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Toubia J, Conn VM, Conn SJ. Don't go in circles: confounding factors in gene expression profiling. EMBO J 2018; 37:embj.201797945. [PMID: 29735571 DOI: 10.15252/embj.201797945] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- John Toubia
- ACRF Cancer Genomics Facility, SA Pathology, Adelaide, SA, Australia.,Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Vanessa M Conn
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine & Public Health, Flinders University, Adelaide, SA, Australia
| | - Simon J Conn
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine & Public Health, Flinders University, Adelaide, SA, Australia
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Thorey IS, Grote M, Mayer K, Brinkmann U. Hapten-Binding Bispecific Antibodies for the Targeted Delivery of SiRNA and SiRNA-Containing Nanoparticles. Methods Mol Biol 2016; 1364:219-234. [PMID: 26472454 DOI: 10.1007/978-1-4939-3112-5_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Hapten-binding bispecific antibodies (bsAbs) are effective and versatile tools for targeting diverse payloads, including siRNAs, to specific cells and tissues. In this chapter, we provide examples for successful SiRNA delivery using this powerful targeting platform. We further provide protocols for designing and producing bsAbs, for combining bsAbs with SiRNA into functional complexes, and achieving specific mRNA knockdown in cells by using these functional complexes.
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Affiliation(s)
- Irmgard S Thorey
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Nonnenwald 2, 82377, Penzberg, Germany
| | - Michael Grote
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Nonnenwald 2, 82377, Penzberg, Germany
| | - Klaus Mayer
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Nonnenwald 2, 82377, Penzberg, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Nonnenwald 2, 82377, Penzberg, Germany.
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TriFabs--Trivalent IgG-Shaped Bispecific Antibody Derivatives: Design, Generation, Characterization and Application for Targeted Payload Delivery. Int J Mol Sci 2015; 16:27497-507. [PMID: 26593903 PMCID: PMC4661895 DOI: 10.3390/ijms161126037] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/28/2015] [Accepted: 11/05/2015] [Indexed: 02/06/2023] Open
Abstract
TriFabs are IgG-shaped bispecific antibodies (bsAbs) composed of two regular Fab arms fused via flexible linker peptides to one asymmetric third Fab-sized binding module. This third module replaces the IgG Fc region and is composed of the variable region of the heavy chain (VH) fused to CH3 with “knob”-mutations, and the variable region of the light chain (VL) fused to CH3 with matching “holes”. The hinge region does not contain disulfides to facilitate antigen access to the third binding site. To compensate for the loss of hinge-disulfides between heavy chains, CH3 knob-hole heterodimers are linked by S354C-Y349C disulphides, and VH and VL of the stem region may be linked via VH44C-VL100C disulphides. TriFabs which bind one antigen bivalent in the same manner as IgGs and the second antigen monovalent “in between” these Fabs can be applied to simultaneously engage two antigens, or for targeted delivery of small and large (fluorescent or cytotoxic) payloads.
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Microarray experiments and factors which affect their reliability. Biol Direct 2015; 10:46. [PMID: 26335588 PMCID: PMC4559324 DOI: 10.1186/s13062-015-0077-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 08/24/2015] [Indexed: 12/12/2022] Open
Abstract
Oligonucleotide microarrays belong to the basic tools of molecular biology and allow for simultaneous assessment of the expression level of thousands of genes. Analysis of microarray data is however very complex, requiring sophisticated methods to control for various factors that are inherent to the procedures used. In this article we describe the individual steps of a microarray experiment, highlighting important elements and factors that may affect the processes involved and that influence the interpretation of the results. Additionally, we describe methods that can be used to estimate the influence of these factors, and to control the way in which they affect the expression estimates. A comprehensive understanding of the experimental protocol used in a microarray experiment aids the interpretation of the obtained results. By describing known factors which affect expression estimates this article provides guidelines for appropriate quality control and pre-processing of the data, additionally applicable to other transcriptome analysis methods that utilize similar sample handling protocols.
