Shreyas Dahotre

BME PhD Proposal Presentation

July 24th, 2019, 11 am

Marcus Nanotechnology Building, Rm 1116

Advisor: Gabe Kwong

Committee: James Dahlman (GT/Emory BME), Yonggang Ke (GT/Emory BME), Julie Champion (GT ChBE), John Altman (Emory Microbiology and Immunology)

Title: Programmable DNA barcoded platforms to monitor and modulate T cell responses

Abstract: Increasing our ability to broadly monitor T cell responses at depth throughout the course of a disease has provided clinicians with valuable new insights. For example, technologies that enable tracking of clonal expansion and contraction of T cells have revealed useful clinical biomarkers such as T cell counts for assessing disease burden and progression. Furthermore, the ability to manipulate these T cell responses in vivo has enabled new therapeutic approaches, including transformative immunotherapies such as immune checkpoint blockade that have led to potent and durable responses for chronic diseases such as infection and cancer. While these methods have revolutionized immunotherapy, detecting and modifying disease-specific T cells is still challenging because antigen-specific subsets are found at low frequency and current platforms such as flow cytometry lack the capacity to monitor more than a few clones at one time. By contrast, emerging analytical and therapeutic platforms based on DNA and RNA leverage the programmable properties of nucleic acids to enable ultrasensitive, multiplexed detection and selective gene modulation. In this thesis, I will establish a framework whereby programmable platforms based on nucleic acids are used to detect, isolate, and modulate T cell populations, providing scalable approaches that are not limited by biophysical constraints. In Aim 1, I will build a library of DNA barcoded peptide-MHC tetramers for multiplexed monitoring of viral-specific T cells during infection using digital PCR. To provide the ability to isolate these T cell subsets, in Aim 2, I will design and implement an extensible library of programmable DNA gates, comprising dynamic and orthogonal DNA strand displacement reactions, for sorting multiple T cell populations from a single sample. In Aim 3, to modulate the activity of specific T cell subsets, I will construct pMHC-targeted polyplexes as gene modulators to improve antiviral T cell memory responses during infection. Completion of these aims will provide new programmable technologies to track and modulate T cell responses to guide the development of a new generation of immunotherapies.