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Lin H, Guo X, Liu J, Tang Y, Chen L, Chen H, Zhao Y, Wang L, Li H, Yu J, Yao P. Ethanol-Induced Hepatic Ferroptosis Is Mediated by PERK-Dependent MAMs Formation: Preventive Role of Quercetin. Mol Nutr Food Res 2024; 68:e2300343. [PMID: 38501770 DOI: 10.1002/mnfr.202300343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 11/05/2023] [Indexed: 03/20/2024]
Abstract
SCOPE Iron deposition is frequently observed in alcoholic liver disease (ALD), which indicates a potential role of ferroptosis in its development. This study aims to explore the effects of quercetin on ferroptosis in ALD and elucidates the underlying mechanism involving the formation of mitochondria-associated endoplasmic reticulum membranes (MAMs) mediated by protein kinase RNA-like endoplasmic reticulum kinase (PERK). METHODS AND RESULTS C57BL/6J mice are fed either a regular or an ethanol-containing liquid diet (with 28% energy form ethanol) with or without quercetin supplementation (100 mg kg-1 BW) for 12 weeks. Ethanol feeding or treatment induced ferroptosis in mice and AML12 cells, which is associated with increased MAMs formation and PERK expression within MAMs. Quercetin attenuates these changes and protects against ethanol-induced liver injury. The antiferroptotic effect of quercetin is abolished by ferroptosis inducers, but mimicked by ferroptosis inhibitors and PERK knockdown. The study demonstrates that PERK structure, rather than its kinase activity (transfected with the K618A site mutation that inhibits kinase activity-ΔK plasmid or protein C terminal knockout-ΔC plasmid of PERK), mediates the enhanced MAMs formation and ferroptosis during the ethanol exposure. CONCLUSION Quercetin ameliorates ethanol-induced liver injury by inhibiting ferroptosis via modulating PERK-dependent MAMs formation.
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Affiliation(s)
- Hongkun Lin
- Department of Nutrition and Food Hygiene, School of Public Health,Tongji Medical College, Huazhong University of Science & Technology, 13 Hangkong Road, Wuhan, 430030, P. R. China
- Department of Nutrition, School of Public Health, Wuhan University, Wuhan, 430071, P. R. China
| | - Xiaoping Guo
- Department of Nutrition and Food Hygiene, School of Public Health,Tongji Medical College, Huazhong University of Science & Technology, 13 Hangkong Road, Wuhan, 430030, P. R. China
| | - Jingjing Liu
- Henan Provincial Center for Disease Control and Prevention, Zhengzhou, 450016, P. R. China
| | - Yuhan Tang
- Department of Nutrition and Food Hygiene, School of Public Health,Tongji Medical College, Huazhong University of Science & Technology, 13 Hangkong Road, Wuhan, 430030, P. R. China
| | - Li Chen
- Department of Nutrition and Food Hygiene, School of Public Health,Tongji Medical College, Huazhong University of Science & Technology, 13 Hangkong Road, Wuhan, 430030, P. R. China
| | - Huimin Chen
- Department of Nutrition and Food Hygiene, School of Public Health,Tongji Medical College, Huazhong University of Science & Technology, 13 Hangkong Road, Wuhan, 430030, P. R. China
| | - Ying Zhao
- Department of Nutrition and Food Hygiene, School of Public Health,Tongji Medical College, Huazhong University of Science & Technology, 13 Hangkong Road, Wuhan, 430030, P. R. China
| | - Lili Wang
- Department of Nutrition and Food Hygiene, School of Public Health,Tongji Medical College, Huazhong University of Science & Technology, 13 Hangkong Road, Wuhan, 430030, P. R. China
| | - Hongxia Li
- Department of Nutrition and Food Hygiene, School of Public Health,Tongji Medical College, Huazhong University of Science & Technology, 13 Hangkong Road, Wuhan, 430030, P. R. China
| | - Jiasheng Yu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
| | - Ping Yao
- Department of Nutrition and Food Hygiene, School of Public Health,Tongji Medical College, Huazhong University of Science & Technology, 13 Hangkong Road, Wuhan, 430030, P. R. China
- Ministry of Education Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science & Technology, 13 Hangkong Road, Wuhan, 430030, P. R. China
- Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science & Technology, 13 Hangkong Road, Wuhan, 430030, P. R. China
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2
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Xia X, Jiang M, Lin C, Ke R. Visualization of Individual RNA Molecules by Proximity Ligation-Based Chromogenic In Situ Hybridization Assay. Methods Mol Biol 2024; 2822:143-156. [PMID: 38907917 DOI: 10.1007/978-1-0716-3918-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
RNA in situ hybridization reveals the abundance and location of gene expression in cells or tissues, providing a technical basis for the clinical diagnosis of diseases. In this chapter, we show a "V" shape probe-mediated single-molecule chromogenic in situ hybridization (vsmCISH) technique for bright-field visualization of individual RNA molecules. In our method, several pairs of target hybridization probes are hybridized to RNA molecules and each probe pair forms a "V" shape overhang. The overhang oligonucleotides then mediated the proximity ligation to form DNA circles, followed by rolling circle amplification for signal enhancement and enzyme-catalyzed chromogenic reaction-based readout. The colorimetric assay avoids problems such as photobleaching and autofluorescence of current fluorescent in situ hybridization-based single-molecule RNA detection techniques. Furthermore, the relatively straightforward protocol makes the method useful for biological research and clinical diagnosis applications.
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Affiliation(s)
- Xueqian Xia
- School of Medicine, Huaqiao University, Xiamen, Fujian, China
| | - Meng Jiang
- School of Medicine, Huaqiao University, Xiamen, Fujian, China
- College of Materials Science and Engineering, Huaqiao University, Xiamen, Fujian, China
| | - Chen Lin
- School of Medicine, Huaqiao University, Xiamen, Fujian, China
| | - Rongqin Ke
- School of Medicine, Huaqiao University, Xiamen, Fujian, China.
