hypoxia. However, hypertrophy is not evidenced on histology. Mild proteinuria is observed; however, no changes in renal glomerular structure are visible via electron microscopy. In skin, proteins associated with cutaneous inflammation, keratinocyte hyper-proliferation, and increased inflammatory response are differentially expressed. CONCLUSIONS AND CLINICAL RELEVANCE It is posited that pre-clinical implementation of a combined histopathological/RPPA approach provides a sensitive method to mechanistically elucidate the early manifestation of TKI on-target/organ off-target toxicities.
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Affiliation(s)
- Alice C O'Farrell
- RCSI Centre for Systems Medicine, Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, D02 HX03, Ireland
| | - Ian S Miller
- RCSI Centre for Systems Medicine, Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, D02 HX03, Ireland
| | - Rhys Evans
- RCSI Centre for Systems Medicine, Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, D02 HX03, Ireland
| | - Marina Alamanou
- OncoMark Ltd., NovaUCD, Bellfield, University College Dublin, Dublin 4, D04 V2P1, Ireland
| | - Maurice Cary
- Pathology Experts GmBH, Basel, CH-4108, Switzerland
| | - Girish Mallya Udupi
- OncoMark Ltd., NovaUCD, Bellfield, University College Dublin, Dublin 4, D04 V2P1, Ireland
| | - Adam Lafferty
- RCSI Centre for Systems Medicine, Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, D02 HX03, Ireland
| | - Naser Monsefi
- RCSI Centre for Systems Medicine, Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, D02 HX03, Ireland
| | - Mattia Cremona
- Beaumont Education Resource Centre, Beaumont Hospital, Dublin 9, D09 YD60, Ireland
| | - Jochen H M Prehn
- RCSI Centre for Systems Medicine, Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, D02 HX03, Ireland
| | - Henk M Verheul
- Department of Medical Oncology, VU University Medical Centre, Amsterdam, 1081HV, The Netherlands
| | - William M Gallagher
- OncoMark Ltd., NovaUCD, Bellfield, University College Dublin, Dublin 4, D04 V2P1, Ireland.,UCD Cancer Biology and Therapeutics Laboratory, School of Biomolecular and Biomedical Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 W6F6, Ireland
| | | | - Annette T Byrne
- RCSI Centre for Systems Medicine, Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, D02 HX03, Ireland
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Dawson JC, Warchal SJ, Carragher NO. Drug Screening Platforms and RPPA. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1188:203-226. [PMID: 31820390 DOI: 10.1007/978-981-32-9755-5_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Since its inception as a scalable and cost-effective method for precise quantification of the abundance of multiple protein analytes and post-translational epitopes across large sample sets, reverse phase protein array (RPPA) has been utilized as a drug discovery tool. Key RPPA drug discovery applications include primary screening of abundance or activation state of nominated protein targets, secondary screening for toxicity and selectivity, mechanism-of-action profiling, biomarker discovery, and drug combination discovery. In recent decades, drug discovery strategies have evolved dramatically in response to continual advances in technology platforms supporting high-throughput screening, structure-based drug design, new therapeutic modalities, and increasingly more complex and disease-relevant cell-based and in vivo preclinical models of disease. Advances in biological laboratory capabilities in drug discovery are complemented by significant developments in bioinformatics and computational approaches for integrating large complex datasets. Bioinformatic and computational analysis of integrated molecular, pathway network and phenotypic datasets enhance multiple stages of the drug discovery process and support more informative drug target hypothesis generation and testing. In this chapter we discuss and present examples demonstrating how the latest advances in RPPA complement and integrate with other emerging drug screening platforms to support a new era of more informative and evidence-led drug discovery strategies.
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Affiliation(s)
- John C Dawson
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Scott J Warchal
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK.
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Byron A. Reproducibility and Crossplatform Validation of Reverse-Phase Protein Array Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1188:181-201. [PMID: 31820389 DOI: 10.1007/978-981-32-9755-5_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Reverse-phase protein array (RPPA) technology is a high-throughput antibody- and microarray-based approach for the rapid profiling of levels of proteins and protein posttranslational modifications in biological specimens. The technology consumes small amounts of samples, can sensitively detect low-abundance proteins and posttranslational modifications, enables measurements of multiple signaling pathways in parallel, has the capacity to analyze large sample numbers, and offers robust interexperimental reproducibility. These features of RPPA experiments have motivated and enabled the use of RPPA technology in various biomedical, translational, and clinical applications, including the delineation of molecular mechanisms of disease, profiling of druggable signaling pathway activation, and search for new prognostic markers. Owing to the complexity of many of these applications, such as developing multiplex protein assays for diagnostic laboratories or integrating posttranslational modification-level data using large-scale proteogenomic approaches, robust and well-validated data are essential. There are many distinct components of an RPPA workflow, and numerous possible technical setups and analysis parameter options exist. The differences between RPPA platform setups around the world offer opportunities to assess and minimize interplatform variation. Crossplatform validation may also aid in the evaluation of robust, platform-independent protein markers of disease and response to therapy.
