Proteomics provides an unbiased window on the workings of the cell, and can provide cues to functional protein complexes, biomarkers and potential therapeutic targets. Since mRNA expression does not correlate with protein expression, detailed, quantitative proteomics analysis is essential to understanding biological processes. Proteomics research requires thoughtful experimental design, protein sample preparation, cutting edge mass spectrometry, and bioinformatics analysis. Several funded programs provide training opportunities in proteomics discovery:
Proteomics of Hepatic Neoplasia: Identification of Therapeutic Targets and Biomarkers in a Synchronous Model System
Early stages of liver carcinogenesis in liver and liver regeneration are among the model systems currently being studied in our group, using a rat model system with synchronous development of cell types and progression to cancer. Preliminary data show an early appearance of markers for angiogenesis and metastasis, and indicate a major shift in cytoskeletal structure. Future studies combined with laser capture microdissection, as well as detailed analysis of experimental sera, may provide early molecular markers with diagnostic and therapeutic potential for human liver cancer. This is a collaboration with Dr. Phyllis Novikoff in the Department of Pathology.
Biodefense Proteomics Center--Target Discovery Proteomics in Waterborne Parasites
The Albert Einstein College of Medicine of Yeshiva University has been awarded a contract from the National Institute of Allergy and Infectious Diseases (NIAID) for identifying therapeutic targets in waterborne parasites by proteomics technologies. This center, under the leadership of Dr. George Orr, brings together Albert Einstein faculty with expertise in apicomplexan parasitology, proteomics and bioinformatics and includes Dr. Louis Weiss, Dr. Kami Kim, Dr. Ruth Hogue Angeletti, Dr. Fang Wang and Dr. Andras Fiser. These investigators will join to identify and validate potential targets, develop novel proteomic and bioinformatics methods to further biodefense and biomedical research efforts, and provide information and unique resources to advance selection of therapeutic targets and design of strategies for disease intervention.
Two waterborne apicomplexan protozoa, Toxoplasma gondii and Cryptosporidium parvum, are potential biological weapons.T. gondii, a ubiquitous parasite of mammals and birds, has long been recognized as an important pathogen of both immune competent and immunocompromised hosts. T.gondii infection during pregnancy can result in congenital toxoplasmosis with associated encephalitis and chorioretinitis. In addition to its effects on children, adults can become infected with T. gondii through water supplies or food. The major syndrome caused by C. parvum is diarrhea, which can last for several weeks and can cause dehydration and death. Like T. gondii, the oocysts of this organism are also environmentally resistant and water-borne outbreaks have been described.
This center will develop an integrated approach to identify and validate new therapeutic drug targets based upon (a) the unique cytoskeletal scaffold that is a defining feature of all Apicomplexa and (b) membrane-associated proteins. The apicomplexan cytoskeletal scaffold is a primary determinant of cell shape, and tethers functional protein assemblies in the cytosol and overlying membranes. Membrane proteins are positioned at the contact interface of parasites and their hosts and are involved in a diverse range of cellular functions including cell signaling/communication, nutrient and ion transport. We will use proteomics approaches to identify the proteins mediating inter- and intramolecular associations within the cytoskeletal complex as well as the overlying membranes. These macromolecular assemblies and membrane protein complexes, given their importance for cell function, will provide a rich source of novel targets for chemotherapy.
Microtubules are important components of the cytoskeleton and play crucial roles in a diverse array of cellular processes including morphogenesis, motility, organelle and vesicle trafficking, and chromosome segregation during mitosis. Microtubules also function as a scaffold for a large number of signaling proteins, and may serve to localize and regulate their activities. The Many possible combinations of tubulin heterdimers, defined by isotype composition and degree/type of posttranslational modifications occur in cells and tissues. Mass spectrometry based methods have been developed to analyze tubulin isotype composition and posttranslational modifications, as well as the associated macromolecular assemblies. Hydrogen/deuterium exchange studies coupled to mass spectrometry are also being used to analyze drug binding as well as tubulin dynamics and assembly. This is a collaboration with Dr. Susan B. Horwitz.
Protein Biomarkers in Head & Neck Squamous Cell Carcinoma
Head and neck squamous cell carcinoma (HNSCC) is the fifth most common malignancy worldwide, representing a major international health problem. These tumors constitute an anatomically heterogeneous group of neoplasms arising from the oral cavity, oropharynx, hypopharynx, larynx and nasopharynx. While all have in common an etiological association with tobacco and/or alcohol exposure, tumors originating from these different locations can exhibit varying behavior that is not predictable by histopathology of the primary tumor but is discernable by gene profiling. Thus, gene expression profiling of primary tumors using sophisticated cDNA microarray and global proteomic analyses will likely yield information that will predict aggressive growth, metastatic potential and responsiveness to several types of therapy. We are using proteomic analysis of primary HNSCC to identify proteins that will differentiate tumor types and be used to predict tumor behavior. While surgery can cure early stage disease, multimodality therapy is of limited success in later stage HNSCC. Thus, new diagnostics that can predict tumor behavior including response to therapy will have high clinical impact. Our goal is to identify specific changes in the proteome that predict tumor behavior and patient outcome in HNSCC, and to develop new, simple diagnostic tests that will enhance patient care and improve clinical outcome. This is a collaboration with Dr. Michael Prystowsky, chair of the Department of Pathology.