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Mansoor A, Kamran H, Akhter A, Seno R, Torlakovic EE, Roshan TM, Shabani-Rad MT, Elyamany G, Minoo P, Stewart D. Identification of Potential Therapeutic Targets for Plasmablastic Lymphoma Through Gene Expression Analysis: Insights into RAS and Wnt Signaling Pathways. Mod Pathol 2023; 36:100198. [PMID: 37105495 DOI: 10.1016/j.modpat.2023.100198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/20/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023]
Abstract
Plasmablastic lymphoma (PBL) is a rare and aggressive B-cell lymphoma with overlapping characteristics with diffuse large B-cell lymphoma (DLBCL) and multiple myeloma. Hyperactive Wnt signaling derails homeostasis and promotes oncogenesis and chemoresistance in DLBCL and multiple myeloma. Evidence suggests active cross-talk between the Wnt and RAS pathways impacting metastasis in solid cancers in which combined targeted therapies show effective results. Recent genomic studies in PBL demonstrated a high frequency of mutations linked with the RAS signaling pathway. However, the role of RAS and Wnt signaling pathway molecule expression in PBL remained unknown. We examined the expression of Wnt and RAS pathway-related genes in a well-curated cohort of PBL. Because activated B cells are considered immediate precursors of plasmablasts in B cell development, we compared this data with activated B-cell type DLBCL (ABC-DLBCL) patients, employing NanoString transcriptome analysis (770 genes). Hierarchical clustering revealed distinctive differential gene expression between PBL and ABC-DLBCL. Gene set enrichment analysis labeled the RAS signaling pathway as the most enriched (37 genes) in PBL, including upregulating critical genes, such as NRAS, RAF1, SHC1, and SOS1. Wnt pathway genes were also enriched (n = 22) by gene set enrichment analysis. Molecules linked with Wnt signaling activation, such as ligands or targets (FZD3, FZD7, c-MYC, WNT5A, WNT5B, and WNT10B), were elevated in PBL. Our data also showed that, unlike ABC-DLBCL, the deranged Wnt signaling activity in PBL was not linked with hyperactive nuclear factor κB and B-cell receptor signaling. In divergence, Wnt signaling inhibitors (CXXC4, SFRP2, and DKK1) also showed overexpression in PBL. The high expression of RAS signaling molecules reported may indicate linkage with gain-in-function RAS mutations. In addition, high expression of Wnt and RAS signaling molecules may pave pathways to explore benefiting from combined targeted therapies, as reported in solid cancer, to improve prognosis in PBL patients.
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Affiliation(s)
- Adnan Mansoor
- Department of Pathology & Laboratory Medicine, University of Calgary, and Alberta Precision Laboratories (APL), Calgary, Alberta, Canada.
| | - Hamza Kamran
- Department of Pathology & Laboratory Medicine, University of Calgary, and Alberta Precision Laboratories (APL), Calgary, Alberta, Canada
| | - Ariz Akhter
- Department of Pathology & Laboratory Medicine, University of Calgary, and Alberta Precision Laboratories (APL), Calgary, Alberta, Canada
| | - Rommel Seno
- Department of Pathology & Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Emina E Torlakovic
- Department of Pathology & Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tariq Mahmood Roshan
- Department of Pathology & Laboratory Medicine, University of Calgary, and Alberta Precision Laboratories (APL), Calgary, Alberta, Canada
| | - Meer-Taher Shabani-Rad
- Department of Pathology & Laboratory Medicine, University of Calgary, and Alberta Precision Laboratories (APL), Calgary, Alberta, Canada
| | - Ghaleb Elyamany
- Department of Pathology & Laboratory Medicine, University of Calgary, and Alberta Precision Laboratories (APL), Calgary, Alberta, Canada
| | - Parham Minoo
- Department of Pathology & Laboratory Medicine, University of Calgary, and Alberta Precision Laboratories (APL), Calgary, Alberta, Canada
| | - Douglas Stewart
- Department of Oncology, University of Calgary, Tom Baker Cancer Centre, Calgary, Alberta, Canada
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Ramos De Dios SM, Tiwari VK, McCune CD, Dhokale RA, Berkowitz DB. Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization. Chem Rev 2022; 122:13800-13880. [PMID: 35904776 DOI: 10.1021/acs.chemrev.2c00213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.
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Affiliation(s)
| | - Virendra K Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Christopher D McCune
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ranjeet A Dhokale
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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5
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Åberg M, Edén D, Siegbahn A. Activation of β1 integrins and caveolin-1 by TF/FVIIa promotes IGF-1R signaling and cell survival. Apoptosis 2021; 25:519-534. [PMID: 32458278 PMCID: PMC7347522 DOI: 10.1007/s10495-020-01611-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tissue factor/coagulation factor VIIa (TF/FVIIa) complex induces transactivation of the IGF-1 receptor (IGF-1R) in a number of different cell types. The mechanism is largely unknown. The transactivation leads to protection from apoptosis and nuclear translocation of the IGF-1R. The aim of this study was to clarify the signaling pathway between TF and IGF-1R after FVIIa treatment with PC3 and DU145 prostate or MDA-MB-231 breast cancer cells as model systems. Protein interactions, levels, and phosphorylations were assessed by proximity ligation assay or flow cytometry in intact cells and by western blot on cell lysates. The transactivation of the IGF-1R was found dependent on TF/FVIIa-induced activation of β1-integrins. A series of experiments led to the conclusion that the caveolae protein caveolin-1 prevented IGF-1R activation in resting cells via its scaffolding domain. TF/FVIIa/β1-integrins terminated this inhibition by activation of Src family kinases and subsequent phosphorylation of caveolin-1 on tyrosine 14. This phosphorylation was not seen after treatment with PAR1 or PAR2 agonists. Consequently, the protective effect of FVIIa against apoptosis induced by the death receptor agonist TRAIL and the de novo synthesis of cyclin D1 induced by nuclear IGF-1R accumulation were both significantly reduced by down-regulation of β1-integrins or overexpression of the caveolin-1 scaffolding domain. In conclusion, we present a plausible mechanism for the interplay between TF and IGF-1R involving FVIIa, β1-integrins, Src family proteins, and caveolin-1. Our results increase the knowledge of diseases associated with TF and IGF-1R overexpression in general but specifically of TF-mediated signaling with focus on cell survival.
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Affiliation(s)
- Mikael Åberg
- Department of Medical Sciences, Clinical Chemistry and Science for Life Laboratory, Uppsala University Hospital, Entr. 61 3rd floor, 751 85, Uppsala, Sweden.
| | - Desirée Edén
- Department of Medical Sciences, Clinical Chemistry and Science for Life Laboratory, Uppsala University Hospital, Entr. 61 3rd floor, 751 85, Uppsala, Sweden
| | - Agneta Siegbahn
- Department of Medical Sciences, Clinical Chemistry and Science for Life Laboratory, Uppsala University Hospital, Entr. 61 3rd floor, 751 85, Uppsala, Sweden
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6
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Lindskog C, Backman M, Zieba A, Asplund A, Uhlén M, Landegren U, Pontén F. Proximity Ligation Assay as a Tool for Antibody Validation in Human Tissues. J Histochem Cytochem 2020; 68:515-529. [PMID: 32602410 DOI: 10.1369/0022155420936384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Immunohistochemistry (IHC) is the accepted standard for spatial analysis of protein expression in tissues. IHC is widely used for cancer diagnostics and in basic research. The development of new antibodies to proteins with unknown expression patterns has created a demand for thorough validation. We have applied resources from the Human Protein Atlas project and the Antibody Portal at National Cancer Institute to generate protein expression data for 12 proteins across 39 cancer cell lines and 37 normal human tissue types. The outcome of IHC on consecutive sections from both cell and tissue microarrays using two independent antibodies for each protein was compared with in situ proximity ligation (isPLA), where binding by both antibodies is required to generate detection signals. Semi-quantitative scores from IHC and isPLA were compared with expression of the corresponding 12 transcripts across all cell lines and tissue types. Our results show a more consistent correlation between mRNA levels and isPLA as compared to IHC. The main benefits of isPLA include increased detection specificity and decreased unspecific staining compared to IHC. We conclude that implementing isPLA as a complement to IHC for analysis of protein expression and in antibody validation pipelines can lead to more accurate localization of proteins in tissue.