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Affiliation(s)
- Adam Byron
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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15
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Liao H, Xie X, Xu Y, Huang G. Identification of driver genes associated with chemotherapy resistance of Ewing's sarcoma. Onco Targets Ther 2018; 11:6947-6956. [PMID: 30410352 PMCID: PMC6199211 DOI: 10.2147/ott.s172190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Background The aim of this study was to identify the driver genes associated with chemotherapy resistance of Ewing’s sarcoma and potential targets for Ewing’s sarcoma treatment. Methods Two mRNA microarray datasets, GSE12102 and GSE17679, were downloaded from the Gene Expression Omnibus database, which contain 94 human Ewing’s sarcoma samples, including 65 from those who experienced a relapse and 29 from those with no evidence of disease. The differen tially expressed genes (DEGs) were identified using LIMMA package R. Subsequently, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed for DEGs using Database for Annotation, Visualization and Integrated Analysis. The protein–protein interaction network was constructed using Cytoscape software, and module analysis was performed using Molecular Complex Detection. Results A total of 206 upregulated DEGs and 141 downregulated DEGs were identified. Upregulated DEGs were primarily enriched in DNA replication, nucleoplasm and protein kinase binding for biological processes, cellular component and molecular functions, respectively. Downregulated DEGs were predominantly involved in receptor clustering, membrane raft, and ligand-dependent nuclear receptor binding. The protein–protein interaction network of DEGs consisted of 150 nodes and 304 interactions. Thirteen hub genes were identified, and biological analysis revealed that these genes were primarily enriched in cell division, cell cycle, and mitosis. Furthermore, based on closeness centrality, betweenness centrality, and degree centrality, the three most significant genes were identified as GAPDH, AURKA, and EHMT2. Furthermore, the significant network module was composed of nine genes. These genes were primarily enriched in mitotic nuclear division, mitotic chromosome condensation, and nucleoplasm. Conclusion These hub genes, especially GAPDH, AURKA, and EHMT2, may be closely associated with the progression of Ewing’s sarcoma chemotherapy resistance, and further experiments are needed for confirmation.
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Affiliation(s)
- Hongyi Liao
- Department of Orthopedic Surgery, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Xianbiao Xie
- Department of Orthopedic Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China,
| | - Yuanyuan Xu
- Department of Pediatrics, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Gang Huang
- Department of Orthopedic Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China,
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16
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Santacatterina F, Torresano L, Núñez-Salgado A, Esparza-Molto PB, Olive M, Gallardo E, García-Arumi E, Blazquez A, González-Quintana A, Martín MA, Cuezva JM. Different mitochondrial genetic defects exhibit the same protein signature of metabolism in skeletal muscle of PEO and MELAS patients: A role for oxidative stress. Free Radic Biol Med 2018; 126:235-248. [PMID: 30138712 DOI: 10.1016/j.freeradbiomed.2018.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/15/2018] [Accepted: 08/17/2018] [Indexed: 12/13/2022]
Abstract
A major challenge in mitochondrial diseases (MDs) is the identification of biomarkers that could inform of the mechanisms involved in the phenotypic expression of genetic defects. Herein, we have investigated the protein signature of metabolism and of the antioxidant response in muscle biopsies of clinically and genetically diagnosed patients with Progressive External Ophthalmoplegia due to single large-scale (PEO-sD) or multiple (PEO-mD) deletions of mtDNA and Mitochondrial Encephalopathy Lactic Acidosis and Stroke-like episode (MELAS) syndrome, and healthy donors. A high-throughput immunoassay technique that quantitates the expression of relevant proteins of glycolysis, glycogenolysis, pentose phosphate pathway, oxidative phosphorylation, pyruvate and fatty acid oxidation, tricarboxylic acid cycle and the antioxidant response in two large independent and retrospectively collected cohorts of PEO-sD, PEO-mD and MELAS patients revealed that despite the heterogeneity of the genetic alterations, the three MDs showed the same metabolic signatures in both cohorts of patients, which were highly divergent from those of healthy individuals. Linear Discriminant Analysis and Support Vector Machine classifier provided a minimum of four biomarkers to discriminate healthy from pathological samples. Regardless of the induction of a large number of enzymes involved in ameliorating oxidative stress, the down-regulation of mitochondrial superoxide dismutase (SOD2) and catalase expression favored the accumulation of oxidative damage in patients' proteins. Down-regulation of SOD2 and catalase expression in MD patients is not due to relevant changes in the availability of their mRNAs, suggesting that oxidative stress regulates the expression of the two enzymes post-transcriptionally. We suggest that SOD2 and catalase could provide specific targets to improve the detoxification of reactive oxygen species that affects muscle proteins in these patients.
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Affiliation(s)
- Fulvio Santacatterina
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Hospital, 12 de Octubre (i+12), Madrid, Spain
| | - Laura Torresano
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Hospital, 12 de Octubre (i+12), Madrid, Spain
| | - Alfonso Núñez-Salgado
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Spain
| | - Pau B Esparza-Molto
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Hospital, 12 de Octubre (i+12), Madrid, Spain
| | - Montse Olive
- Servicio de Anatomía Patológica, Unidad Patología Neuromuscular, IDIBELL-Hospital Universitario de Bellvitge, Spain
| | - Eduard Gallardo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Elena García-Arumi
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Laboratorio de Patología Mitocondrial y Neuromuscular, Área de Genética Clínica y Molecular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alberto Blazquez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Hospital, 12 de Octubre (i+12), Madrid, Spain; Laboratorio de Enfermedades Mitocondriales y Neuromusculares, Hospital Universitario, 12 de Octubre, Madrid, Spain
| | - Adrián González-Quintana
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Hospital, 12 de Octubre (i+12), Madrid, Spain; Laboratorio de Enfermedades Mitocondriales y Neuromusculares, Hospital Universitario, 12 de Octubre, Madrid, Spain
| | - Miguel A Martín
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Hospital, 12 de Octubre (i+12), Madrid, Spain; Laboratorio de Enfermedades Mitocondriales y Neuromusculares, Hospital Universitario, 12 de Octubre, Madrid, Spain
| | - José M Cuezva
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Hospital, 12 de Octubre (i+12), Madrid, Spain.
