Research

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Our laboratory develops novel chemical tools to address important questions in biology and medicine with the aim of advancing our understanding of underlying mechanisms of human diseases. Currently, we are focusing on four major projects described below.

Project 1. Cancer Metabolic Reprogramming

Cancer metabolic reprogramming has been recently recognized as an important hallmark of cancer. It relies of the fact that cancer tissue possesses several important metabolic features, such as differential utilization of many essential metabolites. Cancer metabolic reprogramming is known to be required for malignant transformation, tumor development, invasion and metastasis. Its complex and dynamic nature has been recognized as one of the major challenges for effective cancer treatment. Therefore, a better understanding of metabolic dependencies in specific tumor types can provide a path for improved cancer treatments.

However, no efficient methodologies currently exist that allow noninvasive imaging and quantification of the uptake of essential metabolites in animal models of disease. Current strategies rely on either nuclear imaging techniques such as PET/SPECT/MRI or endpoint ex vivo quantification of metabolites (ex. MS). All of these methods have significant limitations, resulting in a lack of understanding of tumor metabolism and, consequently, poor predictability and efficacy of cancer therapies.

To address the unmet need for nutrient uptake imaging tools, we decided to develop a novel platform based on a combination of versatile “click” chemistry reactions with noninvasive, ultrasensitive bioluminescent imaging techniques. The applications of the novel platform are focused on tumor uptake measurements of glucose, fatty acids, amino acids, and nucleosides previously reported to play important roles in cancer metabolism. The results will lead to the generation of novel, effective treatments; therefore, this novel platform has high clinical applicability. Due to its versatile nature, application of the platform can be expended to studies of many other important human pathologies in which changes in metabolism play a key role, such as diabetes, neurodegenerative diseases, nonalcoholic steatohepatitis, and many others.

Please see the first demonstration of the platform recently published in Nature Methods (link)


Project 2. Development of new tools for probing mitochondrial activity in cells and living animals

In addition to studies of metabolite uptake, we are developing a novel set of tools for studies of mitochondrial functions, which are also known to play a central role in cancer metabolism. We will then use this novel tool to investigate the metabolic reprogramming of different types of cancers.

Mitochondria are essential organelles that provide eukaryotic cells with energy in the form of ATP generated through aerobic respiration. Electrons harvested from the oxidation of carbon food sources are utililized to pump protons across the inner membrane and store the energy in a proton gradient, which is then used to produce ATP through chemiosmosis. Aside from this critical role of ATP production, mitochondria are also important in multiple biological processes including cell differentiation, cell cycle control, cell survival, neuronal protection, and aging.

Mitochondrial dysfunction contributes to a remarkably wide range of human diseases including cancer, Alzheimer’s disease, Parkinson’s disease, diabetes, ischemia perfusion injury, steatohepatitis, sepsis, Huntington’s disease, and many others. As more information associating mitochondrial dysfunction with human diseases emerges, the development of new tools to interrogate this important organelle becomes increasingly important. Since it is not possible to mimic the complexity of these diseases in cell culture, many animal models that closely reflect these important human pathologies have recently been developed. Mitochondrial membrane potential (ΔΨm) is one of the main indicators of mitochondrial function but its direct role in many human pathologies still remain illusive due to  the lack of tools for the sensitive, noninvasive, longitudinal, and nonradioactive imaging of ΔΨm levels both in vitro and in vivo. This issue represents a major obstacle to our understanding of the role of this important function in a range of important human diseases, making the drug discovery process complex and less efficient. To address this unmet need, our lab develops novel chemical biology tools that allow noninvasive longitudinal imaging and quantification of ΔΨm levels both in vitro and in vivo. The approach is based on combination of sensitive bioluminescent imaging and a powerful “click” reaction chemical tool and has wide applicability in the field of biomedical research.


Project 3. Development of probes for image guided surgery in oncology

Surgery still plays a central role in modern cancer treatment. A complete curative microscopic tumor resection is the single most important prognostic factor for disease-free survival in virtually all solid tumors. However, there are very few tools currently available to surgeons that would help them to achieve this important goal. The vast majority of surgeons still have to use their naked eye and tactile information to determine the extent of local invasion in surrounding tissues during the operation and the final outcome of surgery is evaluated post-operatively by immune-histopathology. As a result, even in highly expert surgical procedures, incomplete microscopic resections may lead to cancer re-growth in 40-60% of cases for several types of cancer. Moreover, in most cases, significantly more healthy tissues and organs are removed during the surgery than it is really necessary. These compromised surgical procedures dramatically decrease the prognostic outcome of patients with cancer and significantly decrease their quality of life. Therefore, development of probes providing surgeons with clear visual feedback of cancer margins during the surgery would greatly enhance the ability to achieve complete curative treatment for many solid tumors and at the same time leave healthy tissues intact. One such probe has been recently developed for image guided surgery of ovarian cancer. 

One such probe has been recently developed for image guided surgery of ovarian cancer (link).

This technique is summarized in the video below (courtesy of Dr. Go van Dam)


Project 4. Novel tools to unravel enzymatic functions of gut microbiota

The gut microbiota plays a major role in human health and has been characterized as an extremely dynamic and chemically diverse community. Gut microbes significantly impact host physiology by influencing host homeostasis including metabolism, neurobiology, and immune function. The microbiome-produced enzymes play central role in regulation of many essential functions of gut microbiome. For example, bile salt hydrolase (BSH) is thought to play a central role in human health and is responsible for modulation of multiple host signaling pathways, bile detoxification, and gastrointestinal persistence of bacteria. Despite the importance of BAs in host health and disease, the underlying mechanisms by which the gut microbiota enzymes drive their composition and modification are largely unknown. Another important family of gut microbiota enzymes is nitroreductase (NTR) that is known to metabolize nitrosubstituted compounds and quinones using NADH or NADPH as reducing agents. They are important for the development of novel antibiotics being the main target for the treatment of infections caused by bacteria, e.g. Helicobacter pylori, Mycobacterium tuberculosis and by parasites, e.g. Giardia, Trypanosoma and Entamoeba. NTR enzymatic activity in gut microbiota is also linked to carcinogen production and etiology of colorectal cancer.

Estimation of enzymatic activity in the gastro-intestinal tract is very challenging given the unique chemical environment, variable distribution of the microbiota, and highly dynamic nature of the microbiota. Currently, no methods exist for noninvasive real-time evaluation of the BSH activity of the gut microbiota in its intact environment. The existing methods involve ex vivo evaluation of fecal samples, studies of isolated cultured bacteria (in vitro tests), and in silico methods. However, all of these approaches have significant drawbacks for assessment of the composition and function of the microbiota. For example, fecal samples represent only a small portion of the environmental, chemical and microbial complexity that can be found along the length of the GI tract, limiting our knowledge to a very small part of the microbiome contributing to host health. In addition, none of the common methods are practical for the analysis of intact fecal samples because these methods are associated with significant assay interference.

To address this unmet need, we developed a novel quantitative optical readout-based method that is bereft of these disadvantages. The design of the method is based on bioluminescence imaging (BLI) and caged-luciferin approach that relies on “caging” luciferin with a small chemical group. Here, we adopted this strategy to create a novel assay for non-invasive real-time imaging of NTR activity of gut microbiota (link). Several other imaging reagents are currently in the developmental pipeline such as probes for studies BSH activity.