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Affiliation(s)
- Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Max Backman
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Agata Zieba
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Asplund
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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7
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Xie Y, Perrino BA. Quantitative in situ proximity ligation assays examining protein interactions and phosphorylation during smooth muscle contractions. Anal Biochem 2019; 577:1-13. [PMID: 30981700 DOI: 10.1016/j.ab.2019.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/21/2019] [Accepted: 04/10/2019] [Indexed: 12/26/2022]
Abstract
Antibody-based in situ proximity ligation assays (isPLA) have the potential to study protein phosphorylation and protein interactions with spatial resolution in intact tissues. However, the application of isPLA at the tissue level is limited by a lack of appropriate positive and negative controls and the difficulty in accounting for changes in tissue shape. Here we demonstrate a set of experimental and computational approaches using gastric fundus smooth muscles to improve the validity of quantitative isPLA. Appropriate positive and negative biological controls and PLA technical controls were selected to ensure experimental rigor. To account for changes in morphology between relaxed and contracted smooth muscles, target PLA spots were normalized to smooth muscle myosin light chain 20 PLA spots or the cellular cross-sectional areas. We describe the computational steps necessary to filter out false-positive improperly sized spots and set the thresholds for counting true positive PLA spots to quantify the PLA signals. We tested our approach by examining protein phosphorylation and protein interactions in smooth muscle myofilament Ca2+ sensitization pathways from resting and contracted gastric fundus smooth muscles. In conclusion, our tissue-level isPLA method enables unbiased quantitation of protein phosphorylation and protein-protein interactions in intact smooth muscle tissues, suggesting the potential for quantitative isPLA applications in other types of intact tissues.
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Affiliation(s)
- Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada Reno, School of Medicine, MS 0352, 1664 N Virginia St, Reno, NV, 89557, USA
| | - Brian A Perrino
- Department of Physiology and Cell Biology, University of Nevada Reno, School of Medicine, MS 0352, 1664 N Virginia St, Reno, NV, 89557, USA.
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Exploring Protein⁻Protein Interaction in the Study of Hormone-Dependent Cancers. Int J Mol Sci 2018; 19:ijms19103173. [PMID: 30326622 PMCID: PMC6213999 DOI: 10.3390/ijms19103173] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 12/20/2022] Open
Abstract
Estrogen receptors promote target gene transcription when they form a dimer, in which two identical (homodimer) or different (heterodimer) proteins are bound to each other. In hormone-dependent cancers, hormone receptor dimerization plays pivotal roles, not only in the pathogenesis or development of the tumors, but also in the development of therapeutic resistance. Protein–protein interactions (PPIs), including dimerization and complex formation, have been also well-known to be required for proteins to exert their functions. The methods which could detect PPIs are genetic engineering (i.e., resonance energy transfer) and/or antibody technology (i.e., co-immunoprecipitation) using cultured cells. In addition, visualization of the target proteins in tissues can be performed using antigen–antibody reactions, as in immunohistochemistry. Furthermore, development of microscopic techniques (i.e., electron microscopy and confocal laser microscopy) has made it possible to visualize intracellular and/or intranuclear organelles. We have recently reported the visualization of estrogen receptor dimers in breast cancer tissues by using the in situ proximity ligation assay (PLA). PLA was developed along the lines of antibody technology development, and this assay has made it possible to visualize PPIs in archival tissue specimens. Localization of PPI in organelles has also become possible using super-resolution microscopes exceeding the resolution limit of conventional microscopes. Therefore, in this review, we summarize the methodologies used for studying PPIs in both cells and tissues, and review the recently reported studies on PPIs of hormones.
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Jedinak A, Loughlin KR, Moses MA. Approaches to the discovery of non-invasive urinary biomarkers of prostate cancer. Oncotarget 2018; 9:32534-32550. [PMID: 30197761 PMCID: PMC6126692 DOI: 10.18632/oncotarget.25946] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/23/2018] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer (PCa) continues to be one of the most common cancers in men worldwide. Prostate specific antigen (PSA) measured in blood has been used for decades as an aid for physicians to detect the presence of prostate cancer. However, the PSA test has limited sensitivity and specificity, leading to unnecessary biopsies, overdiagnosis and overtreatment of patients. For these reasons, there is an urgent need for more accurate PCa biomarkers that can detect PCa with high sensitivity and specificity. Urine is a unique source of potential protein biomarkers that can be measured in a non-invasive way. This review comprehensively summarizes state of the art approaches used in the discovery and validation of urinary biomarkers for PCa. Numerous strategies are currently being used in the discovery of urinary biomarkers for prostate cancer including gel-based separation techniques, mass spectrometry, activity-based proteomic assays and software approaches. Antibody-based approaches remain preferred method for validation of candidate biomarkers with rapidly advancing multiplex immunoassays and MS-based targeted approaches. In the last decade, there has been a dramatic acceleration in the development of new techniques and approaches in the discovery of protein biomarkers for prostate cancer including computational, statistical and data mining methods. Many urinary-based protein biomarkers have been identified and have shown significant promise in initial studies. Examples of these potential biomarkers and the methods utilized in their discovery are also discussed in this review.
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Affiliation(s)
- Andrej Jedinak
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Kevin R Loughlin
- Department of Surgery, Harvard Medical School, Boston, MA, USA.,Department of Urology, Brigham and Women's Hospital, Boston, MA, USA
| | - Marsha A Moses
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
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10
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de Marco A. Nanomaterial bio-activation and macromolecules functionalization: The search for reliable protocols. Protein Expr Purif 2018; 147:49-54. [DOI: 10.1016/j.pep.2018.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 02/24/2018] [Indexed: 02/08/2023]
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11
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Brand S, Roy S, Schröder P, Rathmer B, Roos J, Kapoor S, Patil S, Pommerenke C, Maier T, Janning P, Eberth S, Steinhilber D, Schade D, Schneider G, Kumar K, Ziegler S, Waldmann H. Combined Proteomic and In Silico Target Identification Reveal a Role for 5-Lipoxygenase in Developmental Signaling Pathways. Cell Chem Biol 2018; 25:1095-1106.e23. [PMID: 30251630 DOI: 10.1016/j.chembiol.2018.05.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 02/26/2018] [Accepted: 05/22/2018] [Indexed: 12/21/2022]
Abstract
Identification and validation of the targets of bioactive small molecules identified in cell-based screening is challenging and often meets with failure, calling for the development of new methodology. We demonstrate that a combination of chemical proteomics with in silico target prediction employing the SPiDER method may provide efficient guidance for target candidate selection and prioritization for experimental in-depth evaluation. We identify 5-lipoxygenase (5-LO) as the target of the Wnt pathway inhibitor Lipoxygenin. Lipoxygenin is a non-redox 5-LO inhibitor, modulates the β-catenin-5-LO complex and induces reduction of both β-catenin and 5-LO levels in the nucleus. Lipoxygenin and the structurally unrelated 5-LO inhibitor CJ-13,610 promote cardiac differentiation of human induced pluripotent stem cells and inhibit Hedgehog, TGF-β, BMP, and Activin A signaling, suggesting an unexpected and yet unknown role of 5-LO in these developmental pathways.