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17
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Kuang Z, Huang R, Yang Z, Lv Z, Chen X, Xu F, Yi YH, Wu J, Huang RP. Quantitative screening of serum protein biomarkers by reverse phase protein arrays. Oncotarget 2018; 9:32624-32641. [PMID: 30220970 PMCID: PMC6135697 DOI: 10.18632/oncotarget.25976] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/19/2018] [Indexed: 12/28/2022] Open
Abstract
Screening biomarkers in serum samples for different diseases has always been of great interest because it presents an early, reliable, and, most importantly, noninvasive means of diagnosis and prognosis. Reverse phase protein arrays (RPPAs) are a high-throughput platform that can measure single or limited sets of proteins from thousands of patients' samples in parallel. They have been widely used for detection of signaling molecules involved in diseases, especially cancers, and related regulation pathways in cell lysates. However, this approach has been difficult to adapt to serum samples. Previously, we developed a sensitive method called the enhanced protein array to quantitatively measure serum protein levels from large numbers of patient samples. Here, we further refine the technology on several fronts: 1. simplifying the experimental procedure; 2. optimizing multiple parameters to make the assay more robust, including the support matrix, signal reporting method, background control, and antibody validation; and 3. establishing a method for more accurate quantification. Using this technology, we quantitatively measured the expression levels of 10 proteins: alpha-fetoprotein (AFP), beta 2 microglobulin (B2M), Carcinoma Antigen 15-3(CA15-3), Carcinoembryonic antigen (CEA), golgi protein 73 (GP73), Growth differentiation factor 15 (GDF15), Human Epididymis Protein 4 (HE4), Insulin Like Growth Factor Binding Protein 2 (IGFBP2), osteopontin (OPN) and Beta-type platelet-derived growth factor receptor (PDGFRB) from serum samples of 132 hepatocellular carcinoma (HCC) patients and 78 healthy volunteers. We found that 6 protein expression levels are significantly increased in HCC patients. Statistical and bioinformatical analysis has revealed decent accuracy rates of individual proteins, ranging from 0.617 (B2M) to 0.908 (AFP) as diagnostic biomarkers to distinguish HCC from healthy controls. The combination of these 6 proteins as a specific HCC signature yielded a higher accuracy of 0.923 using linear discriminant analysis (LDA), logistic regression (LR), random forest (RF) and support vector machine (SVM) predictive model analyses. Our work reveals promise for using reverse phase protein arrays for biomarker discovery and validation in serum samples.
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Affiliation(s)
- Zhizhou Kuang
- RayBiotech Inc, Guangzhou, China.,RayBiotech Inc, Parkway Lane, Norcross, GA, USA
| | - Ruochun Huang
- RayBiotech Inc, Guangzhou, China.,RayBiotech Inc, Parkway Lane, Norcross, GA, USA
| | - Zhimin Yang
- Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China.,Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | | | - Xinyan Chen
- Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China.,Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Fuping Xu
- Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China.,Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Yu-Hua Yi
- RayBiotech Inc, Guangzhou, China.,South China Biochip Research Center, Guangzhou, China
| | - Jian Wu
- The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Ruo-Pan Huang
- RayBiotech Inc, Guangzhou, China.,RayBiotech Inc, Parkway Lane, Norcross, GA, USA.,South China Biochip Research Center, Guangzhou, China
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18
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Tong L, Liu J, Yan W, Cao W, Shen S, Li K, Li L, Niu G. RDM1 plays an oncogenic role in human lung adenocarcinoma cells. Sci Rep 2018; 8:11525. [PMID: 30069034 PMCID: PMC6070564 DOI: 10.1038/s41598-018-30071-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/23/2018] [Indexed: 12/14/2022] Open
Abstract
RAD52 motif containing 1 (RDM1) is involved in DNA damage repair pathway and RDM1−/− cells increase sensitivity to cisplatin, a common chemotherapy drug. Lung cancer is the leading cause of cancer death worldwide. However, the role of RDM1 in lung cancer is unknown. Here, we find that the mRNA and protein expression levels of RDM1 are significantly increased in human lung tumors, especially in lung adenocarcinoma. The lung adenocarcinoma patients with higher mRNA expression of RDM1 show the worse clinical outcomes. Knockdown of RDM1 in lung adenocarcinoma cells reduces cell proliferation and promotes apoptosis, consistent with the role RDM1 in the overexpression experiments. Xenograft mouse model shows stable knockdown of RDM1 significantly inhibits lung adenocarcinoma tumor growth. These in vitro and in vivo results conclude that RDM1 plays an oncogenic role in human lung adenocarcinoma. Interestingly, P53/RAD51/RAD52 can be regulated by RDM1, and the negative regulation of P53 by RDM1 may be one of major mechanisms for RDM1 to accomplish its oncogenic functions in lung adenocarcinoma. Therefore, RDM1 may be a new target for the treatment of lung adenocarcinoma.
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Affiliation(s)
- Lu Tong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Jian Liu
- Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Prk, NC, 27709, USA
| | - Wangjun Yan
- Department of Musculoskeletal Tumor, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wenjiao Cao
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, The China Welfare Institute, Shanghai, China
| | - Shihui Shen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Kun Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Lei Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Guoping Niu
- The Affiliated XuZhou Hospital of Medical College of Southeast University, Xuzhou, People's Republic of China.
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19
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Ranjitha Dhanasekaran A, Gardiner KJ. RPPAware: A software suite to preprocess, analyze and visualize reverse phase protein array data. J Bioinform Comput Biol 2018; 16:1850001. [PMID: 29478376 DOI: 10.1142/s0219720018500014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
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. The ease of use and efficiency of RPPAware can accelerate data analysis to facilitate biological discovery. RPPAware 1.0 is freely available under GNU General Public License from the project website at http://downsyndrome.ucdenver.edu/iddrc/rppaware/home.htm along with a full documentation of the tool.
