Overview
The Gomes group develops mass-spectrometry (MS)-based strategies to elucidate the structure of intact proteins and their complexes within the cellular environment. Of great interest is to understand how protein structural deviations (e.g., posttranslational modifications, truncations, and mutations) and ligands (e.g., small molecule inhibitors, metals, and lipids) drive the activity, formation, and stability of functional protein assemblies. Our long-term goal is to understand the molecular basis of fundamental cellular processes to tackle important biological problems.
Native Top-Down Characterization of Proteins and their Complexes
While native MS provides unparalleled information on the architecture, stoichiometry, and binding partners of intact protein complexes and their modified forms (complexoforms), top-down proteomics enables in-depth characterization of intact monomeric proteins and their modified forms (proteoforms). Recently, these two powerful MS strategies have been combined in a single MS strategy “native top-down proteomics (nTDP)” to provide detailed structural information about proteoforms and their complexoforms. We are currently developing innovative nTDP strategies for the characterization of these macromolecules in mammalian cells.
Top-Down Analysis of Single Cells
Responses of subcellular populations are typically measured as an average of the signals of individual cells. But communication between individual cells can generate unique cell-to-cell information that cannot be obtained from the bulk analysis of cells due to the distinctive molecular compositions of each cell. Our group is currently developing innovative TDP strategies for the characterization of proteoforms in single mammalian cells.
Our MS workflows benefit significantly from the development of more efficient separation strategies for liquid-chromatography, capillary-electrophoresis, and ion-mobility, which serve to decrease sample complexity and increase MS detectability of intact proteoforms and complexoforms in the intracellular space.
Breast Cancer
In most breast cancer patients, estrogen receptor alpha (ER) plays a key role in signaling and transcription, as the genes it targets control cell growth and endocrine responses. As a result, most patients with ER-positive tumors receive endocrine therapy that targets the ER-estradiol cell growth. This approach often yields promising results initially and, occasionally, complete clinical responses. However, 30-40% of these cancers recur - sometimes after years of apparent indolence. Thus, resistance to endocrine therapy is a major cause of breast cancer mortality. Our group is currently developing nTDP approaches to investigate the hypothesis that the biological actions of estrogen and antiestrogen drugs in the development of metastatic breast tumors and drug resistance are regulated by ER proteoforms and complexoforms.
Breast cancer is a heterogeneous disease with diverse clinical behaviors and patient outcomes. The breast cancer’s heterogeneity gives rise to cells with different degrees of metastatic capability and drug resistance. We are currently developing innovative TDP strategies to evaluate the proteoform landscape of individual breast cancer cells.
Multiple Sclerosis
Multiple sclerosis is the most common progressive neurological disease in young adults worldwide. Although significant advances in therapy have been made, treatment choices still pose a significant biomedical challenge due to the lack of a basic understanding of disease progression mechanisms. The sphingosine-1-phosphate receptors (S1PRs) constitute a class of G-protein coupled receptors that show promise for the treatment of multiple sclerosis. This protein family is a target for lipid bioactive molecules such as lysophospholipids (LPs). We are currently developing nTDP strategies to characterize the S1PR1's higher order organizations and interactions with receptor modulators/lipids within the cells.