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Conformation-dependent binding and tumor-targeted delivery of siRNA by a designed TRBP2: Affibody fusion protein. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2015; 11:1455-66. [DOI: 10.1016/j.nano.2015.01.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 12/18/2014] [Accepted: 01/19/2015] [Indexed: 12/21/2022]
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Kuballa P, Baumann AL, Mayer K, Bär U, Burtscher H, Brinkmann U. Induction of heat shock protein HSPA6 (HSP70B′) upon HSP90 inhibition in cancer cell lines. FEBS Lett 2015; 589:1450-8. [DOI: 10.1016/j.febslet.2015.04.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 04/10/2015] [Accepted: 04/27/2015] [Indexed: 10/23/2022]
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Koti M, Gooding RJ, Nuin P, Haslehurst A, Crane C, Weberpals J, Childs T, Bryson P, Dharsee M, Evans K, Feilotter HE, Park PC, Squire JA. Identification of the IGF1/PI3K/NF κB/ERK gene signalling networks associated with chemotherapy resistance and treatment response in high-grade serous epithelial ovarian cancer. BMC Cancer 2013; 13:549. [PMID: 24237932 PMCID: PMC3840597 DOI: 10.1186/1471-2407-13-549] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/31/2013] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Resistance to platinum-based chemotherapy remains a major impediment in the treatment of serous epithelial ovarian cancer. The objective of this study was to use gene expression profiling to delineate major deregulated pathways and biomarkers associated with the development of intrinsic chemotherapy resistance upon exposure to standard first-line therapy for ovarian cancer. METHODS The study cohort comprised 28 patients divided into two groups based on their varying sensitivity to first-line chemotherapy using progression free survival (PFS) as a surrogate of response. All 28 patients had advanced stage, high-grade serous ovarian cancer, and were treated with standard platinum-based chemotherapy. Twelve patient tumours demonstrating relative resistance to platinum chemotherapy corresponding to shorter PFS (< eight months) were compared to sixteen tumours from platinum-sensitive patients (PFS > eighteen months). Whole transcriptome profiling was performed using an Affymetrix high-resolution microarray platform to permit global comparisons of gene expression profiles between tumours from the resistant group and the sensitive group. RESULTS Microarray data analysis revealed a set of 204 discriminating genes possessing expression levels which could influence differential chemotherapy response between the two groups. Robust statistical testing was then performed which eliminated a dependence on the normalization algorithm employed, producing a restricted list of differentially regulated genes, and which found IGF1 to be the most strongly differentially expressed gene. Pathway analysis, based on the list of 204 genes, revealed enrichment in genes primarily involved in the IGF1/PI3K/NF κB/ERK gene signalling networks. CONCLUSIONS This study has identified pathway specific prognostic biomarkers possibly underlying a differential chemotherapy response in patients undergoing standard platinum-based treatment of serous epithelial ovarian cancer. In addition, our results provide a pathway context for further experimental validations, and the findings are a significant step towards future therapeutic interventions.
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Affiliation(s)
- Madhuri Koti
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada
| | - Robert J Gooding
- Department of Physics, Engineering Physics and Astronomy, Queen’s University, Kingston, ON, Canada
| | - Paulo Nuin
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
- Ontario Cancer Biomarker Network, Toronto, ON, Canada
| | - Alexandria Haslehurst
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
| | - Colleen Crane
- Department of Pathology, The Ottawa Hospital, Ottawa, ON, Canada
| | - Johanne Weberpals
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Timothy Childs
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
| | - Peter Bryson
- Department of Obstetrics and Gynecology, Queen’s University, Kingston, ON, Canada
| | - Moyez Dharsee
- Ontario Cancer Biomarker Network, Toronto, ON, Canada
| | - Kenneth Evans
- Ontario Cancer Biomarker Network, Toronto, ON, Canada
| | - Harriet E Feilotter
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
| | - Paul C Park
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
| | - Jeremy A Squire
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
- Departments of Genetics and Pathology, Faculdade de Medicina de Ribeirão Preto, University of Sao Paulo, Brazil
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