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Affiliation(s)
- A Ranjitha Dhanasekaran
- * Rocky Mountain Alzheimer's Disease Center, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado 80045, USA
- † Department of Neurology, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado 80045, USA
- ‡ Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Katheleen J Gardiner
- ‡ Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado 80045, USA
- § Department of Pediatrics, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado 80045, USA
- ¶ Human Medical Genetics and Genomics and Neuroscience Programs, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado 80045, USA
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20
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Barbhuiya MA, Kashyap MK, Puttamallesh VN, Kumar RV, Wu X, Pandey A, Gowda H. Identification of spleen tyrosine kinase as a potential therapeutic target for esophageal squamous cell carcinoma using reverse phase protein arrays. Oncotarget 2018; 9:18422-18434. [PMID: 29719615 PMCID: PMC5915082 DOI: 10.18632/oncotarget.24853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/06/2018] [Indexed: 02/07/2023] Open
Abstract
The vast majority of esophageal cancers in China, India and Iran are esophageal squamous cell carcinomas (ESCC). A timely diagnosis provides surgical removal as the main therapeutic option for patients with ESCC. Currently, there are no targeted therapies available for ESCC. We carried out reverse phase protein array-based protein expression profiling of seven ESCC-derivedcell lines and a non-neoplastic esophageal epithelial cell line (Het-1A) to identify differentially expressed proteins in ESCC. SYK non-receptortyrosine kinase was overexpressed in six out of seven ESCC cell lines that were used in the study. We evaluated the role of SYK in ESCC using the pharmacological inhibitor entospletinib (GS-9973) and siRNA-based knock down studies. Entospletinib is a selective inhibitor of SYK, which is currently being evaluated in phase II clinical trials for hematological malignancies. Using in vivo subcutaneous tumor xenografts in mice, we demonstrate that treatment with entospletinib significantly inhibits tumor growth. Further clinical studies are needed to prove the efficacy of entospletinib as a targeted therapeutic agent for treating ESCC.
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Affiliation(s)
- Mustafa A. Barbhuiya
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Centre, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Manoj K. Kashyap
- School of Life and Allied Health Sciences, Glocal University, Saharanpur, India
| | - Vinuth N. Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Rekha Vijay Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Xinyan Wu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Centre, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
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21
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Barbhuiya MA, Kashyap MK, Puttamallesh VN, Kumar RV, Wu X, Pandey A, Gowda H. Identification of spleen tyrosine kinase as a potential therapeutic target for esophageal squamous cell carcinoma using reverse phase protein arrays. Oncotarget 2018. [PMID: 29719615 DOI: 10.18632/oncotarget.24853,] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The vast majority of esophageal cancers in China, India and Iran are esophageal squamous cell carcinomas (ESCC). A timely diagnosis provides surgical removal as the main therapeutic option for patients with ESCC. Currently, there are no targeted therapies available for ESCC. We carried out reverse phase protein array-based protein expression profiling of seven ESCC-derivedcell lines and a non-neoplastic esophageal epithelial cell line (Het-1A) to identify differentially expressed proteins in ESCC. SYK non-receptortyrosine kinase was overexpressed in six out of seven ESCC cell lines that were used in the study. We evaluated the role of SYK in ESCC using the pharmacological inhibitor entospletinib (GS-9973) and siRNA-based knock down studies. Entospletinib is a selective inhibitor of SYK, which is currently being evaluated in phase II clinical trials for hematological malignancies. Using in vivo subcutaneous tumor xenografts in mice, we demonstrate that treatment with entospletinib significantly inhibits tumor growth. Further clinical studies are needed to prove the efficacy of entospletinib as a targeted therapeutic agent for treating ESCC.
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Affiliation(s)
- Mustafa A Barbhuiya
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Sidney Kimmel Comprehensive Cancer Centre, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Manoj K Kashyap
- School of Life and Allied Health Sciences, Glocal University, Saharanpur, India
| | - Vinuth N Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Rekha Vijay Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Xinyan Wu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Sidney Kimmel Comprehensive Cancer Centre, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Institute of Bioinformatics, International Technology Park, Bangalore, India.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
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22
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Ren Y, Zhao S, Jiang D, Feng X, Zhang Y, Wei Z, Wang Z, Zhang W, Zhou QF, Li Y, Hou H, Xu Y, Zhou F. Proteomic biomarkers for lung cancer progression. Biomark Med 2018; 12:205-215. [DOI: 10.2217/bmm-2018-0015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: Lung adenocarcinoma (LUAD) and lung squamous-cell carcinoma (LUSC) are two major subtypes of lung cancer and constitute about 70% of all the lung cancer cases. The patient's lifespan and living quality will be significantly improved if they are diagnosed at an early stage and adequately treated. Methods & results: This study comprehensively screened the proteomic dataset of both LUAD and LUSC, and proposed classification models for the progression stages of LUAD and LUSC with accuracies 86.51 and 89.47%, respectively. Discussion & conclusion: A comparative analysis was also carried out on related transcriptomic datasets, which indicates that the proposed biomarkers provide discerning power for accurate stage prediction, and will be improved when larger-scale proteomic quantitative technologies become available.
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Affiliation(s)
- Yanjiao Ren
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Shishun Zhao
- Center for Applied Statistical Research, College of Mathematics, Jilin University, Changchun, Jilin 130012, PR China
| | - Dandan Jiang
- Center for Applied Statistical Research, College of Mathematics, Jilin University, Changchun, Jilin 130012, PR China
| | - Xin Feng
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Yexian Zhang
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Zhipeng Wei
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Zhongyu Wang
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Wenniu Zhang
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Qing F Zhou
- School of Electrical Engineering & Intelligentization, Dongguan University of Technology, Dongguan 523000, PR China
| | - Yong Li
- Department of Electronic Engineering, Tsinghua University, Beijing 100084, PR China
| | - Hanxu Hou
- School of Electrical Engineering & Intelligentization, Dongguan University of Technology, Dongguan 523000, PR China
| | - Ying Xu
- Computational Systems Biology Lab, Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
- College of Computer Science & Technology, & College of Public Health, Jilin University, Changchun, Jilin 130012, PR China
| | - Fengfeng Zhou
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
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23
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Shin J, Song SY, Ahn HS, An BC, Choi YD, Yang EG, Na KJ, Lee ST, Park JI, Kim SY, Lee C, Lee SW. Integrative analysis for the discovery of lung cancer serological markers and validation by MRM-MS. PLoS One 2017; 12:e0183896. [PMID: 28837649 PMCID: PMC5570484 DOI: 10.1371/journal.pone.0183896] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 08/14/2017] [Indexed: 12/18/2022] Open
Abstract
Non-small-cell lung cancer (NSCLC) constitutes approximately 80% of all diagnosed lung cancers, and diagnostic markers detectable in the plasma/serum of NSCLC patients are greatly needed. In this study, we established a pipeline for the discovery of markers using 9 transcriptome datasets from publicly available databases and profiling of six lung cancer cell secretomes. Thirty-one out of 312 proteins that overlapped between two-fold differentially expressed genes and identified cell secretome proteins were detected in the pooled plasma of lung cancer patients. To quantify the candidates in the serum of NSCLC patients, multiple-reaction-monitoring mass spectrometry (MRM-MS) was performed for five candidate biomarkers. Finally, two potential biomarkers (BCHE and GPx3; AUC = 0.713 and 0.673, respectively) and one two-marker panel generated by logistic regression (BCHE/GPx3; AUC = 0.773) were identified. A validation test was performed by ELISA to evaluate the reproducibility of GPx3 and BCHE expression in an independent set of samples (BCHE and GPx3; AUC = 0.630 and 0.759, respectively, BCHE/GPx3 panel; AUC = 0.788). Collectively, these results demonstrate the feasibility of using our pipeline for marker discovery and our MRM-MS platform for verifying potential biomarkers of human diseases.
