Episode 1 - Dr. Stephanie Gaglione: Scaling TCR–Antigen Mapping from Sequence to Function
Availabe at Oxford podcast, iTune and Spotify
About this episode
In this first episode of Immunity by Design, I speak with Dr Stephanie Gaglione about a central challenge in immunology: how to map T cell receptors (TCRs) to their target antigens at scale.
Despite major advances in sequencing, our ability to link TCR sequences to antigen specificity remains extremely limited. This gap constrains both mechanistic understanding and the development of predictive models.
We discuss a recent study introducing TCRAFT, a scalable and cost-effective approach for synthesising and screening thousands of TCRs, enabling large-scale mapping of antigen reactivity and opening new avenues for data-driven immunology.
Key themes
Why mapping TCRs to antigens remains a fundamental bottleneck in immunology
The limitations of existing screening approaches (one-vs-many vs many-vs-many)
TCRAFT: a modular and scalable strategy for reconstructing large TCR libraries
Integrating synthesis with high-throughput screening (RAPTR) to enable many-to-many mapping
Linking antigen specificity to transcriptional phenotype
Implications for computational modelling, immunotherapy, and data generation
From sequence to function: the core problem
A recurring theme in the discussion is the disconnect between data abundance and functional understanding.
While high-throughput sequencing allows us to capture vast numbers of TCR sequences, translating this information into antigen specificity remains extremely challenging due to:
The enormous diversity of TCRs (up to ~10⁸ per individual)
The combinatorial complexity of antigen space
The lack of scalable experimental systems to map interactions
As highlighted in the study, existing datasets remain sparse and biased, limiting both experimental insight and computational progress.
What this study changes
The work introduces a complete workflow that connects:
TCR sequencing → synthesis → functional screening → antigen mapping → phenotype
At its core is TCRAFT (TCR Rapid Assembly for Functional Testing), a method that enables:
Rapid pooled synthesis of thousands of TCRs
Preservation of α/β chain pairing
Dramatic reduction in cost (scalable to < $1 per TCR)
High-fidelity assembly suitable for downstream screening
This is integrated with RAPTR, allowing library-on-library screening of TCRs against large antigen panels.
Together, these advances enable, for the first time, practical many-to-many mapping at scale.
Key biological insights
Applying this framework to vitiligo, the study reveals that:
Autoreactive T cells show clonal expansion
Their transcriptional profiles resemble melanoma-reactive T cells
This suggests shared functional programs across autoimmunity and cancer, providing new insight into disease mechanisms and therapeutic opportunities.
Episode structure
Past — Why TCR–antigen mapping has remained intractable despite sequencing advances
Present — How TCRAFT and RAPTR enable scalable synthesis and screening
Future — What this means for data-driven immunology, modelling, and immunotherapy
About the guest
Dr Stephanie Gaglione is a postdoctoral researcher at the Gladstone Institutes (UCSF), working in the Marson lab. She completed her PhD at MIT in the Birnbaum lab, where she led the development of TCRAFT.
With a background in chemical engineering and immunology, her work focuses on building experimental systems to decode T cell specificity and enable scalable, data-driven approaches to immune biology.
Links and references
Paper: Scalable TCR synthesis and screening enable antigen reactivity mapping in vitiligo
Podcast: Here