Date of Award

January 2026

Document Type

Thesis

Degree Name

Medical Doctor (MD)

Department

Medicine

First Advisor

Aaron M. Ring

Abstract

Multimodal single-cell tools have been instrumental in resolving cellular heterogeneity and identifying causal regulatory mechanisms. Despite comprehensive coverage of the transcriptome and substantial progress capturing other biomolecular layers, protein measurements lag significantly behind. Even the most advanced single-cell methods survey only a small fraction of the surfaceome and are hindered by binder availability and the resource-intensive requirements to generate large panels. Here, we introduce POETIC (Profiling of Epitopes and Transcriptome with Indexed-Cassettes), a modular platform designed to scale binder barcoding and protein quantification for multimodal single-cell analysis. POETIC leverages a single-batch bacterial expression system to generate comprehensive binder libraries that self-assemble with barcoded cassettes, enabling highly multiplexed profiling of epitopes and transcriptome across individual cells. The platform supports diverse binder formats, including VHHs, scFvs, and de novo designed miniproteins, as well as cassettes such as dCas9 and TrmA. We demonstrate its utility for validating binders experimentally and mapping reactivities against native conformational epitopes. POETIC’s low cost, rapid production time, and streamlined workflow makes it widely adoptable and positions it as a scalable platform for single-cell surfaceome profiling.

Comments

This thesis is restricted to Yale network users only. It will be made publicly available on 07/14/2028

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