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Affiliation(s)
- Jihye Shin
- Center for Theragnosis, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul, Korea
| | - Sang-Yun Song
- Department of Thoracic and Cardiovascular Surgery, Chonnam National University Hwasun Hospital, Hwasun-gun, Jeollanam-do, Korea
| | - Hee-Sung Ahn
- Center for Theragnosis, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
- KIST School, Korea University of Science and Technology, Daejeon, Korea
| | - Byung Chull An
- Department of Anatomy, Chonnam National University Medical School, Hwasun-gun, Jeollanam-do, Korea
| | - Yoo-Duk Choi
- Department of Pathology, Chonnam National University Hospital, Dong-gu, Gwangju, Korea
| | - Eun Gyeong Yang
- Center for Theragnosis, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
| | - Kook-Joo Na
- Department of Thoracic and Cardiovascular Surgery, Chonnam National University Hwasun Hospital, Hwasun-gun, Jeollanam-do, Korea
| | - Seung-Taek Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul, Korea
| | - Jae-Il Park
- Animal Facility of Aging Science, Korea Basic Science Institute, Buk-gu, Gwangju, Korea
| | - Seon-Young Kim
- Personalized Genomic Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
- KIST School, Korea University of Science and Technology, Daejeon, Korea
- * E-mail: (SL); (CL)
| | - Seung-won Lee
- Department of Anatomy, Chonnam National University Medical School, Hwasun-gun, Jeollanam-do, Korea
- * E-mail: (SL); (CL)
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24
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Emdal KB, Dittmann A, Reddy RJ, Lescarbeau RS, Moores SL, Laquerre S, White FM. Characterization of In Vivo Resistance to Osimertinib and JNJ-61186372, an EGFR/Met Bispecific Antibody, Reveals Unique and Consensus Mechanisms of Resistance. Mol Cancer Ther 2017; 16:2572-2585. [PMID: 28830985 DOI: 10.1158/1535-7163.mct-17-0413] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/21/2017] [Accepted: 08/10/2017] [Indexed: 12/28/2022]
Abstract
Approximately 10% of non-small cell lung cancer (NSCLC) patients in the United States and 40% of NSCLC patients in Asia have activating epidermal growth factor receptor (EGFR) mutations and are eligible to receive targeted anti-EGFR therapy. Despite an extension of life expectancy associated with this treatment, resistance to EGFR tyrosine kinase inhibitors and anti-EGFR antibodies is almost inevitable. To identify additional signaling routes that can be cotargeted to overcome resistance, we quantified tumor-specific molecular changes that govern resistant cancer cell growth and survival. Mass spectrometry-based quantitative proteomics was used to profile in vivo signaling changes in 41 therapy-resistant tumors from four xenograft NSCLC models. We identified unique and tumor-specific tyrosine phosphorylation rewiring in tumors resistant to treatment with the irreversible third-generation EGFR-inhibitor, osimertinib, or the novel dual-targeting EGFR/Met antibody, JNJ-61186372. Tumor-specific increases in tyrosine-phosphorylated peptides from EGFR family members, Shc1 and Gab1 or Src family kinase (SFK) substrates were observed, underscoring a differential ability of tumors to uniquely escape EGFR inhibition. Although most resistant tumors within each treatment group displayed a marked inhibition of EGFR as well as SFK signaling, the combination of EGFR inhibition (osimertinib) and SFK inhibition (saracatinib or dasatinib) led to further decrease in cell growth in vitro This result suggests that residual SFK signaling mediates therapeutic resistance and that elimination of this signal through combination therapy may delay onset of resistance. Overall, analysis of individual resistant tumors captured unique in vivo signaling rewiring that would have been masked by analysis of in vitro cell population averages. Mol Cancer Ther; 16(11); 2572-85. ©2017 AACR.
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Affiliation(s)
- Kristina B Emdal
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Antje Dittmann
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Raven J Reddy
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Rebecca S Lescarbeau
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Sheri L Moores
- Oncology, Janssen Research and Development, LLC, Spring House, Pennsylvania
| | - Sylvie Laquerre
- Oncology, Janssen Research and Development, LLC, Spring House, Pennsylvania
| | - Forest M White
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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Pool M, de Boer HR, Hooge MNLD, van Vugt MA, de Vries EG. Harnessing Integrative Omics to Facilitate Molecular Imaging of the Human Epidermal Growth Factor Receptor Family for Precision Medicine. Theranostics 2017; 7:2111-2133. [PMID: 28638489 PMCID: PMC5479290 DOI: 10.7150/thno.17934] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 03/02/2017] [Indexed: 12/13/2022] Open
Abstract
Cancer is a growing problem worldwide. The cause of death in cancer patients is often due to treatment-resistant metastatic disease. Many molecularly targeted anticancer drugs have been developed against 'oncogenic driver' pathways. However, these treatments are usually only effective in properly selected patients. Resistance to molecularly targeted drugs through selective pressure on acquired mutations or molecular rewiring can hinder their effectiveness. This review summarizes how molecular imaging techniques can potentially facilitate the optimal implementation of targeted agents. Using the human epidermal growth factor receptor (HER) family as a model in (pre)clinical studies, we illustrate how molecular imaging may be employed to characterize whole body target expression as well as monitor drug effectiveness and the emergence of tumor resistance. We further discuss how an integrative omics discovery platform could guide the selection of 'effect sensors' - new molecular imaging targets - which are dynamic markers that indicate treatment effectiveness or resistance.