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Affiliation(s)
- Silke Brand
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany; Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
| | - Sayantani Roy
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Peter Schröder
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany; Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
| | - Bernd Rathmer
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
| | - Jessica Roos
- Goethe Universität, Institut für Pharmazeutische Chemie, Max-von-Laue-Strasse 9, Frankfurt am Main 60438, Germany
| | - Shobhna Kapoor
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sumersing Patil
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Claudia Pommerenke
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, Braunschweig 38124, Germany
| | - Thorsten Maier
- Department for Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Theodor-Stern-Kai 7, Frankfurt 60590, Germany; Aarhus University, Department of Biomedicine, Bartholins Allé 6, Aarhus C 8000, Denmark
| | - Petra Janning
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sonja Eberth
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, Braunschweig 38124, Germany
| | - Dieter Steinhilber
- Goethe Universität, Institut für Pharmazeutische Chemie, Max-von-Laue-Strasse 9, Frankfurt am Main 60438, Germany
| | - Dennis Schade
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
| | - Gisbert Schneider
- ETH Zürich, Institut für Pharmazeutische Wissenschaften, Vladimir-Prelog-Weg 1-5/10, Zürich CH-8093, Switzerland
| | - Kamal Kumar
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Slava Ziegler
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Herbert Waldmann
- Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund 44227, Germany; Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, Dortmund 44227, Germany.
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12
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Homogeneous and digital proximity ligation assays for the detection of Clostridium difficile toxins A and B. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 10:2-8. [PMID: 27990343 PMCID: PMC5154635 DOI: 10.1016/j.bdq.2016.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/22/2016] [Accepted: 06/27/2016] [Indexed: 12/22/2022]
Abstract
Background The proximity ligation assay (PLA) detects proteins via their interaction with pairs of proximity probes, which are antibodies coupled to noncomplementary DNA oligonucleotides. The binding of both proximity probes to their epitopes on the target protein brings the oligonucleotides together, allowing them to be bridged by a third oligonucleotide with complementarity to the other two. This enables their ligation and the detection of the resulting amplicon by real-time quantitative PCR (qPCR), which acts as a surrogate marker for the protein of interest. Hence PLA has potential as a clinically relevant diagnostic tool for the detection of pathogens where nucleic acid based tests are inconclusive proof of infection. Methods We prepared monoclonal and polyclonal proximity probes targeting Clostridium difficile toxins A (TcdA) and B (TcdB) and used hydrolysis probe-based qPCR and digital PCR (dPCR) assays to detect antibody/antigen interactions. Results The performance of the PLA assays was antibody-dependent but both TcdA and TcdB assays were more sensitive than comparable ELISAs in either single- or dualplex formats. Both PLAs could be performed using single monoclonal antibodies coupled to different oligonucleotides. Finally, we used dPCR to demonstrate its potential for accurate and reliable quantification of TcdA. Conclusions PLA with either qPCR or dPCR readout have potential as new diagnostic applications for the detection of pathogens where nucleic acid based tests do not indicate viability or expression of toxins. Importantly, since it is not always necessary to use two different antibodies, the pool of potential antibodies useful for PLA diagnostic assays is usefully enhanced.
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13
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Spengler M, Adler M, Niemeyer CM. Highly sensitive ligand-binding assays in pre-clinical and clinical applications: immuno-PCR and other emerging techniques. Analyst 2016. [PMID: 26196036 DOI: 10.1039/c5an00822k] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Recombinant DNA technology and corresponding innovations in molecular biology, chemistry and medicine have led to novel therapeutic biomacromolecules as lead candidates in the pharmaceutical drug development pipelines. While monoclonal antibodies and other proteins provide therapeutic potential beyond the possibilities of small molecule drugs, the concomitant demand for supportive bioanalytical sample testing creates multiple novel challenges. For example, intact macromolecules can usually not be quantified by mass-spectrometry without enzymatic digestion and isotopically labeled internal standards are costly and/or difficult to prepare. Classical ELISA-type immunoassays, on the other hand, often lack the sensitivity required to obtain pharmacokinetics of low dosed drugs or pharmacodynamics of suitable biomarkers. Here we summarize emerging state-of-the-art ligand-binding assay technologies for pharmaceutical sample testing, which reveal enhanced analytical sensitivity over classical ELISA formats. We focus on immuno-PCR, which combines antibody specificity with the extremely sensitive detection of a tethered DNA marker by quantitative PCR, and alternative nucleic acid-based technologies as well as methods based on electrochemiluminescence or single-molecule counting. Using case studies, we discuss advantages and drawbacks of these methods for preclinical and clinical sample testing.
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Affiliation(s)
- Mark Spengler
- Chimera Biotec GmbH, Emil-Figge-Str. 76 A, D-44227 Dortmund, Germany.
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14
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Bagchi S, Fredriksson R, Wallén-Mackenzie Å. In Situ Proximity Ligation Assay (PLA). Methods Mol Biol 2016; 1318:149-59. [PMID: 26160573 DOI: 10.1007/978-1-4939-2742-5_15] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In situ proximity ligation assay (PLA) is a method to identify physical closeness of proteins, where a signal will only be produced if the two proteins are closer than 40 nm, in tissue section or cell cultures. Modifications of the PLA method can also be used to increase specificity or sensitivity of standard immunohistochemistry protocols.
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Affiliation(s)
- Sonchita Bagchi
- Department of Neuroscience, Uppsala biomedicinska centrum BMC, Uppsala University, Husarg. 3, 593, Uppsala, 751 24, Sweden
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15
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Zetterberg H, Morris HR, Hardy J, Blennow K. Update on fluid biomarkers for concussion. Concussion 2016; 1:CNC12. [PMID: 30202555 PMCID: PMC6094065 DOI: 10.2217/cnc-2015-0002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 01/14/2016] [Indexed: 12/14/2022] Open
Abstract
Concussions are difficult to diagnose and symptoms may not appear immediately. As an accurate initial diagnosis has profound implications for the clinical management, there is an unmet need for better diagnostic tools. Fluid biomarkers for CNS injury may represent such tools. These markers are often proteins, peptides or other molecules with selective or high expression in the brain, which can be measured in the cerebrospinal fluid or blood as they leak out or get secreted into the biofluid in response to the injury. Here, we review the literature on fluid markers of neuronal, axonal and astroglial injury and response mechanisms to diagnose CNS injury upon head impact and to determine when the injurious process has resolved.
