Membrane proteins play essential roles in driving intra- and inter-cellular function that are heavily influenced by the surrounding protein microenvironments they inherently experience. This inherent protein proximity is not only crucial for impacting how proteins function but also informs our ability to effectively target/modulate cell surface environments for therapeutic benefit.  This talk will describe the development of a novel light-mediated catalytic microenvironment labeling toolbox for identifying proximal protein environments within intra and intercellular regions as well as downstream applications of the technology.

Spatial profiling technologies like hyper-plex immunostaining in tissue, spatial transcriptomics have the potential to enable a multi-factorial, multi-modal characterization of the tissue microenvironment. Objective scoring methods inspired by recent advances in statistics and machine learning can serve to aid the interpretation of these datasets, as well as their integration with other, companion data like genomics. In this talk, we will discuss elements of spatial profiling from multiple studies as well as paradigms from statistics and machine learning in the context of these problems.

Here, we’ll describe a new technology called Slide-tags in which single nuclei within an intact tissue section are "tagged" with spatial barcode oligonucleotides derived from DNA-barcoded beads with known positions. We adapted Slide-tags for T cell receptor sequencing to spatially map T cell clonality in single nuclei. We also implemented Slide-tags to quantify genetic alterations at single-nucleus spatial resolution by targeted sequencing of single-nucleotide variations captured in the transcriptome. Slide-tags offers a universal platform for importing established single cell measurements of gene expression, epigenetic regulation, and antibody-based quantification into the spatial genomics repertoire.

Current approaches to treating autoimmune disease and attenuating immunogenicity of therapeutics broadly suppress the immune system. These approaches leave patients vulnerable to infection, cancer, and metabolic dysregulation. Further, such approaches only modify symptoms rather than treat underlying disease. Tolerizing patients to specific antigens is a holy-grail challenge that can displace systemic immunosuppression. GRObio’s ProGly approach to immunotolerization enables reversal of autoimmune disease and elimination of anti-drug antibodies without systemic immunosuppression.

Cytokines are very potent and can steer many related unwanted effects. By concentrating treatment directly in the tumor environment, the safety profile significantly improves, and cytokines can change this micro-environment by getting efficient activation of tumor cell destruction. Deka has designed novel immunotherapies targeted to the tumor environment using known receptors like EGFR, HER2, and VEGFR. Labelling studies are illustrative for targeted dosing and better drug distribution and kinetics.

We have developed synthetic cancer-targeting gene circuits that specifically target cancer cells. Once the circuits enter cells, they will sense the activity of several cancer-associated transcription factors and get activated in tumor cells to trigger tumor-localized combinatorial immunotherapy. Circuits mediate robust therapeutic efficacy in ovarian cancer mouse models. This platform can be adjusted to treat multiple cancer types and can potentially trigger genetically encodable immunomodulators as therapeutic outputs.

Bispecific antibodies (bsAbs) used in cancer treatments require functional T cells; however, in patients, T cells are often damaged and depleted. Allogeneic T cells from healthy donors could enhance bsAb treatment, but they carry a high risk of GvHD. To address this, we developed Allogeneic-Engineered-Decoupled (AED) T cells. AED T cells can be activated via bsAb, but do not respond to host antigens, eliminating the risk of GvHD. This combination approach of healthy and safe donor T cells with bsAbs could lead to development of new and more effective cancer therapies.

In this presentation, I will describe our work on engineering chimeric antigen receptor circuits and biomaterials in T cells and NK cells to improve their tumor-targeting specificity.