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Affiliation(s)
- Martin Pool
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - H. Rudolf de Boer
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marjolijn N. Lub-de Hooge
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marcel A.T.M. van Vugt
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Elisabeth G.E. de Vries
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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26
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Pan L, Aguilar HA, Wang L, Iliuk A, Tao WA. Three-Dimensionally Functionalized Reverse Phase Glycoprotein Array for Cancer Biomarker Discovery and Validation. J Am Chem Soc 2016; 138:15311-15314. [PMID: 27933927 DOI: 10.1021/jacs.6b10239] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Glycoproteins have vast structural diversity that plays an important role in many biological processes and have great potential as disease biomarkers. Here, we report a novel functionalized reverse phase protein array (RPPA), termed polymer-based reverse phase glycoprotein array (polyGPA), to capture and profile glycoproteomes specifically, and validate glycoproteins. Nitrocellulose membrane functionalized with globular hydroxyaminodendrimers was used to covalently capture preoxidized glycans on glycoproteins from complex protein samples such as biofluids. The captured glycoproteins were subsequently detected using the same validated antibodies as in RPPA. We demonstrated the outstanding specificity, sensitivity, and quantitative capabilities of polyGPA by capturing and detecting purified as well as endogenous α-1-acid glycoprotein (AGP) in human plasma. We further applied quantitative N-glycoproteomics and the strategy to validate a panel of glycoproteins identified as potential biomarkers for bladder cancer by analyzing urine glycoproteins from bladder cancer patients or matched healthy individuals.
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Affiliation(s)
| | | | | | - Anton Iliuk
- Tymora Analytical Operations , West Lafayette, Indiana 47906, United States
| | - W Andy Tao
- Tymora Analytical Operations , West Lafayette, Indiana 47906, United States.,Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907, United States
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27
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Aslam B, Basit M, Nisar MA, Khurshid M, Rasool MH. Proteomics: Technologies and Their Applications. J Chromatogr Sci 2016; 55:182-196. [PMID: 28087761 DOI: 10.1093/chromsci/bmw167] [Citation(s) in RCA: 470] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 07/25/2016] [Accepted: 09/08/2016] [Indexed: 12/12/2022]
Abstract
Proteomics involves the applications of technologies for the identification and quantification of overall proteins present content of a cell, tissue or an organism. It supplements the other "omics" technologies such as genomic and transcriptomics to expound the identity of proteins of an organism, and to cognize the structure and functions of a particular protein. Proteomics-based technologies are utilized in various capacities for different research settings such as detection of various diagnostic markers, candidates for vaccine production, understanding pathogenicity mechanisms, alteration of expression patterns in response to different signals and interpretation of functional protein pathways in different diseases. Proteomics is practically intricate because it includes the analysis and categorization of overall protein signatures of a genome. Mass spectrometry with LC-MS-MS and MALDI-TOF/TOF being widely used equipment is the central among current proteomics. However, utilization of proteomics facilities including the software for equipment, databases and the requirement of skilled personnel substantially increase the costs, therefore limit their wider use especially in the developing world. Furthermore, the proteome is highly dynamic because of complex regulatory systems that control the expression levels of proteins. This review efforts to describe the various proteomics approaches, the recent developments and their application in research and analysis.
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Affiliation(s)
- Bilal Aslam
- Department of Microbiology, Government College University, Faisalabad, Pakistan
| | - Madiha Basit
- Department of Microbiology, Government College University, Faisalabad, Pakistan
| | - Muhammad Atif Nisar
- Department of Microbiology, Government College University, Faisalabad, Pakistan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University, Faisalabad, Pakistan .,College of Allied Health Professionals, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan
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28
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Oh S, Kim HS. Emerging power of proteomics for delineation of intrinsic tumor subtypes and resistance mechanisms to anti-cancer therapies. Expert Rev Proteomics 2016; 13:929-939. [PMID: 27599289 DOI: 10.1080/14789450.2016.1233063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Despite extreme genetic heterogeneity, tumors often show similar alterations in the expression, stability, and activation of proteins important in oncogenic signaling pathways. Thus, classifying tumor samples according to shared proteomic features may help facilitate the identification of cancer subtypes predictive of therapeutic responses and prognostic for patient outcomes. Meanwhile, understanding mechanisms of intrinsic and acquired resistance to anti-cancer therapies at the protein level may prove crucial to devising reversal strategies. Areas covered: Herein, we review recent advances in quantitative proteomic technology and their applications in studies to identify intrinsic tumor subtypes of various tumors, to illuminate mechanistic aspects of pharmacological and oncogenic adaptations, and to highlight interaction targets for anti-cancer compounds and cancer-addicted proteins. Expert commentary: Quantitative proteomic technologies are being successfully employed to classify tumor samples into distinct intrinsic subtypes, to improve existing DNA/RNA based classification methods, and to evaluate the activation status of key signaling pathways.