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Affiliation(s)
- Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Institute of Neuroscience & Physiology, Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden.,Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK.,Clinical Neurochemistry Laboratory, Institute of Neuroscience & Physiology, Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden.,Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Huw R Morris
- Department of Clinical Neuroscience, UCL Institute of Neurology, Queen Square, London, UK.,Department of Clinical Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - John Hardy
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK.,Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Institute of Neuroscience & Physiology, Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Institute of Neuroscience & Physiology, Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden
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16
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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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17
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Leng Y, Sun K, Chen X, Li W. Suspension arrays based on nanoparticle-encoded microspheres for high-throughput multiplexed detection. Chem Soc Rev 2015; 44:5552-95. [PMID: 26021602 PMCID: PMC5223091 DOI: 10.1039/c4cs00382a] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Spectrometrically or optically encoded microsphere based suspension array technology (SAT) is applicable to the high-throughput, simultaneous detection of multiple analytes within a small, single sample volume. Thanks to the rapid development of nanotechnology, tremendous progress has been made in the multiplexed detecting capability, sensitivity, and photostability of suspension arrays. In this review, we first focus on the current stock of nanoparticle-based barcodes as well as the manufacturing technologies required for their production. We then move on to discuss all existing barcode-based bioanalysis patterns, including the various labels used in suspension arrays, label-free platforms, signal amplification methods, and fluorescence resonance energy transfer (FRET)-based platforms. We then introduce automatic platforms for suspension arrays that use superparamagnetic nanoparticle-based microspheres. Finally, we summarize the current challenges and their proposed solutions, which are centered on improving encoding capacities, alternative probe possibilities, nonspecificity suppression, directional immobilization, and "point of care" platforms. Throughout this review, we aim to provide a comprehensive guide for the design of suspension arrays, with the goal of improving their performance in areas such as multiplexing capacity, throughput, sensitivity, and cost effectiveness. We hope that our summary on the state-of-the-art development of these arrays, our commentary on future challenges, and some proposed avenues for further advances will help drive the development of suspension array technology and its related fields.
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Affiliation(s)
- Yuankui Leng
- The State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
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18
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Greenwood C, Ruff D, Kirvell S, Johnson G, Dhillon HS, Bustin SA. Proximity assays for sensitive quantification of proteins. BIOMOLECULAR DETECTION AND QUANTIFICATION 2015; 4:10-6. [PMID: 27077033 PMCID: PMC4822221 DOI: 10.1016/j.bdq.2015.04.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 04/23/2015] [Indexed: 12/22/2022]
Abstract
Proximity assays are immunohistochemical tools that utilise two or more DNA-tagged aptamers or antibodies binding in close proximity to the same protein or protein complex. Amplification by PCR or isothermal methods and hybridisation of a labelled probe to its DNA target generates a signal that enables sensitive and robust detection of proteins, protein modifications or protein-protein interactions. Assays can be carried out in homogeneous or solid phase formats and in situ assays can visualise single protein molecules or complexes with high spatial accuracy. These properties highlight the potential of proximity assays in research, diagnostic, pharmacological and many other applications that require sensitive, specific and accurate assessments of protein expression.
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Affiliation(s)
- Christina Greenwood
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
| | - David Ruff
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Sara Kirvell
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
| | - Gemma Johnson
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
| | - Harvinder S Dhillon
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
| | - Stephen A Bustin
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
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19
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Ho-Yen CM, Jones JL, Kermorgant S. The clinical and functional significance of c-Met in breast cancer: a review. Breast Cancer Res 2015; 17:52. [PMID: 25887320 PMCID: PMC4389345 DOI: 10.1186/s13058-015-0547-6] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 03/05/2015] [Indexed: 02/05/2023] Open
Abstract
c-Met is a receptor tyrosine kinase that upon binding of its ligand, hepatocyte growth factor (HGF), activates downstream pathways with diverse cellular functions that are important in organ development and cancer progression. Anomalous c-Met signalling has been described in a variety of cancer types, and the receptor is regarded as a novel therapeutic target. In breast cancer there is a need to develop new treatments, particularly for the aggressive subtypes such as triple-negative and basal-like cancer, which currently lack targeted therapy. Over the last two decades, much has been learnt about the functional role of c-Met signalling in different models of breast development and cancer. This work has been complemented by clinical studies, establishing the prognostic significance of c-Met in tissue samples of breast cancer. While the clinical trials of anti-c-Met therapy in advanced breast cancer progress, there is a need to review the existing evidence so that the potential of these treatments can be better appreciated. The aim of this article is to examine the role of HGF/c-Met signalling in in vitro and in vivo models of breast cancer, to describe the mechanisms of aberrant c-Met signalling in human tissues, and to give a brief overview of the anti-c-Met therapies currently being evaluated in breast cancer patients. We will show that the HGF/c-Met pathway is associated with breast cancer progression and suggest that there is a firm basis for continued development of anti-c-Met treatment, particularly for patients with basal-like and triple-negative breast cancer.
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Affiliation(s)
- Colan M Ho-Yen
- Department of Cellular Pathology, St George's Healthcare NHS Trust, Blackshaw Road, Tooting, London, SW17 0QT, UK.
| | - J Louise Jones
- Centre for Tumour Biology, Barts Cancer Institute, Charterhouse Square, London, EC1M 6BQ, UK.
| | - Stephanie Kermorgant
- Centre for Tumour Biology, Barts Cancer Institute, Charterhouse Square, London, EC1M 6BQ, UK.
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20
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Kaehler C, Guenther A, Uhlich A, Krobitsch S. PRMT1-mediated arginine methylation controls ATXN2L localization. Exp Cell Res 2015; 334:114-25. [PMID: 25748791 DOI: 10.1016/j.yexcr.2015.02.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/20/2015] [Accepted: 02/25/2015] [Indexed: 01/02/2023]
Abstract
Arginine methylation is a posttranslational modification that is of importance in diverse cellular processes. Recent proteomic mass spectrometry studies reported arginine methylation of ataxin-2-like (ATXN2L), the paralog of ataxin-2, a protein that is implicated in the neurodegenerative disorder spinocerebellar ataxia type 2. Here, we investigated the methylation state of ATXN2L and its significance for ATXN2L localization. We first confirmed that ATXN2L is asymmetrically dimethylated in vivo, and observed that the nuclear localization of ATXN2L is altered under methylation inhibition. We further discovered that ATXN2L associates with the protein arginine-N-methyltransferase 1 (PRMT1). Finally, we showed that neither mutation of the arginine-glycine-rich motifs of ATXN2L nor methylation inhibition alters ATXN2L localization to stress granules, suggesting that methylation of ATXN2L is probably not mandatory.
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Affiliation(s)
- Christian Kaehler
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Anika Guenther
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Anja Uhlich
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Sylvia Krobitsch
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany.
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21
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Chan AI, McGregor LM, Liu DR. Novel selection methods for DNA-encoded chemical libraries. Curr Opin Chem Biol 2015; 26:55-61. [PMID: 25723146 DOI: 10.1016/j.cbpa.2015.02.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 01/31/2015] [Accepted: 02/09/2015] [Indexed: 02/02/2023]
Abstract
Driven by the need for new compounds to serve as biological probes and leads for therapeutic development and the growing accessibility of DNA technologies including high-throughput sequencing, many academic and industrial groups have begun to use DNA-encoded chemical libraries as a source of bioactive small molecules. In this review, we describe the technologies that have enabled the selection of compounds with desired activities from these libraries. These methods exploit the sensitivity of in vitro selection coupled with DNA amplification to overcome some of the limitations and costs associated with conventional screening methods. In addition, we highlight newer techniques with the potential to be applied to the high-throughput evaluation of DNA-encoded chemical libraries.
