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1. Protein microarray technology development and application
Fueled by the ever-growing DNA sequence information, the field of proteomics has become one of the most important disciplines to characterize protein function and activity and provide insight into functional networks on a global scale. Because of the power of high-throughput, miniaturization, and parallel analysis, protein microarray is one of the most promising technologies for proteomics study (ABBS, 2011; Frontiers in Biology, 2012; Curr Pharm Des, 2013). Our laboratory is focusing on protein microarray technology development and its applications in biological and clinical studies. Specifically, our current studies include:

Proteome microarray. We've already setup a variety of proteome microarray platforms, such as E.coli proteome microarray (>4,200 proteins) (Nature methods, 2008) and yeast proteome microarray (>5,800 proteins) (Molecular systems biology, 2009). We are de novo constructing other proteome microarrays. Based on these microarrays, we are perfoming systems biology. The microarray platforms are and will be used for serum biomarker screening, host-pathogen interaction study, protein post translational modification study(e.g., such as glycosylation and acetylation) (FEBS J. 2014; ABBS, 2014), protein-protein interaction study (Molecular cellular proteomics, 2013), protein-DNA interaction study, and etc.

Lectin microarray. Glycosylation is among the most complex posttranslational modifications with an extremely high level of diversity that has made it refractory to high-throughput analyses. Despite its resistance to high-throughput techniques, glycosylation is important in many critical cellular processes that necessitate a productive approach to their analysis. To facilitate studies in glycosylation, we have developed a most comprehensive lectin microarray with about 91 lectins for defining cell surface glycan signatures (Glycobiology, 2008; COMB CHEM HIGH T SCR, 2011). By using this lectin microarray, we have successfully identified novel lectin biomarkers for for sperm (Clinical proteomics, 2014) and cancer metastasis (Breast cancer research, 2015 in press). Currently, we are trying to add about 90 human lectins and lectin like proteins to the lectin microarrays and make this platform more human relevant.

Cutting edge microarray related technology development. About 2,500 years ago, the Chinese Saint Confucius said "If you want to do a good job, please sharpen your tool first". Technology development is one of the major driving forces for biological and clinical researches. Based on our microarray platforms, we are developing several cutting edge technologies, such as on-chip protein microarray fabrication (Nature biotechnology, 2006), high density antibody microarray, e.g. 1000~30000 antibodies on a single microarray for convenient global protein level monitoring and comparison, microarray based technologies for global PTM enzyme and key regulator discovery, and microarray system for >100 plex nucleic acid detection (Lab on a chip, 2011; Analytcial chemistry, 2014).
2. Mycobacterium tuberculosis systems biology
the outline here



Mycobacterium tuberculosis (MTB), the etiological agent of tuberculosis and one of the most successful human pathogens, caused 8.6 million incident cases of tuberculosis (TB) and claimed 1.3 million lives in 2012, in spite of century-long efforts to combat it. New drugs, vaccines and diagnostic tests for TB are clearly needed, but their development is hampered by poor understanding of the basic biology of this pathogen. Global studies on MTB at the systems level rather than traditional one gene or one protein approaches should lead to breakthroughs, however, new tools with which to investigate the basic biology of MTB and its interactions with the host at the systems level are urgently needed.

To address this problem, we have just constructed a functional MTB proteome microarray covering 95% of the proteome, and a complete ORFome library (Cell reports, 2014). We demonstrate the broad applicability of the microarray by investigating global protein-protein interactions, small molecule-protein binding, and serum biomarker discovery, identifying 59 PknG-interacting proteins, 30 c-di-GMP binding proteins, and 14 MTB proteins that together differentiate between TB patients with active disease and recovered individuals. Results suggest that the MTB rhamnose pathway is likely regulated by both the serine/threonine kinase PknG and c-di-GMP. This new resource has potential to generate greater understanding of key biological processes in the pathogenesis of tuberculosis, possibly leading to new therapies for the treatment of this ancient disease.


Based on this powerful platform, we are now trying to tackle Mtb on a systems level. Several systems biology projects are now ongoing in our laboratory, e.g., global host-pathogen protein-protein interaction, phosphorylation network, pupylation regulation network, drug mechanism, as well as serum biomarker identification.



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Tao Lab, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University
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