Characterization of Complex Immune Cell Phenotypes and Spatial Interactions in the Tumor Immune Microenvironment Using Imaging Mass Cytometry
The Merchant Laboratory investigates the mechanism for disease progression and treatment resistance in diffuse large B-cell lymphomas, Hodgkin's lymphomas, multiple myeloma and myelofibrosis by characterizing the composition and complexity as well as spatial interactions among tumor and immune cells in the tumor microenvironment using imaging mass cytometry (IMC), a multiplex imaging platform that allows concurrent detection of 40+ markers and enables high-dimensional, single-cell analysis with spatial information of the different cell types at sub-cellular resolution.
The advancement of mass cytometry using Fluidigm's Helios (CyTOF) platform enables the detection of a large number of surface markers, transcription factors and intracellular cytokines without the need for compensation due to spectral overlap as with traditional flow cytometry. In the Merchant Lab, immune system monitoring of leukemia and lymphoma patients enrolled in clinical trials is performed using mass cytometry and a variety of other techniques. We are able to characterize and track the makeup and functionality of the patients' immune systems, with resolution down to a single cell level, before, during and after treatment/intervention. This information provides critical insights and may enable us to pinpoint key factors differentiating responders and non-responders.
This platform is rapidly expanding—increasing the number of possible targets—and can be applied to many other studies involving the identification, quantification or characterization of a heterogenous cell population. Additional complementary experiments including single-cell RNA sequencing, proteomics/metabolomics profiling as well as in vitro cytotoxic killing assays and culturing of tumors in the presence of small molecule immune checkpoint inhibitors give a more complete picture and a deeper understanding of what is taking place inside the body. The Merchant Lab hopes to use the results to identify patients who have biomarkers of poor prognosis that may require alternative or additional interventions or monitoring and ultimately enable doctors to provide less toxic, more targeted treatment strategies.
Research in the Merchant Laboratory is focused on understanding how signaling pathways critical to the establishment and maintenance of normal hematopoiesis and hematopoietic stem cell function become deregulated in disease states such as myeloid proliferative diseases or leukemia. Our research has established that Hedgehog (Hh) signaling is present in most blood cells, and we were the first to report that the Hedgehog transcription factors Gli1, Gli2 and Gli3 are required for normal hematopoiesis and stem cell self-renewal1,2. We were also the first group to demonstrate that primary cilia are present on blood cells in humans and mice, where they mediate Hh signaling3. Previous work using knockouts of SMO, the upstream activator of Hh signaling, had led some to conclude that Hh signaling was not involved in hematopoiesis4. While the complete role of Hh signaling in hematopoiesis is not fully understood, our work has significantly clarified the controversy surrounding this topic.
In acute myeloid leukemia (AML), a central question has been the apparent paradox between high levels of Hedgehog pathway activation and the relative insensitivity of primary AML samples to Hedgehog pathway (Smoothened (SMO)) inhibitors. In previously presented work, now under review for publication, we show that in most AML, the hedgehog pathway is activated independently of SMO primarily through loss of GLI3 repressor5. This work is the first description of GLI3R as a tumor suppressor in any cancer and is of critical importance because all Hedgehog pathway inhibitors currently in clinical development target SMO. Our findings provide a mechanism for the widespread clinical resistance to SMO inhibitors seen in a variety of tumors and a potential biomarker for selection of patients likely to response to SMO inhibitors.
Currently, the Merchant Lab has two projects in the lab focused on Hedgehog signaling. The first is focused on understanding how loss of Gli2 and Gli3 disrupts stem cell function in normal hematopoietic stem cells. The aim of the second project is to understand how mutant JAK/STAT (JAK2V617F) signaling interacts with Hh/SMO activity in myeloproliferative neoplasms. We believe that SMO inhibitors, such as glasdegib, have enormous therapeutic potential for patients with myeloproliferative diseases and leukemia.
Statistical Learning Algorithm Development in the Context of Lymphomas
Currently, the Merchant Lab is constructing machine-learning methodologies that learn from both single-cell sequencing technology and in situ spatial interactions designed to inform and challenge the current understanding of lymphoma cancers.
Our aim is to generalize spatial genomic models and identify pan-cancer and disease specific features that motivate targetable intervention therapy.
Contact the Merchant Lab
127 S. San Vicente Blvd.
Los Angeles, CA 90048