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Affiliation(s)
- Alix I Chan
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St, Cambridge, MA 02138, United States
| | - Lynn M McGregor
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St, Cambridge, MA 02138, United States
| | - David R Liu
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St, Cambridge, MA 02138, United States.
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22
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Flanders KC, Heger CD, Conway C, Tang B, Sato M, Dengler SL, Goldsmith PK, Hewitt SM, Wakefield LM. Brightfield proximity ligation assay reveals both canonical and mixed transforming growth factor-β/bone morphogenetic protein Smad signaling complexes in tissue sections. J Histochem Cytochem 2014; 62:846-63. [PMID: 25141865 PMCID: PMC4244299 DOI: 10.1369/0022155414550163] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 07/18/2014] [Indexed: 11/22/2022] Open
Abstract
Transforming growth factor-β (TGF-β) is an important regulator of cellular homeostasis and disease pathogenesis. Canonical TGF-β signaling occurs through Smad2/3-Smad4 complexes; however, recent in vitro studies suggest that elevated levels of TGF-β may activate a novel mixed Smad complex (Smad2/3-Smad1/5/9), which is required for some of the pro-oncogenic activities of TGF-β. To determine if mixed Smad complexes are evident in vivo, we developed antibodies that can be used with a proximity ligation assay to detect either canonical or mixed Smad complexes in formalin-fixed paraffin-embedded sections. We demonstrate high expression of mixed Smad complexes in the tissues from mice genetically engineered to express high levels of TGF-β1. Mixed Smad complexes were also prominent in 15-16 day gestation mouse embryos and in breast cancer xenografts, suggesting important roles in embryonic development and tumorigenesis. In contrast, mixed Smad complexes were expressed at extremely low levels in normal adult mouse tissue, where canonical complexes were correspondingly higher. We show that this methodology can be used in archival patient samples and tissue microarrays, and we have developed an algorithm to quantitate the brightfield read-out. These methods will allow quantitative analysis of cell type-specific Smad signaling pathways in physiological and pathological processes.
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Affiliation(s)
- Kathleen C Flanders
- Laboratory of Cancer Biology and Genetics (KCF, BT, MS, SLD, LMW), Center for Cancer Research, National Cancer Institute, Bethesda, MDAntibody and Protein Purification Unit (CDH, PKG), Center for Cancer Research, National Cancer Institute, Bethesda, MDLaboratory of Pathology (CC, SMH), Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Christopher D Heger
- Laboratory of Cancer Biology and Genetics (KCF, BT, MS, SLD, LMW), Center for Cancer Research, National Cancer Institute, Bethesda, MDAntibody and Protein Purification Unit (CDH, PKG), Center for Cancer Research, National Cancer Institute, Bethesda, MDLaboratory of Pathology (CC, SMH), Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Catherine Conway
- Laboratory of Cancer Biology and Genetics (KCF, BT, MS, SLD, LMW), Center for Cancer Research, National Cancer Institute, Bethesda, MDAntibody and Protein Purification Unit (CDH, PKG), Center for Cancer Research, National Cancer Institute, Bethesda, MDLaboratory of Pathology (CC, SMH), Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Binwu Tang
- Laboratory of Cancer Biology and Genetics (KCF, BT, MS, SLD, LMW), Center for Cancer Research, National Cancer Institute, Bethesda, MDAntibody and Protein Purification Unit (CDH, PKG), Center for Cancer Research, National Cancer Institute, Bethesda, MDLaboratory of Pathology (CC, SMH), Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Misako Sato
- Laboratory of Cancer Biology and Genetics (KCF, BT, MS, SLD, LMW), Center for Cancer Research, National Cancer Institute, Bethesda, MDAntibody and Protein Purification Unit (CDH, PKG), Center for Cancer Research, National Cancer Institute, Bethesda, MDLaboratory of Pathology (CC, SMH), Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Samuel L Dengler
- Laboratory of Cancer Biology and Genetics (KCF, BT, MS, SLD, LMW), Center for Cancer Research, National Cancer Institute, Bethesda, MDAntibody and Protein Purification Unit (CDH, PKG), Center for Cancer Research, National Cancer Institute, Bethesda, MDLaboratory of Pathology (CC, SMH), Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Paul K Goldsmith
- Laboratory of Cancer Biology and Genetics (KCF, BT, MS, SLD, LMW), Center for Cancer Research, National Cancer Institute, Bethesda, MDAntibody and Protein Purification Unit (CDH, PKG), Center for Cancer Research, National Cancer Institute, Bethesda, MDLaboratory of Pathology (CC, SMH), Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Stephen M Hewitt
- Laboratory of Cancer Biology and Genetics (KCF, BT, MS, SLD, LMW), Center for Cancer Research, National Cancer Institute, Bethesda, MDAntibody and Protein Purification Unit (CDH, PKG), Center for Cancer Research, National Cancer Institute, Bethesda, MDLaboratory of Pathology (CC, SMH), Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Lalage M Wakefield
- Laboratory of Cancer Biology and Genetics (KCF, BT, MS, SLD, LMW), Center for Cancer Research, National Cancer Institute, Bethesda, MDAntibody and Protein Purification Unit (CDH, PKG), Center for Cancer Research, National Cancer Institute, Bethesda, MDLaboratory of Pathology (CC, SMH), Center for Cancer Research, National Cancer Institute, Bethesda, MD
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23
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Abstract
Optical imaging is crucial for addressing fundamental problems in all areas of life science. With the use of confocal and two-photon fluorescence microscopy, complex dynamic structures and functions in a plethora of tissue and cell types have been visualized. However, the resolution of 'classical' optical imaging methods is poor due to the diffraction limit and does not allow resolution of the cellular microcosmos. On the other hand, the novel stimulated emission depletion (STED) microscopy technique, because of its targeted on/off-switching of fluorescence, is not hampered by a diffraction-limited resolution barrier. STED microscopy can therefore provide much sharper images, permitting nanoscale visualization by sequential imaging of individual-labelled biomolecules, which should allow previous findings to be reinvestigated and provide novel information. The aim of this review is to highlight promising developments in and applications of STED microscopy and their impact on unresolved issues in biomedical science.
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Affiliation(s)
- H Blom
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
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24
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O'Hurley G, Sjöstedt E, Rahman A, Li B, Kampf C, Pontén F, Gallagher WM, Lindskog C. Garbage in, garbage out: a critical evaluation of strategies used for validation of immunohistochemical biomarkers. Mol Oncol 2014; 8:783-98. [PMID: 24725481 PMCID: PMC5528533 DOI: 10.1016/j.molonc.2014.03.008] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 03/10/2014] [Indexed: 12/19/2022] Open
Abstract
The use of immunohistochemistry (IHC) in clinical cohorts is of paramount importance in determining the utility of a biomarker in clinical practice. A major bottleneck in translating a biomarker from bench-to-bedside is the lack of well characterized, specific antibodies suitable for IHC. Despite the widespread use of IHC as a biomarker validation tool, no universally accepted standardization guidelines have been developed to determine the applicability of particular antibodies for IHC prior to its use. In this review, we discuss the technical challenges faced by the use of immunohistochemical biomarkers and rigorously explore classical and emerging antibody validation technologies. Based on our review of these technologies, we provide strict criteria for the pragmatic validation of antibodies for use in immunohistochemical assays.
