Yu laboratory interests are to develop new high-throughput proteomics technology to learn the mechanism and find biomarkers for the early diagnostics, prognosis and therapeutic treatment of different diseases.
1. Protein microarray technology and functional proteomics discovery
Protein microarrays have often been applied in basic science and translational research. Benefitting from their high throughput capability, protein microarrays are often used to measure protein interactions where they have aided in the unbiased (i.e., concentration-independent) discovery of target proteins regulated by different molecules (i.e. DNA, protein, compounds), and allowed the study of specific protein families or signaling pa
thways. Protein microarrays have helped address routine challenges in other proteomics technologies, including low protein abundance, complicated assay procedures, difficulty in modulating assay environment, low sensitivity, and low throughput screen of targets-of-interest
We are working on the development high-throughput and high-sensitive protein microarray technologies that facilitate the protein function and translational studies. The human (14K), tuberculosis (4K), Vibro Cholera and panviral proteome microarrays (1K, ~20 viruses) by NAPPA (Nucleic Acid Programmable Protein Arrays) technology (Figure 1) have been available and can be used in protein interactions, post-translational modifications, drug discovery immune profiling and biomarker discovery studies.
2. Translational research
The human immune system responds to exogenous pathogens (e.g., bacteria, parasites, viruses) as well as endogenous anomalies that pose a threat to the body’s natural homeostasis. An inadequate immune response or disorders of the immune system may result in disease, including the manifestation of infectious diseases; the destruction of healthy endogenous cells, tissues, or organs in autoimmune disorders; or the inability to control neoplastic cell proliferation and growth during the progression and development of cancer (Figure 1 and 2). Our research is to investigate the changes of antibody immune system by exogenous and endogenous factors and to find antibody biomarkers aiding the early diagnostics, treatment and prognosis of cancer, autoimmune and infectious diseases.
3. High-throughput cloning, construction of gene repository
A comprehensive collection of fully sequence-verified open reading frames (ORFs) clone repositories is invaluable to basic biology, drug discovery and diagnostic reagent development. Our interests are to construct a high-throughput gene-cloning platform, build human and pathogen gene plasmids collections that support functional and translational proteomics studies in China.
1. Xiaofang Bian, Garrick Wallstrom, Amy Davis, Jin Park, Andrea Throoph, Jason Steel, Xiaobo Yu, Clive Wasserfall, Desmond Schatz, Mark Atkinson, Ji Qiu, Joshua LaBaer. Immunoproteomic Profiling of Anti-Viral Antibodies in New-Onset Type 1 Diabetes Using Protein Arrays, Diabetes, in press.
2. Xiaofang Bian, Peter Wiktor, Peter Kahn, Al Brunner, Amritpal Khela, Kailash Karthikeyan, Kristi Barker, Xiaobo Yu, Mitch Magee, Clive H. Wasserfall, David Gibson, Madeleine E Rooney, Ji Qiu,*, Joshua LaBaer, (2015) Anti-Viral Antibody Profiling by High Density Protein Arrays. Proteomics, DOI: 10.1002/pmic.201400612.
3. Xiaobo Yu, Kimberly B. Decker, Kristi Baker, M. Ramona Neunuebel, Morgan Graves, Nathan Westcott, Howard Hang, Joshua LaBaer, Ji Qiu, Matthias P. Machner. (2015) Host-Pathogen Interaction Profiling Using Self-Assembling Human Protein Arrays. J Proteome Res., 14(4):1920-36.
4. Xiaobo Yu and Joshua LaBaer (2015) High-throughput identification of proteins with AMPylation using self-assembled human protein microarrays. Nature Protocols, 10(5):756-67.
5. Xiaobo Yu, Poulami Talukder, Chandrabali Bhattacharya, Nour Eddine Fahmi, Jamie A. Lines, Larisa M. Dedkova, Joshua LaBaer, Sidney M. Hecht, Shengxi Chen. Incorporation of phenylalanine derivatives into human CD4 protein to increase the binding ability with HIV gp120 protein. Bioorganic & Medicinal Chemistry Letters, 2014 24(24): 5699-703.
6. Andrew R. Woolery, Xiaobo Yu, Joshua LaBaer, Kim Orth* (2014) Varied cellular consequences of Rac inhibition by VopS AMPylation. J Biol Chem. 2014 289(47):32977-88.
7. Rafael Prados-Rosales, Leandro J. Carre?o, Ana Batista-Gonzalez, Andres Baena, Manjunatha M. Venkataswamy Jiayong Xu, Xiaobo Yu, Garrick Wallstrom, D. Mitchell Magee, Joshua LaBaer, Jacqueline M. Achkar, William R. Jacobs Jr, John Chan, Steven A. Porcelli and Arturo Casadevall (2014) Immunization with Mycobacterial membrane vesicles protect against Mycobacterium tuberculosis in mice. mBio, 5(5):e01921-14.
8. Wang, Wei, Yin, Linliang, Gonzalez, Laura, Wang, Shaopeng, Yu, Xiaobo, Eaton, Seron, Zhang, Shengtao, Chen, Hong-Yuan; LaBaer, Joshua; Tao, Nongjian (2014) Label-free Study of Drug-Receptor Binding Kinetics, Receptor Expression Levels and Drug Resistance in Single Cells. Scientific Reports, 4:6609.
9. Xiaobo Yu, Andrew R. Woolery, Phi Luong, Yi Heng Hao, Markus Gramme, Nathan Westcott, Jin Park, Jie Wang, Xiaofang Bian, Gokhan Demirkan, Howard C. Hang, Kim Orth, Joshua LaBaer (2014) Click chemistry-based detection of global pathogen-host AMPylation on self-assembled human protein microarrays. Mol. Cell. Proteomics, 13(11):3164-76. (Highlight from the journal)
10. Xiaobo Yu, Xiaofang Bian, Andrea Throop, Lusheng Song, Lerys Del Moral, Jin Park, Catherine Seiler, Michael Fiacco, Jason Steel, Preston Hunter, Justin Saul, Jie Wang, Ji Qiu, James M. Pipas, Joshua LaBaer (2014) Exploration of Panviral Proteome: High-Throughput Cloning and Functional Implications in Virus-Host Interactions. Theranostics, 4(8): 808-822. (Highlight by the editor)
11. Xiaobo Yu, Michael Hartmann, Quan Wang, Oliver Poetz, Nicole Schneiderhan-Marra, Dieter Stoll, Cornelia Kazmaier, Thomas O. Joos (2010) μFBI - a microfluidic bead-based immunoassay for multiplexed detection of proteins from a ul-sample volume. PLos One. 5(10): e13125.
12. Xiaobo Yu, Zhe Yu, Li Liu, Jun Chi, Huanhuan Han, Ying Liu, Wei He, Qihong Sun, Jianen Gao, Danke Xu (2010) High-throughput Antibody Generation using Multiplexed Immunization and Immunogen Array Analysis?. J Biomol Screen. 15: 1260-1267.
13. Xiaobo Yu, Nicole Schneiderhan-Marra, Thomas O. Joos (2010) Protein microarrays for personalized medicine. Clin. Chem., 56(3):376-87.
14. Li-Tang Yan and Xiaobo Yu (2009) Enhanced Permeability of Charged Dendrimers across Tense Lipid Bilayer Membranes. ACS Nano, 3 (8), 2171-2176.
15. Dawei Xu, Xiaobo Yu, Zhihong Liu, Wei He and Zhenqiu Ma (2005) Label-free electrochemical detection for aptamer-based array electrodes. Anal. Chem. 77(16), 5107-5113. (One of the Most-Accessed Articles, July-September 2005)