T cells typically recognize their ligands using a defined cell biology – the scanning of their membrane microvilli to palpate their environment – while that same membrane scaffolds T cell receptors (TCRs) that can signal upon ligand binding. Chimeric antigen receptors (CARs) present both a therapeutic promise as well as a tractable means to study the interplay between receptor affinity, microvillar dynamics and T cell function. CARs are often built using single-chain variable fragments (scFvs) with far greater affinity than that of natural TCRs. We used high resolution lattice lightsheet (LLS) and total internal reflection fluorescence (TIRF) imaging to visualize microvillar scanning in the context of variations in CAR design. This demonstrated that conventional CARs hyper-stabilized microvillar contacts relative to TCRs. Reducing the affinity and/or avidity of binding brought synapse microvillar dynamics into natural ranges, normalized synapse resolution and improved downstream effector function. This work highlights the importance of understanding the underlying cell biology when designing receptors for optimal antigen engagement.

T cells typically recognize their ligands using a defined cell biology—the scanning of their membrane microvilli (MV) to palpate their environment—while that same membrane scaffolds T cell receptors (TCRs) that can signal upon ligand binding. Chimeric antigen receptors (CARs) present both a therapeutic promise and a tractable means to study the interplay between receptor affinity, MV dynamics and T cell function. CARs are often built using single-chain variable fragments (scFvs) with far greater affinity than that of natural TCRs. We used high-resolution lattice lightsheet (LLS) and total internal reflection fluorescence (TIRF) imaging to visualize MV scanning in the context of variations in CAR design. This demonstrated that conventional CARs hyper-stabilized microvillar contacts relative to TCRs. Reducing receptor affinity, antigen density, and/or multiplicity of receptor binding sites normalized microvillar dynamics and synapse resolution, and effector functions improved with reduced affinity and/or antigen density, highlighting the importance of understanding the underlying cell biology when designing receptors for optimal antigen engagement.

During immune surveillance, CD8 T cells scan the surface of antigen-presenting cells using dynamic microvillar palpation and movements as well as by having their receptors preconcentrated into patches. Here, we use real-time lattice light-sheet microscopy to demonstrate the independence of microvillar and membrane receptor patch scanning. While T cell receptor (TCR) patches can distribute to microvilli, they do so stochastically and not preferentially as for other receptors such as CD62L. The distinctness of TCR patch movement from microvillar movement extends to many other receptors that form patches that also scan independent of the TCR. An exception to this is the CD8 coreceptor which largely comigrates in patches that overlap with or are closely adjacent to those containing TCRs. Microvilli that assemble into a synapse contain various arrays of the engaged patches, notably of TCRs and the inhibitory receptor PD-1, creating a pastiche of occupancies that vary from microvillar contact to contact. In summary, this work demonstrates that localization of receptor patches within the membrane and on microvillar projections is random prior to antigen detection and that such random variation may play into the generation of many individually composed receptor patch compositions at a single synapse.

T cells typically recognize their ligands using microvilli to scan for cognate antigen and scaffold T cell receptors (TCRs) during antigen recognition. Conventional chimeric antigen receptors (CARs) are often built using single-chain variable fragments (scFvs) with far greater affinity than that of natural TCRs. The implications of this for T cell function are not well understood. Using high-resolution microscopy, we studied the membrane dynamics in cells bearing anti-human epidermal growth factor receptor 2 (HER2) CARs and found these hyper-stabilized microvillar contacts relative to TCRs. While these CARs also impaired synapse resolution, a monomerized CAR with a lower affinity scFv rescued synapse dynamics and improved antigen-dose discrimination. The dimeric low-affinity CAR improved synapse dynamics and minimized early indicators of exhaustion, while maintaining or improving effector functions. This work highlights the importance of designing CAR binding dynamics that more closely resemble natural TCR antigen sensing to optimize T cell quality and function.

Spatial transcriptomics seeks to integrate single cell transcriptomic data within the three-dimensional space of multicellular biology. Current methods to correlate a cell's position with its transcriptome in living tissues have various limitations. We developed an approach, called 'ZipSeq', that uses patterned illumination and photocaged oligonucleotides to serially print barcodes ('zipcodes') onto live cells in intact tissues, in real time and with an on-the-fly selection of patterns. Using ZipSeq, we mapped gene expression in three settings: in vitro wound healing, live lymph node sections and a live tumor microenvironment. In all cases, we discovered new gene expression patterns associated with histological structures. In the tumor microenvironment, this demonstrated a trajectory of myeloid and T cell differentiation from the periphery inward. A combinatorial variation of ZipSeq efficiently scales in the number of regions defined, providing a pathway for complete mapping of live tissues, subsequent to real-time imaging or perturbation. ZipSeq uses patterned illumination and photocaged oligonucleotides to serially print barcodes onto live, intact tissues for spatially mapping single cell transcriptomes.