Interdisciplinary PhD in Structural and Computational Biology and Quantitative Biosciences

Ying Ge

Professor, Cell and Regenerative Biology Lab Website 265-4744

8551 Wi Institute Medical Research
1111 Highland Ave
Madison, WI 53705

Cardiovascular Systems Biology

Our research aims to understand the molecular and cellular mechanisms underlying cardiovascular diseases via systems biology approaches featuring cutting-edge high-resolution mass spectrometry (MS)-based comparative proteomics and metabolomics in conjunction with functional studies. Our research is highly interdisciplinary within the interface of chemistry, biology, and medicine. Success in my proposed research will advance our understanding of the molecular basis of diseases and foster the development of new strategies for early diagnosis, prevention and better treatment of cardiovascular diseases. It is our belief that in order to make significant impact in molecular medicine, we need to combine technological advances with functional studies and bridge the silos between chemical and biological sciences as well as basic and translational/clinical research.

Cardiovascular disease is the leading cause of morbidity and mortality in developed countries and is reaching epidemic proportions. Transformative insights from a holistic approach at the systems level have great potential to elucidate disease mechanisms and to develop new therapeutic treatments. Proteins and metabolites are important molecular entities of the cell downstream of genes. Hence in the post genomic era, proteomics and metabolomics (the large-scale global analysis of proteins and metabolites in a cell, organism, tissue, and biofluid), are essential for deciphering how molecules interact as a system and for understanding the functions of cellular systems in health and disease. However, there are tremendous challenges in proteomics and metabolomics due to the extreme complexity and dynamic nature of the proteome and metabolome.

To address such challenges, we are developing novel ultra high-resolution MS-based top-down comparative proteomics and metabolomics platforms for systems biology studies with high efficiency, specificity, sensitivity, and reproducibility. Specifically we are focusing on the following technology developments:

1) Top-down proteomics: We are establishing a top-down disease proteomics platform to provide a comprehensive tool for separation, detection, identification, quantitation and characterization of intact proteins extracted from tissue samples to reveal all disease-related changes in protein expression and post-translational modifications (PTMs) with high efficiency and reproducibility. Particularly, we are developing novel technologies to address the current challenges in top-down proteomics including protein solubility, proteome complexity, and dynamic range. [Read More]

2) Nanoproteomics: Combining the advances in nanotechnology and proteomics, we are developing “smart” antibody-like multivalent nanomaterials to enrich low abundance proteins or PTMs.  A current focus is to develop multivalent nanoparticle reagents for capturing phosphoproteins globally out of human proteome followed by top-down MS analysis of intact phosphoproteins.

3) Metabolomics: We are establishing an integrated ultra high-resolution MS-based platform for rapid, sensitive, reproducible detection and accurate quantification of diverse metabolites over a wide range of concentrations in a high-throughput and automatic fashion.

We then employ these technology platforms to study heart failure in conjunction with functional assays.  Currently we are focused on two major directions:

i) Cardiac myofilaments:  We are testing the hypothesis that both extrinsic and intrinsic stresses trigger the molecular signaling processes that could result in altered modifications to myofilaments leading to contractile dysfunction and eventually failure. We employ an unbiased top-down proteomics analysis of the myofilaments to globally detect the changes in protein modifications, identify which sites are modified or altered, and elucidate how these alterations act in concert during the transition to the heart failure.  We then mechanistically link the proteomic changes to in vitro, ex vivo, and in vivo cardiac function to assess synergistic changes of myofilaments in regulating contractility during left ventricular remodeling to heart failure using large animal (swine) models and human clinical studies.

ii) Cardiac regeneration: We are testing the hypothesis that transplanted stem cells can trigger the molecular signaling pathways which would protect the native cardiomyocytes from apoptosis and reverse pathological left ventricular remodeling. We aim to gain a holistic view of the molecular signaling pathways underlying cardiac regeneration in response to stem cell therapy through novel systems biology approaches.

Areas of Expertise

  • Biophysical Chemistry
  • Protein Folding Design & Function
  • Synthetic & Systems Biology