Anthony Warford

Application of phage display to high throughput antibody generation and characterization

We have created a high quality phage display library containing over 1010 human antibodies and describe its use in the generation of antibodies on an unprecedented scale. We have selected, screened and sequenced over 38,000 recombinant antibodies to 292 antigens, yielding over 7,200 unique clones. 4,400 antibodies were characterized by specificity testing and detailed sequence analysis and the data/clones are available online. Sensitive detection was demonstrated in a bead based flow cytometry assay. Furthermore, positive staining by immunohistochemistry on tissue microarrays was found for 37% (143/381) of antibodies. Thus, we have demonstrated the potential of and illuminated the issues associated with genome-wide monoclonal antibody generation.

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

One purpose of the biomedical literature is to report results in sufficient detail that the methods of data collection and analysis can be independently replicated and verified. Here we present reporting guidelines for gene expression localization experiments: the minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). MISFISHIE is modeled after the Minimum Information About a Microarray Experiment (MIAME) specification for microarray experiments. Both guidelines define what information should be reported without dictating a format for encoding that information. MISFISHIE describes six types of information to be provided for each experiment: experimental design, biomaterials and treatments, reporters, staining, imaging data and image characterizations. This specification has benefited the consortium within which it was developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal.

Antibody validation of immunohistochemistry for biomarker discovery: Recommendations of a consortium of academic and pharmaceutical based histopathology researchers

As biomarker discovery takes centre-stage, the role of immunohistochemistry within that process is increasing. At the same time, the number of antibodies being produced for “research use” continues to rise and it is important that antibodies to be used as biomarkers are validated for specificity and sensitivity before use. This guideline seeks to provide a stepwise approach for the validation of an antibody for immunohistochemical assays, reflecting the views of a consortium of academic and pharmaceutical based histopathology researchers. We propose that antibodies are placed into a tier system, level 1–3, based on evidence of their usage in immunohistochemistry, and that the degree of validation required is proportionate to their place on that tier.

Cellular expression, trafficking, and function of two isoforms of human ULBP5/RAET1G

Background The activating immunoreceptor NKG2D is expressed on Natural Killer (NK) cells and subsets of T cells. NKG2D contributes to anti-tumour and anti-viral immune responses in vitro and in vivo. The ligands for NKG2D in humans are diverse proteins of the MIC and ULBP/RAET families that are upregulated on the surface of virally infected cells and tumours. Two splicing variants of ULBP5/RAET1G have been cloned previously, but not extensively characterised. Methodology/Principal Findings We pursue a number of approaches to characterise the expression, trafficking, and function of the two isoforms of ULBP5/RAET1G. We show that both transcripts are frequently expressed in cell lines derived from epithelial cancers, and in primary breast cancers. The full-length transcript, RAET1G1, is predicted to encode a molecule with transmembrane and cytoplasmic domains that are unique amongst NKG2D ligands. Using specific anti-RAET1G1 antiserum to stain tissue microarrays we show that RAET1G1 expression is highly restricted in normal tissues. RAET1G1 was expressed at a low level in normal gastrointestinal epithelial cells in a similar pattern to MICA. Both RAET1G1 and MICA showed increased expression in the gut of patients with celiac disease. In contrast to healthy tissues the RAET1G1 antiserum stained a wide variety or different primary tumour sections. Both endogenously expressed and transfected RAET1G1 was mainly found inside the cell, with a minority of the protein reaching the cell surface. Conversely the truncated splicing variant of RAET1G2 was shown to encode a soluble molecule that could be secreted from cells. Secreted RAET1G2 was shown to downregulate NKG2D receptor expression on NK cells and hence may represent a novel tumour immune evasion strategy. Conclusions/Significance We demonstrate that the expression patterns of ULBP5RAET1G are very similar to the well-characterised NKG2D ligand, MICA. However the two isoforms of ULBP5/RAET1G have very different cellular localisations that are likely to reflect unique functionality.

Isolation and tissue profiles of a large panel of phage antibodies binding to the human adipocyte cell surface

Phage display is a powerful technique for the rapid selection and isolation of antibodies to any given target antigen. We have applied this technology to isolate over 100 different human antibodies that bind to antigens expressed in situ on the human adipocyte cell surface. This is a diverse panel of antibodies, as indicated by the V-region sequences. The binding profile of each anti-adipocyte antibody has been characterised using phage antibody immunocytochemistry against a panel of normal human tissues. Although there was some variation in the intensity of the adipocyte staining, each antibody consistently recognised adipocytes, where present, irrespective of the tissue source. In addition, all of the antibodies recognised at least one other cell type other than the adipocyte cell surface. In total, over 50 different tissue-binding profiles were recorded, with the most frequently recognised tissues identified as capillaries or smooth muscle. Extensive tissue binding profiles were generated for some antibodies using a panel of 37 different human tissues. This identified anti-adipocyte antibodies with unexpected profiles, such as FAT.13, which binds only to adipocytes and capillaries in the entire tissue panel. We believe this is the most extensive survey ever undertaken of the human adipocyte cell surface. Moreover, similar methodology could be used to derive complete tissue-binding profiles of antibodies against cell-surface antigens of any cell type. Indeed, by screening antibodies on both normal and diseased tissues, it may be possible to identify antigenic associations between different cell types and the pathologies of many diseases.

Resin tissue microarrays: a universal format for immunohistochemistry.