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Affiliation(s)
- Sejin Oh
- a Brain Korea 21 Project for Medical Science, Severance Biomedical Science Institute , Yonsei University College of Medicine , Seoul , Korea
| | - Hyun Seok Kim
- a Brain Korea 21 Project for Medical Science, Severance Biomedical Science Institute , Yonsei University College of Medicine , Seoul , Korea
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29
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Marrero A, Lawrence S, Wilsker D, Voth AR, Kinders RJ. 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. Semin Oncol 2016; 43:453-63. [PMID: 27663477 PMCID: PMC5065024 DOI: 10.1053/j.seminoncol.2016.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Multiplex pharmacodynamic (PD) assays have the potential to increase sensitivity of biomarker-based reporting for new targeted agents, as well as revealing significantly more information about target and pathway activation than single-biomarker PD assays. Stringent methodology is required to ensure reliable and reproducible results. Common to all PD assays is the importance of reagent validation, assay and instrument calibration, and the determination of suitable response calibrators; however, multiplex assays, particularly those performed on paraffin specimens from tissue blocks, bring format-specific challenges adding a layer of complexity to assay development. We discuss existing multiplex approaches and the development of a multiplex immunofluorescence assay measuring DNA damage and DNA repair enzymes in response to anti-cancer therapeutics and describe how our novel method addresses known issues.
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Affiliation(s)
- Allison Marrero
- Pharmacodynamics Assay Development and Implementation Section, Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Scott Lawrence
- Pharmacodynamics Assay Development and Implementation Section, Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Deborah Wilsker
- Pharmacodynamics Assay Development and Implementation Section, Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Andrea Regier Voth
- Pharmacodynamics Assay Development and Implementation Section, Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Robert J Kinders
- Pharmacodynamics Assay Development and Implementation Section, Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD.
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30
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Tan Z, Chaudhai R, Zhang S. Polypharmacology in Drug Development: A Minireview of Current Technologies. ChemMedChem 2016; 11:1211-8. [PMID: 27154144 DOI: 10.1002/cmdc.201600067] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/21/2016] [Indexed: 01/09/2023]
Abstract
Polypharmacology, the process in which a single drug is able to bind to multiple targets specifically and simultaneously, is an emerging paradigm in drug development. The potency of a given drug can be increased through the engagement of multiple targets involved in a certain disease. Polypharmacology may also help identify novel applications of existing drugs through drug repositioning. However, many problems and challenges remain in this field. Rather than covering all aspects of polypharmacology, this Minireview is focused primarily on recently reported techniques, from bioinformatics technologies to cheminformatics approaches as well as text-mining-based methods, all of which have made significant contributions to the research of polypharmacology.
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Affiliation(s)
- Zhi Tan
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Rajan Chaudhai
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Shuxing Zhang
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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Jiang LP, Zhu ZT, He CY. Expression of miRNA-26b in the diagnosis and prognosis of patients with non-small-cell lung cancer. Future Oncol 2016; 12:1105-15. [PMID: 27033050 DOI: 10.2217/fon.16.21] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE To investigate the correlation between miR-26b and non-small-cell lung cancer (NSCLC). MATERIALS & METHODS NSCLC tissues and normal lung tissues that were more than 7 cm adjacent from tumor were collected from 154 NSCLC patients. Additionally, 63 normal specimens from benign lung disease were selected as the control group. Real-time fluorescent quantitative PCR was used to detect miR-26b expression in tissues. RESULT miR-26b expression in NSCLC tissues was significantly lower than in other two types of tissues. Receiver operating characteristic curve analysis showed that the area under the curve was 0.856 with sensitivity and specificity of 79.9 and 79.4%, respectively. miR-26b expression was a risk factor for poor prognosis of NSCLC. CONCLUSION The expression of miR-26b is downregulated in NSCLC tissues, and it might be useful in the diagnosis and prognosis of NSCLC patients.
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Affiliation(s)
- Li-Peng Jiang
- Department of Radiation Oncology, First Affiliated Hospital of Liaoning Medical University, Jinzhou 121000, PR China
| | - Zhi-Tu Zhu
- Department of Oncology, First Affiliated Hospital of Liaoning Medical University, Jinzhou 121000, PR China
| | - Chun-Yan He
- Department of Prosthodontics, Second Affiliated Hospital of Liaoning Medical University, Jinzhou 121000, PR China
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32
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Nishizuka SS, Mills GB. New era of integrated cancer biomarker discovery using reverse-phase protein arrays. Drug Metab Pharmacokinet 2016; 31:35-45. [DOI: 10.1016/j.dmpk.2015.11.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/26/2015] [Accepted: 11/29/2015] [Indexed: 12/11/2022]
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Kaddi CD, Wang MD. Models for Predicting Stage in Head and Neck Squamous Cell Carcinoma Using Proteomic and Transcriptomic Data. IEEE J Biomed Health Inform 2015; 21:246-253. [PMID: 26462248 DOI: 10.1109/jbhi.2015.2489158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Late diagnosis is one of the reasons that head and neck squamous cell carcinoma (HNSCC) patients experience relative five-year survival rates ranging from 40%-66%. The molecular-level differences between early and advanced stage HNSCC may provide insight into therapeutic targets and strategies. Previous bioinformatics studies have shown mixed or limited results in identifying gene and protein markers and in developing models for discriminating between early and advanced stage HNSCC. Thus, we have investigated models for HNSCC stage prediction using RNAseq and reverse phase protein array data from The Cancer Genome Atlas and The Cancer Proteome Atlas. We systematically assessed individual and ensemble binary classifiers, using filter and wrapper feature selection methods, to develop several well-performing models. In particular, integrated models harnessing both data types consistently resulted in better performance. This study identifies informative protein and gene feature sets which may increase understanding of HNSCC progression.
