BioGPS has become the valuable resource that it is because of the contributions from our wonderful user community. Thank you for contributing plugins, suggestions, and ideas–all of which have improved BioGPS for everyone. In order to celebrate the contributions of BioGPS users to the scientific research community, this series will feature publications and articles generated by BioGPS users. We sincerely hope you will join us in celebrating the fascinating work that YOU do.

This week, we will feature an article by collaborating researchers from three institutions across the US: Multi-omic landscape of rheumatoid arthritis: re-evaluation of drug adverse effects by Paolo Tieri, XiaoYuan Zhou, Lisha Zhu, and Christine Nardini.

Dr. Paolo Tieri and Dr. Christine Nardini kindly answered our inquiries for this series.

  1. Who is the team behind the work that was published in Multi-omic landscape of rheumatoid arthritis: re-evaluation of drug adverse effects?.
    This group is the result of the synergies created with two successful exchange programs: one funded by the Chinese Academy of Sciences (CAS): young researchers fellowship awarded to Paolo Tieri, investigator at the Consiglio Nazionale delle Ricerche (CNR), Rome, Italy, to join Christine Nardini, principal investigator at PICB MPG-CAS institute. The group at PICB is formed by two senior scientists (a bioinformatician, Yuanhua Liu, and a biologist, Valentina Devescovi) and several PhD students (two participated to this project: XiaoYuan Zhou and Lisha Zhu). The second project is a EU funded program for the mobility of researchers (Marie Curie), which permitted two-ways exchanges between the same institutions..

  3. What inspired the work published in Multi-omic landscape of rheumatoid arthritis: re-evaluation of drug adverse effects?
    Christine Nardini’s group working at CAS has developed a strong expertise on rheumatoid arthritis in the past seven years, due to the multifaceted aspects of the disease and to peculiar characteristics of interest that notably include: the possibility to treat the disease with acupuncture (according to the WHO meta-analyses on clinical studies); the involvement of the gut intestinal (GI) microbiome in the etiology and development of the malady; the complex inflammatory and (auto)immune response developed.

    Paolo Tieri’s long dated expertise in the design and analysis of immuno-related complex networks was fundamental in developing a multi-omic network used to simulate complex responses to novel drugs.


  5. Please provide a brief summary of the findings reported in your article, Multi-omic landscape of rheumatoid arthritis: re-evaluation of drug adverse effects.
    With such integrative effort we were able to provide a comprehensive molecular map of rheumatoid arthritis, a multifaceted disease which complexity requires a systemic approach. Our multi-omic landscape provides a reliable platform for in silico hypothesis testing or recommendation on novel therapies, recollecting in a single analytical picture known, yet complex, information like the adverse/side effects of MTX, the identification of GRB2 as a robust potential new target, and the warning on the usage of IRAK4-inhibitors.

  7. How did the team learn about BioGPS?
    As bioinformaticians, we got aware of BioGPS from the publication in 2009, since then we often utilized its annotation services to get more integrative views of many genes. After that, Paolo has also been directly in touch with Andrew Su (back in 2012) to support BioGPS in getting new funding from NIH.

  9. How did your team utilize BioGPS in this research?
    We used it to investigate in deep the content of different data source for RA-related genome-wide association studies in a systems biology perspective, also in parallel with other major databases.

  11. What are some future directions for the team behind this research?
    Taking steps from this effort, we are setting up a larger project consortium to be funded to the extent of validating molecular biomarkers in early RA detection as well as novel RA pharmacological targets, by integrating multiscale and complementary modeling approaches.

Thanks again to Dr. Paolo Tieri and Dr. Christine Nardini for taking the time to answer our questions (and a special thanks to Dr. Tieri for supporting BioGPS). Click here to read their fascinating article. Have a look because these awesome researchers have made their compelling research open access–so you can read the whole exciting article for free!

Used BioGPS and cited it in your publication? Let us know! We would love to feature YOUR work, no matter how long ago it was published. BioGPS Featured Article Series only started recently, but we know your contributions to science is ongoing.