Tissue microarray (TMA) technology allows the miniaturization and characterization of multiple tissue samples on a single slide and commonly uses formalin-fixed paraffin-embedded (FFPE) tissue or acetone-fixed frozen tissue. The former provides good morphology but can compromise antigenicity, whereas the latter provides compromised morphology with good antigenicity. Here, we report the development of TMAs in glycol methacrylate resin, which combine the advantages of both methods in one embedding format. Freshly collected tissue fixed in -20C acetone or 10% neutral buffered formaldehyde were cored and arrayed into an intermediary medium of 2% agarose before infiltration of the agarose array with glycol methacrylate resin. Acetone-fixed resin TMA demonstrated improved morphology over acetone-fixed frozen TMA, with no loss of antigenicity. Staining for extracellular, cell surface, and nuclear antigens could be realized with monoclonal and polyclonal antibodies as well as with monomeric single-chain Fv preparations. In addition, when compared with FFPE TMA, formalin-fixed tissue in a resin TMA gave enhanced morphology and subcellular detail. Therefore, resin provides a universal format for the construction of TMAs, providing improved tissue morphology while retaining antigenicity, allows thin-section preparation, and could be used to replace preparation of frozen and FFPE TMAs for freshly collected tissue.

Antigen retrieval, blocking, detection and visualisation systems in immunohistochemistry: a review and practical evaluation of tyramide and rolling circle amplification systems.

To achieve specificity and sensitivity using immunohistochemistry it is necessary to combine the application of validated primary antibodies with optimised pre-treatment, detection and visualisation steps. The influence of these surrounding procedures is reviewed. A practical evaluation of tyramide signal amplification and rolling circle amplification detection methods is provided in which formalin fixed paraffin embedded sections of adenocarcinomas of breast, colon and lung together with squamous metaplasia of lung were immunostained with CD20 and CK19 primary antibodies. The results indicate that the detection systems are of comparable sensitivity and specificity.

Abstract B42: ATM deficiency sensitizes gastric cancer cells to the PARP inhibitior olaparib

Ataxia telangiectasia mutated (ATM) is a protein kinase that regulates cell‐cycle checkpoints, DNA repair and recombination (1). It has been shown that ATM interacts with and regulates NBS1 and BRCA complex which is essential for the homologous recombination (HR) repair in response to the DNA double‐strand break (DSB) damage (2). These observations suggest that tumor cells with defective ATM expression or activity subsequently leading to HR deficiency are likely more sensitive to the targeted therapeutic/chemotherapeutic agents that cause the accumulation of DNA DSBs during replication. To test this, we studied the growth inhibitory effects of olaparib (AZD2281; KU‐0059436) and SN‐38 (the active metabolite of Irinotecan) on gastric cancer (GC) cells with reduced ATM expression. Olaparib is a potent oral inhibitor of poly(adenosine diphosphate [ADP]‐ribose) polymerase (PARP), which has selective antitumor activity in cancers associated with BRCA1 and BRCA2 mutations (3). Our study here showed that 6 out of 7 GC cell lines with low or no expression of ATM are sensitive to olaparib inhibition with IC50s ≤ 1uM as measured by clonogenic survival assays. In contrast, the majority of other GC cell lines positive for ATM expression (11 out of 13) are less sensitive (1uM 1.5uM) to olaparib with only 2 of 13 lines sensitive. Similar correlation was also observed in these GC cell lines between reduced ATM expression and sensitivity to SN‐38 treatment. In addition, combination of olaparib and SN‐38 had a synergistic and selective inhibitory effect on cell growth of GC cells with low/no expression of ATM. These data suggest that loss of ATM in GC cell can sensitize their cellular response to olaparib or/and SN‐38. Next, we asked whether this finding has clinical relevance in GC therapy. The tumor and tumor adjacent tissue specimens from more than 100 patients with gastric cancer were analyzed for ATM expression by immunohistochemistry. 22% (24/111) of the gastric tumor specimens were found stained ATM negative while the negative rate in the adjacent tissues was only 4% (1/26). These results suggested that loss of ATM expression is frequently associated with gastric tumorigenesis. Loss of ATM function may serve as an important tumor biomarker in GC and a PARP inhibitor as monotherapy or in combination with chemotherapy provides a promising therapeutic in this disease segment. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B42.

In situ hybridisation: Technologies and their application to understanding disease

In situ hybridisation (ISH) is unique amongst molecular analysis methods in providing for the precise microscopic localisation of genes, mRNA and microRNA in metaphase spreads, cell and tissue preparations. The method is well established as a tool to guide appropriate therapeutic intervention in breast, gastric and lung cancer. With the description of ultrasensitive ISH technologies for low copy mRNA demonstration and the relative ease by which microRNA can be visualised, the applications for research and diagnostic purposes is set to increase dramatically. In this review ISH is considered with emphasis on recent technological developments and surveyed for present and future applications in the context of the demonstration of genes, mRNA and microRNA in health and disease.

Impact of Analytical Variables in Breast Cancer Biomarker Analysis

Assessment of biomarkers for tissues is a demanding science. Scientific rigor in the analytical methodology is the key to obtaining standardized and consistent results. In this chapter, we focus on the analytical variables, both assay variables and reporting variables, in biomarker analysis. Each and every step in the assay process needs to be carefully monitored, optimized and standardized. Using immunohistochemistry and in situ methods as a background, we describe in detail the parameters required for staining. Assessment of the staining requires the evaluation of not only the tumor staining but also presence of staining in the internal controls such as normal breast epithelium. Strict laboratory quality control using both internal and external quality assessment metrices is necessary. Adoption of national and international guidelines such as ASCO-CAP guidelines, when available, is necessary to provide high degree of confidence required for biomarker analysis that is critical in this era of precision medicine.