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Araujo TDO, Costa LT, Fernandes J, Aucélio RQ, de Campos RC. Biomarkers to assess the efficiency of treatment with platinum-based drugs: what can metallomics add? Metallomics 2014; 6:2176-88. [PMID: 25387565 DOI: 10.1039/c4mt00192c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Since the approval of cisplatin as an antineoplastic drug, the medical and the scientific communities have been concerned about the side effects of platinum-based drugs, and this has been the dose-limiting factor that leads to reduced treatment efficiency. Another important issue is the intrinsic or acquired resistance of some patients to treatment. Identifying proper biomarkers is crucial in evaluating the efficiency of a treatment, assisting physicians in determining, at early stages, whether or not the patient presents resistance to the drug, minimizing severe side effects, and allowing them to redirect the established course of chemotherapy. A great effort is being made to identify biomarkers that can be used to predict the outcome of the treatment of cancer patients with platinum-based drugs. In this context, the metallomic approach has not yet been used to its full potential. Since the basis of these drugs is platinum, the monitoring of biomarkers containing this metal should be the natural approach to evaluate treatment progress. This review intends to show where the research in this field stands and points out some gaps that can be filled by metallomics.
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35
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Masuda M, Yamada T. Signaling pathway profiling by reverse-phase protein array for personalized cancer medicine. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:651-7. [PMID: 25448010 DOI: 10.1016/j.bbapap.2014.10.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 10/01/2014] [Accepted: 10/20/2014] [Indexed: 11/28/2022]
Abstract
Deregulation of intracellular signaling through accumulation of genetic alterations is a hallmark of cancer. In the past few decades, concerted and systematic efforts have been made to identify key genetic alterations and to develop therapeutic agents targeting active signaling molecules. However, the efficacy of molecular therapeutics often varies among individuals, and precise mapping of active molecules in individual patients is now considered an essential for therapy optimization. Reverse-phase protein array or microarray (RPPA or RPPM) is an emerging antibody-based highly quantitative proteomic technology, especially suitable for profiling of expression and modification of signaling proteins in low abundance. Because the supply of clinical materials is often limited, RPPA technology is highly advantageous for clinical proteomics in view of its high sensitivity as well as accurate quantification. RPPA has now begun to be incorporated into various clinical trials employing molecular-targeted therapeutics. In this article we review and discuss the application of RPPA technology in the fields of basic, preclinical, and clinical research. The RPPA Global Workshop was recently launched to accelerate the exchange of rapidly expanding knowledge of this fascinating technology among academic laboratories and industries worldwide. This article is part of a Special Issue entitled: Medical Proteomics.
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Affiliation(s)
- Mari Masuda
- Division of Chemotherapy and Clinical Research, Translational Research Group, National Cancer Center Research Institute, Tokyo, Japan
| | - Tesshi Yamada
- Division of Chemotherapy and Clinical Research, Translational Research Group, National Cancer Center Research Institute, Tokyo, Japan.
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RPPanalyzer toolbox: an improved R package for analysis of reverse phase protein array data. Biotechniques 2014; 57:125-35. [PMID: 25209047 DOI: 10.2144/000114205] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 07/20/2014] [Indexed: 11/23/2022] Open
Abstract
Analysis of large-scale proteomic data sets requires specialized software tools, tailored toward the requirements of individual approaches. Here we introduce an extension of an open-source software solution for analyzing reverse phase protein array (RPPA) data. The R package RPPanalyzer was designed for data preprocessing followed by basic statistical analyses and proteomic data visualization. In this update, we merged relevant data preprocessing steps into a single user-friendly function and included a new method for background noise correction as well as new methods for noise estimation and averaging of replicates to transform data in such a way that they can be used as input for a new time course plotting function. We demonstrate the robustness of our enhanced RPPanalyzer platform by analyzing longitudinal RPPA data of MET receptor signaling upon stimulation with different hepatocyte growth factor concentrations.
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37
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Newman RH, Zhang J, Zhu H. Toward a systems-level view of dynamic phosphorylation networks. Front Genet 2014; 5:263. [PMID: 25177341 PMCID: PMC4133750 DOI: 10.3389/fgene.2014.00263] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/16/2014] [Indexed: 11/13/2022] Open
Abstract
To better understand how cells sense and respond to their environment, it is important to understand the organization and regulation of the phosphorylation networks that underlie most cellular signal transduction pathways. These networks, which are composed of protein kinases, protein phosphatases and their respective cellular targets, are highly dynamic. Importantly, to achieve signaling specificity, phosphorylation networks must be regulated at several levels, including at the level of protein expression, substrate recognition, and spatiotemporal modulation of enzymatic activity. Here, we briefly summarize some of the traditional methods used to study the phosphorylation status of cellular proteins before focusing our attention on several recent technological advances, such as protein microarrays, quantitative mass spectrometry, and genetically-targetable fluorescent biosensors, that are offering new insights into the organization and regulation of cellular phosphorylation networks. Together, these approaches promise to lead to a systems-level view of dynamic phosphorylation networks.
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Affiliation(s)
- Robert H Newman
- Department of Biology, North Carolina Agricultural and Technical State University Greensboro, NC, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine Baltimore, MD, USA ; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Oncology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Chemical and Biomolecular Engineering, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine Baltimore, MD, USA ; High-Throughput Biology Center, Institute for Basic Biomedical Sciences, Johns Hopkins University Baltimore, MD, USA
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Akbani R, Becker KF, Carragher N, Goldstein T, de Koning L, Korf U, Liotta L, Mills GB, Nishizuka SS, Pawlak M, Petricoin EF, Pollard HB, Serrels B, Zhu J. Realizing the promise of reverse phase protein arrays for clinical, translational, and basic research: a workshop report: the RPPA (Reverse Phase Protein Array) society. Mol Cell Proteomics 2014; 13:1625-43. [PMID: 24777629 DOI: 10.1074/mcp.o113.034918] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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.
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Affiliation(s)
- Rehan Akbani
- From the *University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Neil Carragher
- §Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Ted Goldstein
- ¶Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California
| | | | - Ulrike Korf
- **German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Gordon B Mills
- From the *University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Michael Pawlak
- §§§The Natural and Medical Sciences Institute, Reutlingen, Germany
| | | | - Harvey B Pollard
- ¶¶Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Bryan Serrels
- §Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Jingchun Zhu
- ¶Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California
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