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Affiliation(s)
- Gillian O'Hurley
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland; Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden; OncoMark Ltd, NovaUCD, Belfield Innovation Park, Belfield, Dublin 4, Ireland
| | - Evelina Sjöstedt
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Arman Rahman
- OncoMark Ltd, NovaUCD, Belfield Innovation Park, Belfield, Dublin 4, Ireland
| | - Bo Li
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Caroline Kampf
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden.
| | - William M Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland; OncoMark Ltd, NovaUCD, Belfield Innovation Park, Belfield, Dublin 4, Ireland.
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
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25
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Nong RY, Gu J, Darmanis S, Kamali-Moghaddam M, Landegren U. DNA-assisted protein detection technologies. Expert Rev Proteomics 2014; 9:21-32. [DOI: 10.1586/epr.11.78] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Onstenk W, Gratama J, Foekens J, Sleijfer S. Towards a personalized breast cancer treatment approach guided by circulating tumor cell (CTC) characteristics. Cancer Treat Rev 2013; 39:691-700. [DOI: 10.1016/j.ctrv.2013.04.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 01/16/2023]
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27
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Powers AD, Palecek SP. Protein analytical assays for diagnosing, monitoring, and choosing treatment for cancer patients. JOURNAL OF HEALTHCARE ENGINEERING 2012; 3:503-534. [PMID: 25147725 DOI: 10.1260/2040-2295.3.4.503] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cancer treatment is often hindered by inadequate methods for diagnosing the disease or insufficient predictive capacity regarding therapeutic efficacy. Targeted cancer treatments, including Bcr-Abl and EGFR kinase inhibitors, have increased survival for some cancer patients but are ineffective in other patients. In addition, many patients who initially respond to targeted inhibitor therapy develop resistance during the course of treatment. Molecular analysis of cancer cells has emerged as a means to tailor treatment to particular patients. While DNA analysis can provide important diagnostic information, protein analysis is particularly valuable because proteins are more direct mediators of normal and diseased cellular processes. In this review article, we discuss current and emerging protein assays for improving cancer treatment, including trends toward assay miniaturization and measurement of protein activity.
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Affiliation(s)
- Alicia D Powers
- Department of Chemical and Biological Engineering University of Wisconsin-Madison
| | - Sean P Palecek
- Department of Chemical and Biological Engineering University of Wisconsin-Madison
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28
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Asplund A, Edqvist PHD, Schwenk JM, Pontén F. Antibodies for profiling the human proteome-The Human Protein Atlas as a resource for cancer research. Proteomics 2012; 12:2067-77. [PMID: 22623277 DOI: 10.1002/pmic.201100504] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In this review, we present an update on the progress of the Human Protein Atlas, with an emphasis on strategies for validating immunohistochemistry-based protein expression patterns and on the possibilities to extend the map of protein expression patterns for cancer research projects. The objectives underlying the Human Protein Atlas include (i) the generation of validated antibodies toward a major isoform of all proteins encoded by the human genome, (ii) creating an information database of protein expression patterns in normal human tissues, in cells, and in cancer, and (iii) utilizing generated antibodies and protein expression data as tools to identify clinically useful biomarkers. The success of such an effort is dependent on the validity of antibodies as specific binders of intended targets in applications used to map protein expression patterns. The development of strategies to support specific target binding is crucial and remains a challenge as a large fraction of proteins encoded by the human genome is poorly characterized, including the approximately one-third of all proteins lacking evidence of existence. Conceivable methods for validation include the use of paired antibodies, i.e. two independent antibodies targeting different and nonoverlapping epitopes on the same protein as well as comparative analysis of mRNA expression patterns with corresponding proteins.
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Affiliation(s)
- Anna Asplund
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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29
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Li B, Ellington* AD. Electrochemical Techniques as Powerful Readout Methods for Aptamer-based Biosensors. DNA CONJUGATES AND SENSORS 2012. [DOI: 10.1039/9781849734936-00211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Aptamers are single-stranded nucleic acids that can be selected in vitro with special folding structures to bind to many different small-molecule, protein, and cellular targets. Over the past two decades, aptamers have become novel promising recognition elements for the fabrication of biosensors. These ‘aptasensors’ have several advantages over antibodies in that they are relatively easy to synthesise or modify in vitro, and can be appended with linkers and reporters for adaptation to various sensing strategies. In this chapter, we introduce the various electrochemical techniques that can be used as powerful readout methods for aptasensors, providing a brief introduction to aptamers and related electrochemical techniques, and then a detailed description of various branches within the field, including labelled strategies, unlabelled strategies, and enzyme-amplified strategies. For each type of approach, several basic and improved design principles will be addressed. It is hoped that, through this discussion, readers will get a sense of how several variables (aptamers, targets and redox reporters) are successfully combined with electrochemical techniques in order to produce a series of sensing platforms with high selectivity and sensitivity.
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Affiliation(s)
- Bingling Li
- Institute for Cellular and Molecular Biology Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712 USA
| | - Andrew D. Ellington*
- Institute for Cellular and Molecular Biology Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712 USA
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30
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Jadwin JA, Ogiue-Ikeda M, Machida K. The application of modular protein domains in proteomics. FEBS Lett 2012; 586:2586-96. [PMID: 22710164 DOI: 10.1016/j.febslet.2012.04.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Revised: 04/13/2012] [Accepted: 04/13/2012] [Indexed: 11/19/2022]
Abstract
The ability of modular protein domains to independently fold and bind short peptide ligands both in vivo and in vitro has allowed a significant number of protein-protein interaction studies to take advantage of them as affinity and detection reagents. Here, we refer to modular domain based proteomics as "domainomics" to draw attention to the potential of using domains and their motifs as tools in proteomics. In this review we describe core concepts of domainomics, established and emerging technologies, and recent studies by functional category. Accumulation of domain-motif binding data should ultimately provide the foundation for domain-specific interactomes, which will likely reveal the underlying substructure of protein networks as well as the selectivity and plasticity of signal transduction.
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Affiliation(s)
- Joshua A Jadwin
- Department of Genetics and Developmental Biology, Raymond and Beverly Sackler Laboratory of Genetics and Molecular Medicine, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA
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31
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Borte S, Wang N, Oskarsdóttir S, von Döbeln U, Hammarström L. Newborn screening for primary immunodeficiencies: beyond SCID and XLA. Ann N Y Acad Sci 2012; 1246:118-30. [PMID: 22236436 DOI: 10.1111/j.1749-6632.2011.06350.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Primary immunodeficiencies (PID) encompass more than 250 disease entities, including phagocytic disorders, complement deficiencies, T cell defects, and antibody deficiencies. While differing in clinical severity, early diagnosis and treatment is of considerable importance for all forms of PID to prevent organ damage and life-threatening infections. During the past few years, neonatal screening assays have been developed to detect diseases hallmarked by the absence of T or B lymphocytes, classically seen in severe combined immunodeficiencies (SCID) and X-linked agammaglobulinemia (XLA). As described in this review, a reduction or lack of T and B cells in newborns is also frequently found in several other forms of PID, requiring supplemental investigation and involving the development of additional technical platforms in order to help classify abnormal screening results.
