461 research outputs found
The 6th HUPO Antibody Initiative (HAI) Workshop: Sharing Data About Affinity Reagents and Other Recent Developments September 2009, Toronto, Canada
No full textThe Human Antibody Initiative (HAI) aims to promote and facilitate the use of antibodies for proteomics research. The 6th workshop for the HUPO Antibody Initiative (HAI) held in September 2009 was co-chaired by Michael Snyder and Mathias Uhlen and discussed several aspects of antibody production, their validation, and attempts to standardise this process, in particular, when subsequently described in the literature. An update on the progress of the Human Protein Atlas was also presented to the attendees.</p
Longitudinal big biological data in the AI era
No full textAbstract Generating longitudinal and multi-layered big biological data is crucial for effectively implementing artificial intelligence (AI) and systems biology approaches in characterising whole-body biological functions in health and complex disease states. Big biological data consists of multi-omics, clinical, wearable device, and imaging data, and information on diet, drugs, toxins, and other environmental factors. Given the significant advancements in omics technologies, human metabologenomics, and computational capabilities, several multi-omics studies are underway. Here, we first review the recent application of AI and systems biology in integrating and interpreting multi-omics data, highlighting their contributions to the creation of digital twins and the discovery of novel biomarkers and drug targets. Next, we review the multi-omics datasets generated worldwide to reveal interactions across multiple biological layers of information over time, which enhance precision health and medicine. Finally, we address the need to incorporate big biological data into clinical practice, supporting the development of a clinical decision support system essential for AI-driven hospitals and creating the foundation for an AI and systems biology-based healthcare model
Response to: Should we ignore western blots when selecting antibodies for other applications?
No full textUhlen replies:In the report1 from the International Working Group for Antibody Validation (IWGAV), we concluded that “approaches for antibody validation must be carried out in an application- and context-specific manner.” Our argument is that samples are treated differently in different applications and that this influences the epitopes exposed on the target protein, which might have profound consequences for the ability of a given antibody to bind specifically to its target. As an example, proteins that are analyzed by immunohistochemistry (IHC) are normally first cross-linked with formalin and then heated to very high temperatures (normally >100 °C) in a procedure that is sometimes termed 'epitope retrieval'. Obviously, this procedure might influence the target protein differently than the procedure used to prepare proteins for a western blot, in which the sample is instead treated with a detergent (SDS) before the electrophoresis step. Thus, as concluded by the members of the IWGAV1, the results obtained for a given antibody in western blot applications cannot be used to predict the specificity of the antibody in another assay based on an entirely different epitope-retrieval method, such as IHC.In the Human Protein Atlas (HPA) program, we have validated more than 24,000 in-house-generated antibodies directed to 17,000 human target proteins2. Although there is often a correlation between performance in different applications, we have observed many examples of antibodies that show strong support for specificity in IHC or immunofluorescence microscopy (IF) but which do not stain the correctly sized band in a western blot, and vice versa3, 4, 5. However, as pointed out by Lund-Johansen and Browning, western blot analysis has indeed been found to be useful as a general validation tool for antibody specificity. Many antibody providers use western blot analysis to show whether a band of the right size is stained or whether additional bands are present, the latter indicating off-target binding. This is indeed a practical procedure for a 'first-line' screening of antibodies for specificity. In the HPA program, we always screen our in-house-generated antibodies by western blot analysis.Similarly, protein arrays, in which the target protein is arrayed together with hundreds or thousands of unrelated proteins, are also useful tools for probing antibody specificity6. In this application, however, target proteins are often presented as purified (noncomplex) spots, and the proteins usually have not undergone any prior treatment with denaturing agents. This means that caution should also be applied when using protein arrays for validation of an antibody for its use in other applications, such as IHC and IF.In conclusion, western blot and protein array analyses can indeed be useful tools when selecting specific antibodies for other applications. The use of these methods is encouraged both for antibody providers and users, and antibodies with signs of cross-reactivity in these applications should be treated with caution. However, the formal validation of an antibody for a specific application must be performed in an application- and context-specific manner as suggested by the working group1
The human protein atlas: Implications for human biology, drug development, and precision medicine
Get PDFThe Human Protein Atlas (HPA) is a Swedish-based program with the aim to map of all the human proteins in cells, tissues and organs using integration of various omics technologies, including genomics, transcriptomics, antibody-based imaging, mass spectrometry-based proteomics and systems biology. A Tissue Atlas was launch in 2015 (1) followed by a Cell Atlas in 2016 (2) and a Pathology Atlas in 2017 (3). This open access knowledge-base can be used to explore targets for next generation antibody therapeutics, as well as a discovery tool to find potential biomarkers and drug targets for disease (4,5). A focus has been to use a new drug development platform based on the affibody molecule developed in our group and use this concept for applications in cancer, autoimmune diseases and neurodegenerative diseases. Recently, we have set-up an animal cell factory using CHO cells with the aim to produce full-length proteins representing all the 2,000 secreted proteins encoded in human genome. The Human Protein Atlas program has already contributed to several thousands of publications in the field of human biology and disease and it was recently selected by the organization ELIXIR as a European core resource, due to its fundamental importance for a wider life science community. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.
Selected recent references:
1. Uhlen et al (2015) Science 347: 394
2. Thul et al (2017), Science 356:6340
3. Uhlen et al (2017) Science (August 18)
4. Uhlen et al (2016) Mol Systems Biol. 12: 862
5. Lee et al (2016) Cell Metabolism 12;24(1):172-8
Drug Repositioning for Effective Prostate Cancer Treatment
No full textDrug repositioning has gained attention from both academia and pharmaceutical companies as an auxiliary process to conventional drug discovery. Chemotherapeutic agents have notorious adverse effects that drastically reduce the life quality of cancer patients so drug repositioning is a promising strategy to identify non-cancer drugs which have anti-cancer activity as well as tolerable adverse effects for human health. There are various strategies for discovery and validation of repurposed drugs. In this review, 25 repurposed drug candidates are presented as result of different strategies, 15 of which are already under clinical investigation for treatment of prostate cancer (PCa). To date, zoledronic acid is the only repurposed, clinically used, and approved non-cancer drug for PCa. Anti-cancer activities of existing drugs presented in this review cover diverse and also known mechanisms such as inhibition of mTOR and VEGFR2 signaling, inhibition of PI3K/Akt signaling, COX and selective COX-2 inhibition, NF-kappa B inhibition, Wnt/beta - Catenin pathway inhibition, DNMT1 inhibition, and GSK-3 beta inhibition. In addition to monotherapy option, combination therapy with current anti-cancer drugs may also increase drug efficacy and reduce adverse effects. Thus, drug repositioning may become a key approach for drug discovery in terms of time- and cost-efficiency comparing to conventional drug discovery and development process
Principles of Systems Biology, No. 21
No full textThis month: relating single cells to populations (Cao/Packer, Wu/Altschuler, O'Brien, Friedman), an excess of ribosomes (Barkai), human pathology atlas (Uhlen), signatures of feedback (Rahi), and major genome redesign (Baumgart).</p
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