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Sciomics: antibody microarrays and their broad range of applications

Sciomics GmbH is a start-up biotech from Heidelberg with a special focus on protein microarrays. Sciomics produces complex, high-density antibody microarrays for cancer-relevant proteins and offers services for medical research, diagnostics and the industry, including biomarker screening, the verification of biomarker candidates, the analysis and localization of drug targets and their signalling pathways as well as the characterization of antibodies. In addition, Sciomics produces and markets microarrays that are adapted to the specific research issues of its customers.

Sciomics antibody microarray. © Sciomics GmbH

While DNA and RNA microarrays have long been routine high-throughput technologies for genome analyses and gene expression profiling, affinity microarrays on the basis of proteins, and in particular antibody microarrays, have only been used to any extent for proteome analyses for the past few years. In contrast to DNA arrays, the technical challenges associated with protein microarrays are relatively complex: the microarrays must be able to identify proteins in all their diversity and with all their modifications, and also take into account the fact that the structure, and the biophysical and biochemical characteristics of proteins differ considerably. The concentration of proteins can differ by several magnitudes and undergo constant changes in the same way as the entire proteome constantly undergoes dynamic changes.  

Over the past ten years, the handling and reliability of antibody microarrays has been greatly improved. They have become efficient high-throughput tools for proteome analyses and their applications such as the search for clinically relevant tumour biomarkers. 

Highly parallel – robust – reproducible – cheap

Sciomics GmbH was established in 2013 as a spin-off company of the German Cancer Research Center (DKFZ). The company produces and uses antibody microarrays for proteome analysis at the highest possible technical level in research and clinical application. Sciomics was founded by Dr. Jörg Hoheisel and Dr. Christoph Schröder, two well-known researchers who have gained a worldwide reputation through their numerous key publications on antibody microarrays and their use for the identification of biomarkers for the diagnosis and prognosis of cancer. Hoheisel, head of the Department of Functional Genome Analysis at the DKFZ, has been instrumental in the development of microarray technologies for around 20 years. He is also a world-renowned expert on antibody microarrays and retains close ties with the company as a consultant. Schröder is the CEO of Sciomics GmbH and has for the past decade contributed greatly to the development of antibody arrays and has used them successfully in biomedical studies.

Sciomics GmbH founders Dr. Christoph Schröder (left) and Dr. Jörg Hoheisel. © Sciomics GmbH

Sciomics’ microarrays are robust, easy-to-handle tools with numerous advantages over other proteome analysis techniques. The company’s microarrays enable the highly parallel analysis of different parameters from many molecules in tiny volumes. This makes the tests cheap, and gives them a similar sensitivity to the enzyme-linked immunosorbent assay (ELISA), a test routinely used for the analysis of proteins. In special applications, the sensitivity can be increased up to single-molecule detection. The reproducibility of array measurements has a very good coefficient of variation (CV) of less than 15 percent for all array measuring points. Hoheisel, Schröder and their colleagues have shown that the depletion of excessively abundant proteins in the samples or their fractionation prior to the analysis of the array is not necessary. This does away with time- and labour-intensive steps, increases reproducibility and enables the high throughput of a large number of samples. 

Different microarray technologies for different applications

Sciomics offers three different microarray platforms – antibody microarrays, protein microarrays and peptide microarrays. In antibody microarrays, antibodies are spotted and fixed on a solid surface for the purpose of detecting antigens. They are used for the identification of biomarkers and the highly parallel verification of biomarker candidates, the characterisation of antibodies and the analysis of targets and associated elements, including complete signalling pathways.

The company’s second platform, protein microarrays, consists of proteins that are immobilised on a solid substrate and are mainly used for the detection of autoantibodies and of protein interaction as well as for the assessment of antibody specificity. The third type of microarray offered is peptide microarrays where peptides are immobilised on a solid substrate and interact with antibodies and other proteins. Peptide microarrays are typically used to map antibody epitopes and to study protein-peptide interactions. 

Services and products

Schematic of a microarray, shaped like an IgG antibody. © Sciomics GmbH

Sciomics serves clients ranging from diagnostic companies, the pharmaceutical industry, university hospitals and research centres and offers services such as screening for biomarkers, the localisation of drug targets and of the signalling and metabolic pathways with which the drug interferes. Sciomics also uses gene knock-outs and knock-ins to use the difference between knock-out/knock-in and normal individuals/cells to draw conclusions on the effect of certain genes. Sciomics has developed a 'discovery array' with more than one thousand antibodies directed against more than 900 cancer-relevant proteins. The company also produces smaller specific antibody arrays that are directed against differentiation antigens of the cell membrane (CD antigens) and against cytokines and chemokines. The company has plans to make these microarrays available as kits and also produces microarrays that are made to measure according to client requirements. Sciomics also offers specificity testing of antibodies with protein microarrays with 10,000 to 20,000 recombinant human proteins.

All services and products comply with strict quality criteria and the company hopes to achieve ISO9001 certification in 2014.

Biomarker signatures for diagnosis, prognosis and prediction

With its biomarker screening microarray technology, Sciomics focuses on a key aspect of modern healthcare and patient therapy. Reliable biomarkers are indispensable for the effective treatment of tumours, autoimmune diseases and multiple sclerosis. Biomarkers are used for the diagnosis, prediction and prognosis of diseases. The difference between the latter two is that predictive biomarkers gives information about the effect of a therapeutic intervention, while prognostic biomarkers provide information about the likely course of a disease in an untreated individual.

Over the past few years, the DKFZ team of researchers led by Hoheisel and Schröder has used microarrays to identify biomarker signatures in cancer-relevant antibodies that might contribute to the effective diagnosis, prognosis and prediction of cancer; these signatures have been filed as patents and published. The investigations include altered plasma protein compositions in patients with various B-cell lymphomas, including CLL (chronic lymphocytic leukaemia), which is the most common form of leukaemia in the western world, and cancer-associated proteins for pancreatic cancer, which is one of the deadliest cancers. Pancreatic cancer has a very poor prognosis as most patients are only diagnosed when they are already terminally ill.

In their latest study (2014), the researchers used an antibody microarray for the prediction of bladder cancer recurrence. This cancer recurs in around 60 percent of all patients within five years of the surgical removal of the primary tumour. Due to the lack of reliable biomarkers, patients are recommended to undergo cytological and cytoscopic investigations, which are expensive and very stressful.

The company’s antibody microarray has been used for the identification of variations in the protein composition of patients with and without tumour recurrence. The microarray also identified 255 proteins whose frequency differed between the two patient collectives. In addition, Sciomics has identified a protein pattern consisting of 20 proteins, which, with a specificity of 100 percent and a sensitivity of 80 percent, represents a promising candidate as predictive biomarker signature for the identification of bladder cancer recurrences.

Sciomics is interested in partnerships with investors and the diagnostics and pharmaceutical industry for driving forward the development of such biomarker signatures and their translation into clinically applicable diagnostic tools.

Further information:

Sciomics GmbH
Schneidmühlstr. 19
69115 Heidelberg
Tel.: +49 (0)6221-3271233
E-mail: info(at)sciomics.de

Website address: https://www.gesundheitsindustrie-bw.de/en/article/news/sciomics-antibody-microarrays-and-their-broad-range-of-applications