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Affiliation(s)
- Stephan Borte
- Division of Clinical Immunology and Transfusion Medicine, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
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32
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Zhang A, Sun H, Wang P, Han Y, Wang X. Future perspectives of personalized medicine in traditional Chinese medicine: A systems biology approach. Complement Ther Med 2012; 20:93-9. [DOI: 10.1016/j.ctim.2011.10.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 10/08/2011] [Accepted: 10/19/2011] [Indexed: 10/15/2022] Open
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33
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Zhang H, Li XF, Le XC. Binding-Induced DNA Assembly and Its Application to Yoctomole Detection of Proteins. Anal Chem 2011; 84:877-84. [DOI: 10.1021/ac203207g] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Hongquan Zhang
- Department
of Laboratory Medicine and Pathology, Faculty of Medicine
and Dentistry, and ‡Department of Chemistry, University of Alberta, 10-102 Clinical Sciences Bldg., Edmonton, Alberta,
Canada T6G 2G3
| | - Xing-Fang Li
- Department
of Laboratory Medicine and Pathology, Faculty of Medicine
and Dentistry, and ‡Department of Chemistry, University of Alberta, 10-102 Clinical Sciences Bldg., Edmonton, Alberta,
Canada T6G 2G3
| | - X. Chris Le
- Department
of Laboratory Medicine and Pathology, Faculty of Medicine
and Dentistry, and ‡Department of Chemistry, University of Alberta, 10-102 Clinical Sciences Bldg., Edmonton, Alberta,
Canada T6G 2G3
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34
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Bellucci A, Navarria L, Falarti E, Zaltieri M, Bono F, Collo G, Spillantini MG, Missale C, Spano P. Redistribution of DAT/α-synuclein complexes visualized by "in situ" proximity ligation assay in transgenic mice modelling early Parkinson's disease. PLoS One 2011; 6:e27959. [PMID: 22163275 PMCID: PMC3233557 DOI: 10.1371/journal.pone.0027959] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/28/2011] [Indexed: 01/09/2023] Open
Abstract
Alpha-synuclein, the major component of Lewy bodies, is thought to play a central role in the onset of synaptic dysfunctions in Parkinson's disease (PD). In particular, α-synuclein may affect dopaminergic neuron function as it interacts with a key protein modulating dopamine (DA) content at the synapse: the DA transporter (DAT). Indeed, recent evidence from our “in vitro” studies showed that α-synuclein aggregation decreases the expression and membrane trafficking of the DAT as the DAT is retained into α-synuclein-immunopositive inclusions. This notwithstanding, “in vivo” studies on PD animal models investigating whether DAT distribution is altered by the pathological overexpression and aggregation of α-synuclein are missing. By using the proximity ligation assay, a technique which allows the “in situ” visualization of protein-protein interactions, we studied the occurrence of alterations in the distribution of DAT/α-synuclein complexes in the SYN120 transgenic mouse model, showing insoluble α-synuclein aggregates into dopaminergic neurons of the nigrostriatal system, reduced striatal DA levels and an altered distribution of synaptic proteins in the striatum. We found that DAT/α-synuclein complexes were markedly redistributed in the striatum and substantia nigra of SYN120 mice. These alterations were accompanied by a significant increase of DAT striatal levels in transgenic animals when compared to wild type littermates. Our data indicate that, in the early pathogenesis of PD, α-synuclein acts as a fine modulator of the dopaminergic synapse by regulating the subcellular distribution of key proteins such as the DAT.
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Affiliation(s)
- Arianna Bellucci
- Division of Pharmacology, Department of Biomedical Sciences and Biotechnologies and National Institute of Neuroscience-Italy, School of Medicine, University of Brescia, Brescia, Italy.
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35
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Romer T, Leonhardt H, Rothbauer U. Engineering antibodies and proteins for molecular in vivo imaging. Curr Opin Biotechnol 2011; 22:882-7. [DOI: 10.1016/j.copbio.2011.06.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 06/01/2011] [Accepted: 06/06/2011] [Indexed: 12/31/2022]
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36
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Kasaian K, Jones SJ. A new frontier in personalized cancer therapy: mapping molecular changes. Future Oncol 2011; 7:873-94. [PMID: 21732758 DOI: 10.2217/fon.11.63] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mutations in the genome of a normal cell can affect the function of its many genes and pathways. These alterations could eventually transform the cell from a normal to a malignant state by allowing an uncontrolled proliferation of the cell and formation of a cancer tumor. Each tumor in an individual patient can have hundreds of mutated genes and perturbed pathways. Cancers clinically presenting as the same type or subtype could potentially be very different at the molecular level and thus behave differently in response to therapy. The challenge is to distinguish the key mutations driving the cancer from the background of mutational noise and find ways to effectively target them. The promise is that such a molecular approach to classifying cancer will lead to better diagnostic, prognostic and personalized treatment strategies. This article provides an overview of advances in the molecular characterization of cancers and their applications in therapy.
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Affiliation(s)
- Katayoon Kasaian
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
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37
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Liu Y, Gu J, Hagner-McWhirter Å, Sathiyanarayanan P, Gullberg M, Söderberg O, Johansson J, Hammond M, Ivansson D, Landegren U. Western blotting via proximity ligation for high performance protein analysis. Mol Cell Proteomics 2011; 10:O111.011031. [PMID: 21813417 DOI: 10.1074/mcp.o111.011031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Western blotting is a powerful and widely used method, but limitations in detection sensitivity and specificity, and dependence upon high quality antibodies to detect targeted proteins, are hurdles to overcome. The in situ proximity ligation assay, based on dual antibody recognition and powerful localized signal amplification, offers increased detection sensitivity and specificity, along with an ability to identify complex targets such as phosphorylated or interacting proteins. Here we have applied the in situ proximity ligation assay mechanism in Western blotting. This combination allowed the use of isothermal rolling circle amplification of DNA molecules formed in target-specific ligation reaction, for 16-fold or greater increase in detection sensitivity. The increased specificity because of dual antibody recognition ensured highly selective assays, detecting the specific band when combinations of two cross-reactive antitubulin antibodies were used (i.e. both producing distinct nonspecific bands in traditional Western blotting). We also demonstrated detection of phosphorylated platelet-derived growth factor receptor β by proximity ligation with one antibody directed against the receptor and another directed against the phosphorylated tyrosine residue. This avoided the need for stripping and re-probing the membrane or aligning two separate traditional blots. We demonstrate that the high-performance in situ proximity ligation-based Western blotting described herein is compatible with detection via enhanced chemiluminescence and fluorescence detection systems, and can thus be readily employed in any laboratory.
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Affiliation(s)
- Yanling Liu
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden.
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38
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Saccà B, Niemeyer CM. Functionalization of DNA nanostructures with proteins. Chem Soc Rev 2011; 40:5910-21. [DOI: 10.1039/c1cs15212b] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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