Group of Clinical Genomic Networks - Research

Department of  Molecular Systems Biology - CAS-MPG Partner Institute for Computational Biology

 

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Translational research represents a novel approach to life sciences with the specific goal to enhance and accelerate their applications in healthcare.

In particular, it focuses on multi-disciplinary collaboration among life sciences, exact sciences. and medicine, with the aim of advancing “molecular-based medicine”. In fact, it aims to enable physicians to leverage systems- and computational-biology approaches to allow early detection of complex diseases, increase efficiency in drug development and therapy testing, improve drug efficacy, and enable personalized medicine. Such an approach is necessary

·        to narrow the gap existing between clinical practice and basic research,

·        to accelerate the bidirectional flow of scientific discoveries into the clinic and of clinical findings into novel research directions, and

·        to realize the (crucial !) return on investment made by private and public institutions on life science basic research (as pursued for example by the NIH Clinical and Translational Science Awards network).

To fully realize this vision, translational research requires researchers and clinicians to have access to three types of information

(1)                                                      clinical information, including data contained in hospital systems and medical records, pathology reports and diagnostic labs, clinical trials systems and study participant questionnaires;

(2)                                                      biomolecular information, including genomics, proteomics, medical imaging and other high-throughput molecular and cellular research data;

(3)                                                      methods and tool to synergistically process the data described above.

 

Inflammation is one of the most ubiquitous phenomena occurring in reaction to a variety of events. Although selected by evolution as a defense mechanism, several problem occurring at this level lead to the development of diseases, as a consequence of this mechanism gone awry. This includes complex and chronic maladies such as cancers and autoimmune diseases.

Despite being a very broadly and long-dated studied topic, elucidating the components of the inflammatory response is a complex task and requires the analysis of a variety of information that must be studied at the systemic level, in order to encompass this complexity. The study of inflammation in this light, is indeed very novel, and we want to take adavantage of all the above mentioned information to elucidate it. In fact, thanks to the latest advances in biotechnology, it is nowadays possible to approach this problem with a two-fold systemic perspective: (i) genome-wide screens (systems view at different molecular levels transcriptional, post-transcriptional, translational, etc.); (ii) metagenomic analyses (human microbiome screens).

Our group contributes to this search applied to a systemic, degenerative autoimmune disease: rheumatoid arthritis. Our goal is to tackle this problem from all 3 points of view mentioned above.

 

 

 

Clinical Information:

-                       We have current and past collaborations with several important hospitals in Shanghai (Renji,  Longhua, GuangHua Hospital) to collect blood samples and clinical information from patients, before and after their treatment in the acute stage of RA, either with  variety of treatment. All studies are approved by hospitals’ ethical committees, and enrollment is performed according to the guidelines of ACR

 

 

 

 

 

Biomolecular Information:

-                       We process high-throughput proteomic, transcriptional, and post-transcriptional data from patients in the acute and post-acute phase of RA to infer the differential molecular effect of various treatments. Two pilot study are under way.

-                       To obtain detailed information on the evolution of the therapy we will conduct a parallel trial on animal models (rats) in collaboration with prof. Calza at the university of Bologna. This project has received funding form NSFC (Molecular Interaction Reconstruction of Rheumatoid Arthritis Therapies Using Clinical Data, 2011)

-                       We also plan to integrate microbiome data, thanks to our collaboration with prof. Zhao Liping from SJTU. Recently, we have shown that it is feasible to translate transcriptomic approaches to the analysis of microbiotica data (see Publications), this is the first step to integrate this additional layer to our molecular information analysis.

 

 

Methods and Tools

-                       We develop computational approaches to infer the association between clinical traits and genomic data, by designing and adapting ad-hoc statistics. A R package is available on Bioconductor and on our Software page

-                       We have built a molecular Map of the genes activated during RA, extracted from systemic, high throughput data, we use cell Designer and Cytoscape to characterize and easily export our results. You can access it here on Payao and download the Cytoscape modules in our Software page

-                       We have designed an algorithm for network reconstruction (NTW), the package is available on Bioconductor and on our Software page

-                       We are working on methods to associate different layers of molecular information to extrapolate properties that emerge from the interaction of such layers (i.e. transcriptional, post-transcriptional, translational). This project has received funding from the Sino-Swiss Science and Technology Cooperation Program (SSSTC, NSFC) for an application to stem cells (with the Institute of Electrical Engineering and the Integrated Systems Centre at  EPF Lausanne, Switzerland, Nano structured biochip development for stem cells monitoring, 2009). We will also work on this problem with Dr. Capobianco, thanks to the award of a Senior Scientist CAS Fellowship.