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Detection of cell–cell interactions via photocatalytic cell tagging

Nature Chemical Biology volume 18, pages 850–858 (2022)Cite this article

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Abstract

The growing appreciation of immune cell–cell interactions within disease environments has led to extensive efforts to develop immunotherapies. However, characterizing complex cell–cell interfaces in high resolution remains challenging. Thus, technologies leveraging therapeutic-based modalities to profile intercellular environments offer opportunities to study cell–cell interactions with molecular-level insight. We introduce photocatalytic cell tagging (PhoTag) for interrogating cell–cell interactions using single-domain antibodies (VHHs) conjugated to photoactivatable flavin-based cofactors. Following irradiation with visible light, the flavin photocatalyst generates phenoxy radical tags for targeted labeling. Using this technology, we demonstrate selective synaptic labeling across the PD-1/PD-L1 axis in antigen-presenting cell–T cell systems. In combination with multiomics single-cell sequencing, we monitored interactions between peripheral blood mononuclear cells and Raji PD-L1 B cells, revealing differences in transient interactions with specific T cell subtypes. The utility of PhoTag in capturing cell–cell interactions will enable detailed profiling of intercellular communication across different biological systems.

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Fig. 1: PhoTag.
Fig. 2: Use of flavins for photocatalytic protein labeling.
Fig. 3: Selective biotinylation within cellular immune synapses.
Fig. 4: PhoTag and multiomics single-cell sequencing analysis of transient PBMC–Raji cell interactions.

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Data availability

All supplementary figures, experimental details and synthesis information are included in the Supplementary Information. Raw flow cytometry data, raw and processed bulk RNA-seq data and single-cell sequencing data are available through the Harvard Dataverse62 and also available upon request. The MS proteomics data for peptide mapping in Fig. 2 have been deposited to the ProteomeXchange Consortium via the PRIDE63 partner repository with the dataset identifier PXD032203 at https://doi.org/10.6019/PXD032203. Source data are provided with this paper.

Code availability

Custom processing code used for analysis and figure generation is available upon request.

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Acknowledgements

We are very grateful to N. Haining, S. Lesley, K. Vora, A. Visintin and T. Wang from Merck & Co., Inc., and P. Sage from Brigham and Women’s Hospital and Harvard Medical School for helpful discussions.

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Author notes

  1. Rob C. Oslund & Olugbeminiyi O. Fadeyi

    Present address: InduPro, Cambridge, MA, USA

Authors and Affiliations

  1. Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA

    Rob C. Oslund, Tamara Reyes-Robles, Cory H. White, Jake H. Tomlinson, Kelly A. Crotty, David H. Perlman, Sampat Ingale, Samantha D. O’ Hara, Lee R. Roberts, Grazia Piizzi, Erik C. Hett, Daria J. Hazuda & Olugbeminiyi O. Fadeyi

  2. Discovery Research, Merck & Co., Inc., San Francisco, CA, USA

    Edward P. Bowman

  3. Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA

    Dan Chang, Vanessa M. Peterson & Lixia Li

  4. SpliceBio, Barcelona, Spain

    Silvia Frutos & Miquel Vila-Perelló

  5. Ablynx, A Sanofi Company, Zwijnaarde, Belgium

    David Vlerick & Karen Cromie

  6. Infectious Diseases and Vaccine Research, Merck & Co., Inc., West Point, PA, USA

    Daria J. Hazuda

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Contributions

O.O.F. and R.C.O. conceived of the work. O.O.F., R.C.O., T.R.-R., C.H.W., J.H.T., K.A.C., L.L., D.C. and V.M.P. designed and executed experiments. D.H.P. and S.D.O. interpreted results. S.F. and M.V.-P. designed and engineered the VHH–Fc conjugates. S.I., R.C.O and O.O.F. designed and prepared the peptide-based conjugate. E.P.B., D.V. and K.C. screened and identified the anti-PD-L1 VHH. E.C.H., L.R.R., G.P. and D.J.H. provided insight and direction for experimental design. O.O.F., R.C.O., T.R.-R. and C.H.W. wrote the manuscript with input from all authors.

Corresponding authors

Correspondence to Rob C. Oslund, Tamara Reyes-Robles or Olugbeminiyi O. Fadeyi.

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Competing interests

R.C.O., T.R.-R., C.H.W., J.H.T., K.A.C., D.H.P., S.I., S.D.O., L.R.R., G.P., L.L., D.C., V.M.P., E.P.B., E.C.H., D.J.H. and O.O.F. were employed by Merck & Co., S.F. and M.V.-P. were employed by SpliceBio and D.V. and K.C. were employed by Ablynx, Inc., during the experimental planning, execution and/or preparation of this manuscript. Merck & Co. has filed patents related to the technology and VHH sequences described herein listing R.C.O., T.R.-R. and O.O.F. as inventors (WO2020247725A1) and R.C.O., E.P.B. and O.O.F. as inventors (63/285,520).

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Supplementary information

Supplementary Information

Supplementary Figs. 1–42, Notes 1 and 2 and uncropped western blot images of Supplementary figures.

Reporting Summary

Supplementary Data 1

Excel-based table listing T cell gene expression fold change values in the streptavidin-high versus streptavidin-low groups of naive-like CD4+ T cells (cluster 3) from PD-L1-targeted labeling.

Supplementary Data 2

Excel-based table listing T cell gene expression fold change values in the streptavidin-high versus streptavidin-low groups of TEMRA-like CD8+ T cells (cluster 9) from PD-L1-targeted labeling.

Supplementary Data 3

Source data for Supplementary figures.

Source data

Source Data Fig. 2

Unprocessed western blot_800 channel. Unprocessed western blot_700 channel.

Source Data Fig. 3

Statistical source data for Fig. 3i.

Source Data Fig. 4

Statistical source data for Fig. 4b. Numerical data for Fig. 4g.

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Oslund, R.C., Reyes-Robles, T., White, C.H. et al. Detection of cell–cell interactions via photocatalytic cell tagging. Nat Chem Biol 18, 850–858 (2022). https://doi.org/10.1038/s41589-022-01044-0

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