THE HUMAN PROTEIN ATLAS BLOG
Novel assay concept developed
In an article in a special edition of Proteomics, on protein arrays researchers from the Human Protein Atlas describe the development of a novel assay concept, which combines the flexibility and multiplexing capacity of single-binder assays and the specificity and sensitivity aspects of dual-binder assays. They developed a multiplexed dual-binder assay procedure, which is based on a sequential protein capture.
– This assay is a great addition to the antibody-array toolbox of the Biobank Profiling Group, both to support related assay development activities and for biomarker discovery applications, says Burcu Ayoglu, first author of the study.
Antibody microarrays enable parallelized and miniaturized proteomic analysis of clinical samples. When applying antibody arrays, samples are either labeled in solution to enable a direct read-out in a single-binder assay format, or analyzed by matched pairs of capture and detection antibodies in a dual-binder assay format, also known as sandwich assays. As demonstrated by the outcome of several studies within the Biobank Profiling Group led by Dr. Jochen Schwenk, protein profiling with antibody arrays using a single-binder assay format provides novel and valuable insights in the context of various diseases. Yet, there is ample room for improvement of the performance of the single-binder assays by reducing the off-target binding interactions. Therefore, this technical paper is of great importance.
Burcu Ayoglu is originally from Istanbul where she got her B.Sc. degree in Chemical Engineering. In 2007 she moved to Stockholm and in 2009 she received an M.Sc. degree in Medical Biotechnology from KTH. Following this, she started her Ph.D. work at SciLifeLab-KTH and received a Ph.D. degree in September 2014 for her research with Prof. Peter Nilsson and Dr. Jochen Schwenk in the Affinity Proteomics Group within the Human Protein Atlas.
– My PhD work focused on development and application of protein, peptide and antibody microarrays for profiling autoantibodies and proteins in human body fluids. I worked in various biomarker discovery projects within autoimmune conditions, as well as within neuro- and muscle-degenerative diseases such as multiple sclerosis and Duchenne muscular dystrophy.
Following her PhD, Burcu Ayoglu got awarded a scholarship from the Wallenberg Foundation for a two-year postdoctoral fellowship at Stanford University, with the possibility to receive funding for two more years upon her return to Sweden from USA.
– I saw this as a valuable opportunity to develop my professional skills further and to prepare myself better for an academic career. Since November 2015, I am working at the Immunology Department at Stanford University School of Medicine in California, USA. Here I am continuing to build on my training in establishing multiplexed tools for proteomic analysis of human or animal model body fluid samples within systemic autoimmune diseases and immunodeficiency disorders. Stanford University is a dynamic and stimulating place where you continuously get introduced to interesting concepts, researchers and tools. Thus, in parallel I am also exploring various topics e.g. in neuroimmunology and some wet-lab and biomedical informatics tools with possible applications in systems immunology in order to shape and refine my long-term research program for the coming years.
Coming back to the Proteomics-paper, Burcu Ayoglu explains that with further optimization, the assay described in this technical paper can be applied for the analysis of other body fluids, where an efficient direct labeling approach might not be possible. It can also be applied for protein profiling in extracts of tissues and cells, since this assay offers flexibility in terms of the starting media the cell or tissue lysates could be in.
– We can make use of this assay also for an efficient evaluation of functional antibody pairs for development of more targeted assays, such as sandwich immunoassays. It can also help us to identify those antibodies, which have a higher tendency to reveal off-target interactions in certain sample types such as blood plasma. In that sense, it could be considered as an alternative antibody quality control tool. The Biobank Profiling Group is constantly developing new project ideas where one or several of these possible extensions of this assay concept can be developed and applied.
Read the whole paper in Proteomics.
A portrait of Jochen Schwenk was published earlier this year.
Frida Henningson Johnson